The chromosome band track represents the approximate \ location of bands seen on Giemsa-stained chromosomes.\
\ Data are derived from the ideogram.gz file downloaded from the NCBI ftp \
site ftp://ftp.ncbi.nih.gov/genomes/M_musculus/maps/mapview/ (NCBI current\
version only).
\
Band lengths are estimated based on relative sizes as defined by the\
International System for Cytogenetic Nomenclature (ISCN).\
\
We would like to thank NCBI for providing this information.\ map 1 rikenCageCtssPlus Riken CAGE + bedGraph 4 Riken CAGE Plus Strand - Predicted Gene Start Sites 0 1 109 51 43 182 153 149 0 0 0 rna 0 subTrack rikenCageCtss\ rikenCageCtssMinus Riken CAGE - bedGraph 4 Riken CAGE Minus Strand - Predicted Gene Start Sites 0 2 43 51 109 149 153 182 0 0 0 rna 0 subTrack rikenCageCtss\ stsMapMouseNew STS Markers bed 5 + STS Markers on Genetic and Radiation Hybrid Maps 1 5 0 0 0 128 128 255 0 0 0
This track shows locations of Sequence Tagged Sites (STS) \ along the mouse draft assembly. These markers have been mapped using \ either genetic mapping (WICGR Mouse Genetic Map, MGD Genetic Map) or radiation hybridization mapping (Whitehead/MRC RH Map) techniques.
\ \ Additional data on the individual maps can be found at the following links:\ \ \By default all genetic map markers are shown as blue; only radiation \ hybrid markers and markers that are neither genetic nor radiation hybrid \ are shown as black; markers that map to more than one position are \ shown in lighter colors. Users can choose a color to highlight a subset \ of markers of interest from the Filter options in STS Markers \ Track Setting page.\ \
Positions of STS markers are determined using both full sequences\
and primer information. Full sequences are aligned using The track filter can be used to change the color or include/exclude\
a set of map data within the track. This is helpful when many items\
are shown in the track display, especially when only some are relevant\
to the current task. To use the filter:\
Using the Filter
\
\
When you have finished configuring the filter, click the\ Submit button.
\ \This track was designed and implemented by Terry Furey and Yontao Lu. Many thanks to\ Whitehead Institute (Broad Institute)\ and Jackson Lab for \ contributing the data.\ map 1 ctgPos Map Contigs ctgPos Physical Map Contigs 0 9 150 0 0 202 127 127 0 0 0
\ This track shows the draft assembly of the $organism genome. \ Whole-genome shotgun reads were assembled into contigs. When possible, \ contigs were grouped into scaffolds (also known as "supercontigs").\ The order, orientation and gap sizes between contigs within a scaffold are\ based on paired-end read evidence.
\\ In dense mode, this track depicts the contigs that make up the \ currently viewed scaffold. \ Contig boundaries are distinguished by the use of alternating gold and brown \ coloration. Where gaps\ exist between contigs, spaces are shown between the gold and brown\ blocks. The relative order and orientation of the contigs\ within a scaffold is always known; therefore, a line is drawn in the graphical\ display to bridge the blocks.
\\ All components within this track are of fragment type "W": \ Whole Genome Shotgun contig.
\ \ map 1 gap Gap bed 3 + Gap Locations 0 11 0 0 0 127 127 127 0 0 0\ Gaps are represented as black boxes in this track.\ If the relative order and orientation of the contigs on either side\ of the gap is known, it is a bridged gap and a white line is drawn \ through the black box representing the gap. \
\This assembly contains the following principal types of gaps:\
\ Bacterial artificial chromosomes (BACs) are a key part of many large\ scale sequencing projects. A BAC typically consists of 25 - 350 kb of\ DNA. During the early phase of a sequencing project, it is common\ to sequence a single read (approximately 500 bases) off each end of\ a large number of BACs. Later on in the project, these BAC end reads\ can be mapped to the genome sequence.
\\ This track shows these mappings\ in cases where both ends could be mapped. These BAC end pairs can\ be useful for validating the assembly over relatively long ranges. In some\ cases, the BACs are useful biological reagents. This track can also be\ used for determining which BAC contains a given gene, useful information\ for certain wet lab experiments.
\\ A valid pair of BAC end sequences must be\ at least 25 kb but no more than 350 kb away from each other. \ The orientation of the first BAC end sequence must be "+" and\ the orientation of the second BAC end sequence must be "-".
\\ The scoring scheme used for this annotation assigns 1000 to an alignment \ when the BAC end pair aligns to only one location in the genome (after \ filtering). When a BAC end pair or clone aligns to multiple locations, the \ score is calculated as 1500/(number of alignments).
\ \\ BAC end sequences are placed on the assembled sequence using\ Jim Kent's blat program.
\ \\ Additional information about the clone, including how it\ can be obtained, may be found at the \ NCBI Clone Registry. To view the registry entry for a \ specific clone, open the details page for the clone and click on its name at \ the top of the page.
\ map 1 exonArrows off\ gc5Base GC Percent wig 0 100 GC Percent in 5-Base Windows 0 23.5 0 0 0 128 128 128 0 0 0\ This track may be configured in a variety of ways to highlight different aspects \ of the displayed information. Click the "Graph configuration help" link\ for an explanation of the configuration options.\ \
The data and presentation of this graph were prepared by\ Hiram Clawson.\ \ map 0 autoScaleDefault Off\ defaultViewLimits 30:70\ graphTypeDefault Bar\ gridDefault OFF\ maxHeightPixels 128:36:16\ spanList 5\ windowingFunction Mean\ knownGene Known Genes genePred knownGenePep knownGeneMrna UCSC Known Genes (June, 05) Based on UniProt, RefSeq, and GenBank mRNA 3 34 12 12 120 133 133 187 0 0 0
\ The UCSC Known Genes track shows known protein-coding genes based on\ protein data from UniProt (SWISS-PROT and TrEMBL) and mRNA data from\ the NCBI reference sequences collection (RefSeq) and GenBank. \ Each Known Gene is represented by an mRNA and a protein.\
\ This track follows the display conventions for\ gene prediction\ tracks with the following color scheme:\
\ This track contains an optional codon coloring \ feature that allows users to quickly validate and compare gene predictions.\ To display codon colors, select the genomic codons option from the\ Color track by codons pull-down menu. Click \ here for more \ information about this feature.
\ \This release of UCSC Known Genes was built by a new process, KG II, \ as described below.\
\ UniProt protein sequences (including alternative splicing isoforms) \ and mRNA sequences from RefSeq and GenBank \ were aligned against the base genome using BLAT. \ RefSeq alignments having a base identity level within 0.1% of the best \ and at least 96% base identity with the genomic sequence were kept. \ GenBank mRNA alignments having a base identity level within 0.2% of \ the best and at least 97% base identity with the genomic sequence were kept. \ Protein alignments having a base identity level within 0.2% of the best and \ at least 80% base identity with the genomic sequence were kept.\
Then the genomic mRNA and protein alignments were compared, \ and protein-mRNA pairings were determined from their overlaps. \ mRNA CDS data were obtained from RefSeq and GenBank data \ and supplemented by CDS structures derived from UCSC protein-mRNA BLAT alignments. \ The initial set of UCSC Known Genes candidates consists of \ all protein-mRNA pairs with valid mRNA CDS structures. \ A gene-check program (similar to the one used for the Consensus CDS (CCDS) project) \ is used to remove questionable candidates, such as those with in-frame stop codons, \ missing start or stop codons, etc.\
From each group of gene candidates that share the same CDS structure, \ the protein-mRNA pair having the best ranking and protein-mRNA alignment score \ is selected as a UCSC Known Gene. \ The ranking of a gene candidate depends on its gene-check quality measures. \ When all else is equal, \ a preference is given to RefSeq mRNAs and next to MGC mRNAs. \ Similarly a preference is given to gene candidates represented by Swiss-Prot proteins. \ The protein-mRNA alignment score is calculated based on protein to \ mRNA alignment using TBLASTN, plus weighted sub-scores according \ to the date and length of the mRNA. \
\ The UCSC Known Genes track was produced using protein data from \ UniProt and mRNA \ data from NCBI \ RefSeq\ and GenBank.
\ \\ The UniProt data have the following terms of use, UniProt copyright(c) 2002 - \ 2004 UniProt consortium:
\\ For non-commercial use, all databases and documents in the UniProt FTP\ directory may be copied and redistributed freely, without advance\ permission, provided that this copyright statement is reproduced with\ each copy.
\\ For commercial use, all databases and documents in the UniProt FTP\ directory except the files\
\ From January 1, 2005, all databases and documents in the UniProt FTP\ directory may be copied and redistributed freely by all entities,\ without advance permission, provided that this copyright statement is\ reproduced with each copy.
\ \\ Hsu, F., Kent, W.J., Clawson, H., Kuhn, R.M., Diekhans, M., and Haussler, D. \ The UCSC Known Genes. \ Bioinformatics 22(9), 1036-46 (2006).\
\ Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and \ Wheeler, D.L. \ GenBank: update. Nucleic Acids Res. 32,\ D23-6 (2004).
\\ Kent, W.J.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 12(4), 656-664 (2002).
\ \ genes 1 baseColorDefault genomicCodons\ baseColorUseCds given\ directUrl /cgi-bin/hgGene?hgg_gene=%s&hgg_chrom=%s&hgg_start=%d&hgg_end=%d&hgg_type=%s&db=%s\ hgGene on\ hgsid on\ idXref kgAlias kgID alias\ refGene RefSeq Genes genePred refPep refMrna RefSeq Genes 1 35 12 12 120 133 133 187 0 0 0\ The RefSeq Genes track shows known protein-coding genes taken from \ the NCBI mRNA reference sequences collection (RefSeq). On assemblies in \ which incremental GenBank downloads are supported, the data underlying this \ track are updated nightly.
\ \\ This track follows the display conventions for \ gene prediction \ tracks.\ The color shading indicates the level of review the RefSeq record has \ undergone: predicted (light), provisional (medium), reviewed (dark). \ In some assemblies, non-coding RNA genes are shown in a separate track.
\\ The item labels and display colors of features within this track can be\ configured through the controls at the top of the track description page. \ This page is accessed via the small button to the left of the track's \ graphical display or through the link on the track's control menu. \
\ RefSeq mRNAs were aligned against the $organism genome using blat; those\ with an alignment of less than 15% were discarded. When a single mRNA \ aligned in multiple places, the alignment having the highest base identity \ was identified. Only alignments having a base identity level within 0.1% of \ the best and at least 96% base identity with the genomic sequence were kept.\
\ \ \\ This track was produced at UCSC from mRNA sequence data\ generated by scientists worldwide and curated by the \ NCBI RefSeq project.
\ \\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ \Pruitt KD, Tatusova T, Maglott DR. \ NCBI Reference Sequence (RefSeq): a curated non-redundant \ sequence database of genomes, transcripts and proteins. Nucleic Acids \ Res. 2005 Jan 1;33(Database issue):D501-4.\
\ genes 1 baseColorUseCds given\ idXref refLink mrnaAcc name\ mgcGenes MGC Genes genePred Mammalian Gene Collection Full ORF mRNAs 3 36 34 139 34 144 197 144 0 0 0\ This track shows alignments of $organism mRNAs from the\ Mammalian Gene Collection \ (MGC) having full-length open reading frames (ORFs) to the genome.
\ \\ The track follows the display conventions for \ gene prediction \ tracks.
\\ An optional codon coloring feature is available for quick\ validation and comparison of gene predictions.\ To display codon colors, select the genomic codons option from the\ Color track by codons pull-down menu. Click \ here for more \ information about this feature.
\ \\ GenBank $organism MGC mRNAs identified as having full-length ORFs \ were aligned against the genome using blat. When a single mRNA \ aligned in multiple places, the alignment having the highest base identity was\ found. Only alignments having a base identity level within 1% of\ the best and at least 95% base identity with the genomic sequence \ were kept.
\ \\ The $organism MGC full-length mRNA track was produced at UCSC from \ mRNA sequence data submitted to \ GenBank by the \ Mammalian Gene Collection project.
\ \\ Mammalian Gene Collection project references.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ genes 1 ensGene Ensembl Genes genePred ensPep Ensembl Gene Predictions 1 40 150 0 0 202 127 127 0 0 0\ These gene predictions were generated by Ensembl.
\ \\ For a description of the methods used in Ensembl gene prediction, refer to \ Hubbard, T. et al. (2002) in the References section below.
\ \\ Thanks to Ensembl for providing this annotation.
\ \\ Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J,\ Curwen V, Down T, et al. \ The Ensembl genome database project.\ Nucleic Acids Res. 2002 Jan 1;30(1):38-41.
\ \ genes 1 nscanGene N-SCAN genePred N-SCAN Gene Predictions 0 45.1 34 139 34 144 197 144 0 0 0\ This track shows gene predictions using the N-SCAN gene structure prediction\ software provided by the Computational Genomics Lab at Washington University \ in St. Louis, MO, USA.\
\ \\ N-SCAN combines biological-signal modeling in the target genome sequence along\ with information from a multiple-genome alignment to generate de novo gene\ predictions. It extends the TWINSCAN target-informant genome pair to allow for\ an arbitrary number of informant sequences as well as richer models of\ sequence evolution. N-SCAN models the phylogenetic relationships between the\ aligned genome sequences, context-dependent substitution rates, insertions,\ and deletions.\
\\ Mouse N-SCAN uses human (hg17) as the informant\ and iterative pseudogene masking.\ \
\ Thanks to Michael Brent's Computational Genomics Group at Washington \ University St. Louis for providing this data.\
\ \\ Gross SS, Brent MR.\ Using\ multiple alignments to improve gene prediction. In\ Proc. 9th Int'l Conf. on Research in Computational Molecular Biology\ (RECOMB '05):374-388 and J Comput Biol. 2006 Mar;13(2):379-93.\
\\ Korf I, Flicek P, Duan D, Brent MR.\ Integrating genomic homology into gene structure prediction.\ Bioinformatics. 2001 Jun 1;17(90001)S140-8.
\\ van Baren MJ, Brent MR.\ Iterative gene prediction and pseudogene removal improves\ genome annotation.\ Genome Res. 2006 May;16(5):678-85.
\ genes 1 baseColorDefault genomicCodons\ baseColorUseCds given\ sgpGene SGP Genes genePred sgpPep SGP Gene Predictions Using Mouse/Human Homology 0 47 0 90 100 127 172 177 0 0 0\ This track shows gene predictions from the SGP program, developed at \ the Genome Bionformatics \ Laboratory (GBL), which is part of the Grup de Recerca en Informàtica Biomèdica (GRIB) at Institut \ Municipal d'Investigació Mèdica (IMIM) / Centre de Regulació Genòmica (CGR) in \ Barcelona. To predict genes in a genomic query, SGP combines geneid predictions \ with tblastx comparisons of the genomic query against other genomic sequences.\
\\ Thanks to GBL for providing these gene predictions.\
\ \ \ \ genes 1 geneid Geneid Genes genePred geneidPep Geneid Gene Predictions 0 49 0 90 100 127 172 177 0 0 0\ This track shows gene predictions from the geneid program developed at the \ Genome Bionformatics \ Laboratory (GBL), which is part of the \ Grup de Recerca\ en Informàtica Biomèdica (GRIB) at the Institut Municipal d'Investigació \ Mèdica (IMIM) / Centre de Regulació Genòmica (CRG) in Barcelona."\ \ \
\\ Geneid is a program to predict genes in anonymous genomic sequences designed \ with a hierarchical structure. In the first step, splice sites, start and stop \ codons are predicted and scored along the sequence using Position Weight Arrays \ (PWAs). Next, exons are built from the sites. Exons are scored as the sum of the \ scores of the defining sites, plus the the log-likelihood ratio of a \ Markov Model for coding DNA. Finally, from the set of predicted exons, the gene \ structure is assembled, maximizing the sum of the scores of the assembled exons. \
\\ Thanks to GBL for providing these data.\
\ genes 1 genscan Genscan Genes genePred genscanPep Genscan Gene Predictions 0 50 170 100 0 212 177 127 0 0 0\ This track shows predictions from the \ Genscan program \ written by Chris Burge.\ The predictions are based on transcriptional, \ translational, and donor/acceptor splicing signals, as well as the length \ and compositional distributions of exons, introns and intergenic regions.
\ \\ This track follows the display conventions for \ gene prediction \ tracks. \
\ The track description page offers the following filter and configuration\ options:\
\ For a description of the Genscan program and the model that underlies it, \ refer to Burge and Karlin (1997) in the References section below. \ The splice site models used are described in more detail in Burge (1998)\ below.
\ \\ Burge C. \ Modeling Dependencies in Pre-mRNA Splicing Signals. \ In Salzberg S, Searls D, Kasif S, eds. \ Computational Methods in Molecular Biology, \ Elsevier Science, Amsterdam. 1998;127-163.
\\ Burge C, Karlin S. \ Prediction of Complete Gene Structures in Human Genomic DNA.\ J. Mol. Biol. 1997 Apr 25;268(1):78-94.
\ genes 1 mrna $Organism mRNAs psl . $Organism mRNAs from GenBank 3 54 0 0 0 127 127 127 0 0 0\ The mRNA track shows alignments between $organism mRNAs\ in GenBank and the genome.
\ \\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, the items that\ are more darkly shaded indicate matches of better quality.
\\ The description page for this track has a filter that can be used to change \ the display mode, alter the color, and include/exclude a subset of items \ within the track. This may be helpful when many items are shown in the track \ display, especially when only some are relevant to the current task.
\\ To use the filter:\
\ This track may also be configured to display codon coloring, a feature that\ allows the user to quickly compare mRNAs against the genomic sequence. For more \ information about this option, click \ here.\ Several types of alignment gap may also be colored; \ for more information, click \ here.\
\ \\ GenBank $organism mRNAs were aligned against the genome using the \ blat program. When a single mRNA aligned in multiple places, \ the alignment having the highest base identity was found. \ Only alignments having a base identity level within 0.5% of\ the best and at least 96% base identity with the genomic sequence were kept.\
\ \\ The mRNA track was produced at UCSC from mRNA sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J,\ Wheeler DL.\ GenBank: update. Nucleic Acids Res.\ 2004 Jan 1;32(Database issue):D23-6.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ rna 1 baseColorDefault diffCodons\ baseColorUseCds genbank\ baseColorUseSequence genbank\ indelDoubleInsert on\ indelPolyA on\ indelQueryInsert on\ showDiffBasesAllScales .\ NIAGene NIA Gene Index psl . NIA Mouse Gene Index Version 5 0 54 0 60 120 200 220 255 1 0 0 http://lgsun.grc.nia.nih.gov/geneindex5/bin/giT.cgi?genename=$$\ This track displays alignments of the National Institute on Aging (NIA)\ Mouse Gene Index (Version 5) against the mouse genome.
\ \\ The index was assembled from Blat alignments of the following to the mouse\ genome (mm6/March. 2005):\
\ See the NIA Mouse cDNA Project home page for more information.
\ \\ This track was produced by Alexei A. Sharov, Dawood B. Dudekula and Minoru\ S. H. Ko at the NIA, \ National Institutes of Health. The research was supported by the NIA \ Intramural Research Program.
\ \\ Sharov et al. \ Transcriptome analysis of mouse stem cells and early embryos.\ PLoS Biology 1(3), 410-419 (2003).
\\ Sharov, A.A., Dudekula, D.B. and Ko, M.S.H. \ Genome-wide assembly and analysis of alternative transcripts in mouse. \ Genome Res. 15(5), 748-754 (2005).
\ genes 1 intronEst Spliced ESTs psl est $Organism ESTs That Have Been Spliced 1 56 0 0 0 127 127 127 1 0 0\ This track shows alignments between $organism expressed sequence tags \ (ESTs) in GenBank and the genome that show signs of splicing when\ aligned against the genome. ESTs are single-read sequences, typically about \ 500 bases in length, that usually represent fragments of transcribed genes.\
\\ To be considered spliced, an EST must show \ evidence of at least one canonical intron, i.e. the genomic \ sequence between EST alignment blocks must be at least 32 bases in \ length and have GT/AG ends. By requiring splicing, the level \ of contamination in the EST databases is drastically reduced\ at the expense of eliminating many genuine 3' ESTs.\ For a display of all ESTs (including unspliced), see the \ $organism EST track.
\ \\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, darker shading\ indicates a larger number of aligned ESTs.
\\ The strand information (+/-) indicates the\ direction of the match between the EST and the matching\ genomic sequence. It bears no relationship to the direction\ of transcription of the RNA with which it might be associated.
\\ The description page for this track has a filter that can be used to change \ the display mode, alter the color, and include/exclude a subset of items \ within the track. This may be helpful when many items are shown in the track \ display, especially when only some are relevant to the current task.
\\ To use the filter:\
\ This track may also be configured to display base labeling, a feature that\ allows the user to display all bases in the aligning sequence or only those \ that differ from the genomic sequence. For more information about this option,\ click \ here.\ Several types of alignment gap may also be colored; \ for more information, click \ here.\
\ \\ To make an EST, RNA is isolated from cells and reverse\ transcribed into cDNA. Typically, the cDNA is cloned\ into a plasmid vector and a read is taken from the 5'\ and/or 3' primer. For most — but not all — ESTs, the\ reverse transcription is primed by an oligo-dT, which\ hybridizes with the poly-A tail of mature mRNA. The\ reverse transcriptase may or may not make it to the 5'\ end of the mRNA, which may or may not be degraded.
\\ In general, the 3' ESTs mark the end of transcription\ reasonably well, but the 5' ESTs may end at any point\ within the transcript. Some of the newer cap-selected\ libraries cover transcription start reasonably well. Before the \ cap-selection techniques\ emerged, some projects used random rather than poly-A\ priming in an attempt to retrieve sequence distant from the\ 3' end. These projects were successful at this, but as\ a side effect also deposited sequences from unprocessed\ mRNA and perhaps even genomic sequences into the EST databases.\ Even outside of the random-primed projects, there is a\ degree of non-mRNA contamination. Because of this, a\ single unspliced EST should be viewed with considerable\ skepticism.
\\ To generate this track, $organism ESTs from GenBank were aligned \ against the genome using blat. Note that the maximum intron length\ allowed by blat is 750,000 bases, which may eliminate some ESTs with very \ long introns that might otherwise align. When a single \ EST aligned in multiple places, the alignment having the \ highest base identity was identified. Only alignments having\ a base identity level within 0.5% of the best and at least 96% base identity \ with the genomic sequence are displayed in this track.
\ \\ This track was produced at UCSC from EST sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, \ Wheeler DL. \ GenBank: update. Nucleic Acids Res.\ 2004 Jan 1;32(Database issue):D23-6.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ rna 1 baseColorUseSequence genbank\ indelDoubleInsert on\ indelQueryInsert on\ intronGap 30\ maxItems 300\ showDiffBasesAllScales .\ est $Organism ESTs psl est $Organism ESTs Including Unspliced 0 57 0 0 0 127 127 127 1 0 0\ This track shows alignments between $organism expressed sequence tags \ (ESTs) in GenBank and the genome. ESTs are single-read sequences, \ typically about 500 bases in length, that usually represent fragments of \ transcribed genes.
\ \\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, the items that\ are more darkly shaded indicate matches of better quality.
\\ The strand information (+/-) indicates the\ direction of the match between the EST and the matching\ genomic sequence. It bears no relationship to the direction\ of transcription of the RNA with which it might be associated.
\\ The description page for this track has a filter that can be used to change \ the display mode, alter the color, and include/exclude a subset of items \ within the track. This may be helpful when many items are shown in the track \ display, especially when only some are relevant to the current task.
\\ To use the filter:\
\ This track may also be configured to display base labeling, a feature that\ allows the user to display all bases in the aligning sequence or only those \ that differ from the genomic sequence. For more information about this option,\ click \ here.\ Several types of alignment gap may also be colored; \ for more information, click \ here.\
\ \\ To make an EST, RNA is isolated from cells and reverse\ transcribed into cDNA. Typically, the cDNA is cloned\ into a plasmid vector and a read is taken from the 5'\ and/or 3' primer. For most — but not all — ESTs, the\ reverse transcription is primed by an oligo-dT, which\ hybridizes with the poly-A tail of mature mRNA. The\ reverse transcriptase may or may not make it to the 5'\ end of the mRNA, which may or may not be degraded.
\\ In general, the 3' ESTs mark the end of transcription\ reasonably well, but the 5' ESTs may end at any point\ within the transcript. Some of the newer cap-selected\ libraries cover transcription start reasonably well. Before the \ cap-selection techniques\ emerged, some projects used random rather than poly-A\ priming in an attempt to retrieve sequence distant from the\ 3' end. These projects were successful at this, but as\ a side effect also deposited sequences from unprocessed\ mRNA and perhaps even genomic sequences into the EST databases.\ Even outside of the random-primed projects, there is a\ degree of non-mRNA contamination. Because of this, a\ single unspliced EST should be viewed with considerable\ skepticism.
\\ To generate this track, $organism ESTs from GenBank were aligned \ against the genome using blat. Note that the maximum intron length\ allowed by blat is 750,000 bases, which may eliminate some ESTs with very \ long introns that might otherwise align. When a single \ EST aligned in multiple places, the alignment having the \ highest base identity was identified. Only alignments having\ a base identity level within 0.5% of the best and at least 96% base identity \ with the genomic sequence were kept.
\ \\ This track was produced at UCSC from EST sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J,\ Wheeler DL.\ GenBank: update. Nucleic Acids Res.\ 2004 Jan 1;32(Database issue):D23-6.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ rna 1 baseColorUseSequence genbank\ indelDoubleInsert on\ indelQueryInsert on\ intronGap 30\ maxItems 300\ xenoMrna Other mRNAs psl xeno Non-$Organism mRNAs from GenBank 0 63 0 0 0 127 127 127 1 0 0\ This track displays translated blat alignments of vertebrate and\ invertebrate mRNA in \ GenBank from organisms other than $organism.\ \
\ This track follows the display conventions for \ PSL alignment tracks. In dense display mode, the items that\ are more darkly shaded indicate matches of better quality.
\\ The strand information (+/-) for this track is in two parts. The\ first + indicates the orientation of the query sequence whose\ translated protein produced the match (here always 5' to 3', hence +).\ The second + or - indicates the orientation of the matching \ translated genomic sequence. Because the two orientations of a DNA \ sequence give different predicted protein sequences, there are four \ combinations. ++ is not the same as --, nor is +- the same as -+.
\\ The description page for this track has a filter that can be used to change \ the display mode, alter the color, and include/exclude a subset of items \ within the track. This may be helpful when many items are shown in the track \ display, especially when only some are relevant to the current task.
\\ To use the filter:\
\ This track may also be configured to display codon coloring, a feature that\ allows the user to quickly compare mRNAs against the genomic sequence. For more \ information about this option, click \ here.\ Several types of alignment gap may also be colored; \ for more information, click \ here.\
\ \\ The mRNAs were aligned against the $organism genome using translated blat. \ When a single mRNA aligned in multiple places, the alignment having the \ highest base identity was found. Only those alignments having a base \ identity level within 1% of the best and at least 25% base identity with the \ genomic sequence were kept.
\ \\ The mRNA track was produced at UCSC from mRNA sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, \ Wheeler DL. \ GenBank: update. Nucleic Acids Res.\ 2004 Jan 1;32(Database issue):D23-6.
\\ Kent WJ.\ BLAT - the BLAST-like alignment tool.\ Genome Res. 2002 Apr;12(4):656-64.
\ rna 1 baseColorUseCds genbank\ baseColorUseSequence genbank\ indelDoubleInsert on\ indelQueryInsert on\ showDiffBasesAllScales .\ miRNA miRNA bed 8 . MicroRNAs from miRBase 0 63 255 64 64 255 159 159 1 0 0 http://microrna.sanger.ac.uk/cgi-bin/sequences/mirna_entry.pl?id=$$\ The miRNA track shows microRNAs from the\ \ miRBase at The \ Wellcome Trust Sanger Institute.
\ \\ Mature miRNAs (miRs) are represented by \ thick blocks. The predicted stem-loop portions of the primary transcripts\ are indicated by thinner blocks. miRNAs in the sense orientation are shown in\ black; those in the reverse orientation are colored grey. When a single \ precursor produces two mature miRs from its 5' and 3' parts, it is displayed \ twice with the two different positions of the mature miR.
\\ To display only those items that exceed a specific unnormalized score, enter\ a minimum score between 0 and 1000 in the text box at the top of the track \ description page.\
\ \\ Mature and precursor miRNAs from the miRNA Registry were\ aligned against the genome using blat.\ The extents of the precursor sequences were not generally known, and were\ predicted based on base-paired hairpin structure. \ miRBase is described in Griffiths-Jones, S. et al. (2006).\ The miRNA Registry is\ described in Griffiths-Jones, S. (2004) and Weber, M.J. (2005) in the \ References section below.
\ \\
\
This track was created by Michel Weber of
\ When making use of these data, please cite:
\\ Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ.\ miRBase: microRNA sequences, targets and gene nomenclature.\ Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4.
\\ Griffiths-Jones S. \ The microRNA Registry.\ Nucleic Acids Res. 2004 Jan 1;32(Database issue):D109-11.
\\ Weber MJ. \ New human and mouse microRNA genes found by homology search.\ Febs J. 2005 Jan;272(1):59-73.
\\ You may also want to cite The Wellcome Trust Sanger Institute \ miRNA Registry.
\\
The following publication provides guidelines on miRNA annotation:\
Ambros V, Bartel B, Bartel DP, Burge CB, Carrington JC, Chen X,\
Dreyfuss G, Eddy SR, Griffiths-Jones S, Marshall M et al.\
A uniform system for microRNA annotation. \
RNA. 2003 Mar;9(3):277-9.
\
For more information on blat, see \
Kent WJ.\
BLAT - the BLAST-like alignment tool.\
Genome Res. 2002 Apr;12(4):656-64.
\ This track shows alignments of \ International Gene Trap \ Consortium sequence tags to the $organism genome. \ Items are labeled by cell line and colored by source:\
| BG: | \BayGenomics\ (USA) |
| CMHD: | \Centre \ for Modeling Human Disease (Toronto, Canada) |
| EGTC: | \Exchangeable Gene \ Trap Clones (Kumamoto University, Japan) |
| ESDB: | \Embryonic Stem Cell \ Database (University of Manitoba, Canada) |
| FHCRC: | \Soriano Lab Gene Trap Database (Fred Hutchinson \ Cancer Research Center, Seattle, USA) |
| GGTC: | \German Gene Trap \ Consortium (Germany) |
| SIGTR: | \Sanger Institute Gene Trap Resource \ (Cambridge, UK) |
| TIGEM: | \TIGEM-IRBM Gene Trap (Naples, Italy) |
| TIGM: | \Texas Institute for Genomic Medicine (Houston, Texas) |
\ The \ IGTC \ pipeline\ uses BLAT to align sequence tags from dbGSS to the $organism genome and \ BLAST to match sequence tags to genes. The pipeline filters and reconciles \ the two sets of alignments to associate cell lines with trapped genes. \
\ \\ Thanks to the \ International Gene Trap \ Consortium for providing this track.\
\ genes 1 urlLabel IGTC Cell Line Annotation:\ jaxRepTranscript MGI Rep Transcript genePred Jackson Laboratory / Mouse Genome Informatics Representative Transcript 0 70 0 0 150 127 127 202 0 0 0 http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=markerDetail&id=$$\ This track shows mappings of sequences chosen as "best\ representative transcript" for many highly curated \ Mouse Genome \ Informatics (MGI) genes.\ Representative transcript identifiers are a concatenation of the\ GenBank accession and the MGI gene symbol.
\ \\ Representative transcript sequences were selected by \ MGI.\ The sequences were placed on the assembly using \ Blat \ and filtered to retain the single best hit.
\ \\ Thanks to \ MGI \ at The Jackson Laboratory, \ and Bob Sinclair in particular, for providing these data.
\ \ phenoAllele 1 baseColorUseCds none\ urlLabel MGI Gene Detail:\ jaxPhenotype MGI Phenotype bed 12 + Jackson Laboratory / Mouse Genome Informatics Phenotype 0 71 190 110 0 222 182 127 0 0 0 http://www.informatics.jax.org/searches/allele_report.cgi?markerID=$$\
This track shows \
Mouse Genome \
Informatics (MGI)\
representative transcripts associated with\
Mammalian Phenotype Ontology Top-Level terms.\
The terms have been abbreviated for display as follows:\
\
| Abbreviation | MPO Term |
| Adipose | adipose_tissue_phenotype |
| Behavior | behavior_neurological_phenotype |
| Cardiovascular | cardiovascular_system_phenotype |
| Cellular | cellular_phenotype |
| Craniofacial | craniofacial_phenotype |
| Digestive | digestive_alimentary_phenotype |
| Embryogenesis | embryogenesis_phenotype |
| Embryonic Lethal | lethality-embryonic_perinatal |
| Gland | endocrine_exocrine_gland_phenotype |
| Growth Size | growth_size_phenotype |
| Hearing/Ear | hearing_ear_phenotype |
| Hematopoietic | hematopoietic_system_phenotype |
| Homeostasis | homeostasis_metabolism_phenotype |
| Immune | immune_system_phenotype |
| Life Span | life_span-post-weaning_aging |
| Limbs and Tail | limbs_digits_tail_phenotype |
| Liver and Bile | liver_biliary_system_phenotype |
| Muscle | muscle_phenotype |
| Nervous System | nervous_system_phenotype |
| Pigmentation | pigmentation_phenotype |
| Postnatal Lethal | lethality-postnatal |
| Renal/Urinary | renal_urinary_system_phenotype |
| Reproductive | reproductive_system_phenotype |
| Respiratory | respiratory_system_phenotype |
| Skeleton | skeleton_phenotype |
| Skin/Coat/Nails | skin_coat_nails_phenotype |
| Taste/Smell | taste_olfaction_phenotype |
| Touch | touch_vibrissae_phenotype |
| Tumorigenesis | tumorigenesis |
| Vision/Eye | vision_eye_phenotype |
\ The MGI database report MGI_PhenotypicAllele.rpt was parsed for\ markers and alleles that are associated with representative\ transcripts, and the Top-Level Mammalian Phenotype (MP) terms were\ captured. Note that these top-level terms can be associated with a\ marker multiple times (i.e. via multiple alleles).
\ \\ Thanks to \ MGI \ at The Jackson Laboratory, \ and Bob Sinclair in particular, for providing these data.
\ \ phenoAllele 1 urlLabel MGI Phenotypic Allele(s):\ jaxAllele MGI Allele bed 12 + Jackson Laboratory / Mouse Genome Informatics Allele 0 72 200 0 110 200 0 110 0 0 0 http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=alleleDetail&id=$$\ This track shows \ Mouse Genome \ Informatics (MGI)\ representative transcripts associated with \ MGI-curated alleles. Items are named by concatenating the\ representative transcript ID and allele symbol. \ All chemical- and radiation-induced alleles have been\ combined as type "Induced." \ Floxed/Frt, reporter, knock-out and knock-in\ targeted alleles are combined as type "Targeted." \ Random-expressed, random-gene\ disruption, and Cre/Flp transgenes are combined as\ type "Transgenic".
\ \\ The MGI database report MGI_PhenotypicAllele.rpt was parsed to provide a\ list of all curated alleles that have associated representative \ transcripts.
\ \\ Thanks to \ MGI \ at The Jackson Laboratory, \ and Bob Sinclair in particular, for providing these data.
\ \ phenoAllele 1 urlLabel MGI Phenotypic Allele:\ rikenCageTc Riken CAGE TC bed 6 . Riken CAGE - Associated Transcript Clusters 0 75.1 0 0 0 127 127 127 0 0 0 http://fantom31p.gsc.riken.jp/cage_analysis/mm5/TSSSummary.php?tss_id=$$\ This track shows transcription start points as defined by \ the regions of CAGE (5' Cap Analysis Gene \ Expression) tag clusters. \ CAGE tags are 19-20-mers sequenced from 5' ends of full-length cDNAs \ produced using RIKEN full-length cDNA technology. A CAGE cluster is \ defined as one or more overlapping CAGE tags on the same strand, \ regardless of tissue of origin.\ The full annotation of a cluster, including tissue(s) of origin,\ can be obtained from the \ CAGE Analysis Viewer, via a link on the details\ page for that cluster.\ \
\ The CAGE tags are sequenced from the 5' ends of full-length cDNAs produced using \ RIKEN full-length cDNA technology. \ \ To create the tag, a linker was \ attached to the 5' end of full-length cDNAs which had been selected by cap \ trapping. The first 20 bp of the cDNA were cleaved using the class II \ restriction enzyme, MmeI, followed by PCR amplification. Concatamers\ of the resulting 32 bp tags were then formed for more efficient sequencing. \ \ For more information on \ CAGE, see Shiraki et al. (2003) and Carninci et al (2005). \ \ \ RIKEN \ website\ for information about RIKEN full-length cDNA technologies. \ \ The mapping \ methodology employed in this annotation will be described in upcoming \ publications.
\ \\ These data were contributed by the Functional Annotation of Mouse\ (FANTOM)\ Consortium, RIKEN Genome Science Laboratory and\ RIKEN Genome Exploration Research Group\ (Genome Network Project Core Group).
\ \ \ \ \\ FANTOM Consortium: P. Carninci, T. Kasukawa, S. Katayama, Gough, \ M. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. \ Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. R. \ Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. Allen, \ A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. \ Bansal, K. W. Beisel, T. Bersano, H. Bono, A. M. Chalk, K. P. Chiu, V. \ Choudhary, A. Christoffels, D. R. Clutterbuck, M. L. Crowe, E. Dalla, \ B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down, \ P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, \ M. Furuno, S. Futaki, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, \ T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, V. Harokopos, Y. \ Hayashi, S. Henning, T. K. Hensch, N. Hirokawa, D. Hill, L. Huminiecki, \ M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. \ Katoh, Y. Kawasawa, J. Kelso, H. Kitamura, H. Kitano, G. Kollias, S. \ P. T. Krishnan, A.F. Kruger, K. Kummerfeld, I. V. Kurochkin, \ L. F. Lareau, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, M. Madan \ Babu, M. Madera, L. Marchionni, H. Matsuda, S. Matsuzawa, H. Miki, F. \ Mignone, S. Miyake, K. Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano, \ H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi, S. Nishikawa, F. Nori, \ O. Ohara, Y. Okazaki, V. Orlando, K. C. Pang, W. J. Pavan, G. Pavesi, \ G. Pesole, N. Petrovsky, S. Piazza, W. Qu, J. Reed, J. F. Reid, B. Z. \ Ring, M. Ringwald, B. Rost, Y. Ruan, S. Salzberg, A. Sandelin, C. \ Schneider, C. Schoenbach, K. Sekiguchi, C. A. M. Semple, S. Seno, \ L. Sessa, Y. Sheng, Y. Shibata, H. Shimada, K. Shimada, B. Sinclair, S. \ Sperling, E. Stupka, K. Sugiura, R. Sultana, Y. Takenaka, K. Taki, K. \ Tammoja, S. L. Tan, S. Tang, M. S. Taylor, J. Tegner, S. A. Teichmann, \ H. R. Ueda, E. van Nimwegene, R. Verardo, C. L. Wei, K. Yagi, H. \ Yamanishi, E. Zabarovsky, S. Zhu, A. Zimmer, W. Hide, C. Bult, S. M. \ Grimmond, R. D. Teasdale, E. T. Liu, V. Brusic, J. Quackenbush, C. \ Wahlestedt, J. Mattick, D. Hume.
\\ RIKEN Genome Exploration Research Group: C. Kai, D. Sasaki, Y. \ Tomaru, S. Fukuda, M. Kanamori-Katayama, M. Suzuki, J. Aoki, T. \ Arakawa, J. Iida, K. Imamura, M. Itoh, T. Kato, H. Kawaji, N. \ Kawagashira, T. Kawashima, M. Kojima, S. Kondo, H. Konno, K. Nakano, N. \ Ninomiya, T. Nishio, M. Okada, C. Plessy, K. Shibata, T. Shiraki, S. \ Suzuki, M. Tagami, K Waki, A. Watahiki, Y. Okamura-Oho, H. Suzuki, J. \ Kawai.
\\ General Organizer: Y. Hayashizaki\ \
\ FANTOM Consortium: P. Carninci, et al.\ The transcriptional\ landscape of the mammalian genome. Science 309(5740),\ 1559-63 (2005).\ \
\ Shiraki, T., Kondo, S., Katayama, S., Waki, K., Kasukawa, T., Kawaji, H.,\ Kodzius, R., Watahiki, A., Nakamura, M. et al.\ Cap analysis gene expression for high-throughput analysis of\ transcriptional starting point and identification of promoter usage.\ Proc Natl Acad Sci U S A. 100(26), 15776-81 (2003).
\ rna 1 origAssembly mm5\ rikenCageCtss Riken CAGE bedGraph 4 Riken CAGE - Predicted Gene Start Sites 0 75.2 0 0 0 127 127 127 0 0 0\ This track shows the number of 5' cap analysis gene expression (CAGE) tags \ that map to the genome on the "plus" and "minus" strands at \ a specific location. For clarity, only the first 5' nucleotide in the tag \ (relative to the transcript direction) is considered. Areas in which many tags \ map to the same region may indicate a significant transcription start site.\ The number of tags should be proportional to the expression rate in the \ originating tissues.
\ \\ The position of the first 5' nucleotide in the tag is represented by a solid\ block. The height of the block indicates the number of 5' CAGE tag starts \ that map at that location.
\\ This composite annotation track contains two subtracks that \ may be configured in a variety of ways to highlight different aspects of the \ displayed data. The graphical configuration options are shown at the top of \ the track description page, followed by a list of subtracks. \ For more information about the graphical configuration options, click the \ Graph\ configuration help link. To display only selected subtracks, uncheck the \ boxes next to the tracks you wish to hide.
\ \\ To create the tag, a linker was\ attached to the 5' end of full-length cDNAs which had been selected by cap\ trapping. The first 20 bp of the cDNA were cleaved using the class II\ restriction enzyme, MmeI, followed by PCR amplification. Concatamers\ of the resulting 32 bp tags were then formed for more efficient sequencing.\ A total of 7,151,511 mapped CAGE tags from 145 cDNA libraries, corresponding to \ 22 distinct tissues were produced. \ The tags were mapped to the mm5 assembly and lifted to other\ assemblies using UCSC's liftOver tool.\ For more information on\ CAGE, see Shiraki et al. (2003) and Carninci et al (2005)\ below. The mapping methodology employed in this annotation will be \ described in upcoming publications.
\ \\ These data were contributed by the Functional Annotation of Mouse\ (FANTOM)\ Consortium, RIKEN Genome Science Laboratory and\ \ RIKEN Genome Exploration Research Group\ (Genome Network Project Core Group).
\ \\ FANTOM Consortium: P. Carninci, T. Kasukawa, S. Katayama, Gough, \ M. Frith, N. Maeda, R. Oyama, T. Ravasi, B. Lenhard, C. Wells, R. \ Kodzius, K. Shimokawa, V. B. Bajic, S. E. Brenner, S. Batalov, A. R. R. \ Forrest, M. Zavolan, M. J. Davis, L. G. Wilming, V. Aidinis, J. Allen, \ A. Ambesi-Impiombato, R. Apweiler, R. N. Aturaliya, T. L. Bailey, M. \ Bansal, K. W. Beisel, T. Bersano, H. Bono, A. M. Chalk, K. P. Chiu, V. \ Choudhary, A. Christoffels, D. R. Clutterbuck, M. L. Crowe, E. Dalla, \ B. P. Dalrymple, B. de Bono, G. Della Gatta, D. di Bernardo, T. Down, \ P. Engstrom, M. Fagiolini, G. Faulkner, C. F. Fletcher, T. Fukushima, \ M. Furuno, S. Futaki, M. Gariboldi, P. Georgii-Hemming, T. R. Gingeras, \ T. Gojobori, R. E. Green, S. Gustincich, M. Harbers, V. Harokopos, Y. \ Hayashi, S. Henning, T. K. Hensch, N. Hirokawa, D. Hill, L. Huminiecki, \ M. Iacono, K. Ikeo, A. Iwama, T. Ishikawa, M. Jakt, A. Kanapin, M. \ Katoh, Y. Kawasawa, J. Kelso, H. Kitamura, H. Kitano, G. Kollias, S. \ P. T. Krishnan, A.F. Kruger, K. Kummerfeld, I. V. Kurochkin, \ L. F. Lareau, L. Lipovich, J. Liu, S. Liuni, S. McWilliam, M. Madan \ Babu, M. Madera, L. Marchionni, H. Matsuda, S. Matsuzawa, H. Miki, F. \ Mignone, S. Miyake, K. Morris, S. Mottagui-Tabar, N. Mulder, N. Nakano, \ H. Nakauchi, P. Ng, R. Nilsson, S. Nishiguchi, S. Nishikawa, F. Nori, \ O. Ohara, Y. Okazaki, V. Orlando, K. C. Pang, W. J. Pavan, G. Pavesi, \ G. Pesole, N. Petrovsky, S. Piazza, W. Qu, J. Reed, J. F. Reid, B. Z. \ Ring, M. Ringwald, B. Rost, Y. Ruan, S. Salzberg, A. Sandelin, C. \ Schneider, C. Schoenbach, K. Sekiguchi, C. A. M. Semple, S. Seno, \ L. Sessa, Y. Sheng, Y. Shibata, H. Shimada, K. Shimada, B. Sinclair, S. \ Sperling, E. Stupka, K. Sugiura, R. Sultana, Y. Takenaka, K. Taki, K. \ Tammoja, S. L. Tan, S. Tang, M. S. Taylor, J. Tegner, S. A. Teichmann, \ H. R. Ueda, E. van Nimwegene, R. Verardo, C. L. Wei, K. Yagi, H. \ Yamanishi, E. Zabarovsky, S. Zhu, A. Zimmer, W. Hide, C. Bult, S. M. \ Grimmond, R. D. Teasdale, E. T. Liu, V. Brusic, J. Quackenbush, C. \ Wahlestedt, J. Mattick, D. Hume.
\\ RIKEN Genome Exploration Research Group: C. Kai, D. Sasaki, Y. \ Tomaru, S. Fukuda, M. Kanamori-Katayama, M. Suzuki, J. Aoki, T. \ Arakawa, J. Iida, K. Imamura, M. Itoh, T. Kato, H. Kawaji, N. \ Kawagashira, T. Kawashima, M. Kojima, S. Kondo, H. Konno, K. Nakano, N. \ Ninomiya, T. Nishio, M. Okada, C. Plessy, K. Shibata, T. Shiraki, S. \ Suzuki, M. Tagami, K Waki, A. Watahiki, Y. Okamura-Oho, H. Suzuki, J. \ Kawai.
\\ General Organizer: Y. Hayashizaki\ \
\ FANTOM Consortium: P. Carninci, et al. \ The transcriptional \ landscape of the mammalian genome. Science 309(5740),\ 1559-63 (2005).\ \
\ Shiraki, T., Kondo, S., Katayama, S., Waki, K., Kasukawa, T., Kawaji, H., \ Kodzius, R., Watahiki, A., Nakamura, M. et al.\ Cap analysis gene expression for high-throughput analysis of \ transcriptional starting point and identification of promoter usage.\ Proc Natl Acad Sci U S A. 100(26), 15776-81 (2003).
\ rna 0 autoScale Off\ compositeTrack on\ maxHeightPixels 128:16:16\ maxLimit 4316\ minLimit 1\ origAssembly mm5\ viewLimits 1.0:10.0\ windowingFunction mean\ allenBrainAli Allen Brain psl . Allen Brain Atlas Probes 0 80 50 0 100 152 127 177 0 0 0\ This track provides a link into the \ Allen Brain Atlas (ABA)\ images for this probe. The ABA is an extensive\ database of high resolution in-situ hybridization images of adult\ male mouse brains covering the majority of genes.
\ \\ The ABA created a platform for high-throughput in situ hybridization \ (ISH) that allows a highly systematic approach to analyzing gene expression in \ the brain. ISH is a technique that allows the cellular localization of mRNA \ transcripts for specific genes. Labeled antisense probes, specific to a \ particular gene, are hybridized to cellular (sense) transcripts and subsequent \ detection of the bound probe produces specific labeling in those cells \ expressing the particular gene. This method involves tagged nucleotides \ detected by colorimetric methods.
\ \The platform used for the ABA utilizes this non-isotopic approach, with \ digoxigenin-labeled nucleotides incorporated into a riboprobe produced by in\ vitro transcription. This method produces a label that fills the cell body,\ in contrast to autoradiography that produces scattered silver grains surrounding\ each labeled cell. To enhance the ability to detect low level expression, the \ ABA has incorporated a tyramide signal amplification step into the protocol that\ greatly increases sensitivity. The specific methodology is described in detail \ within the ABA Data Production Processes document.
\ \\ Thanks to the Allen \ Institute for Brain Science in general, and Susan \ Sunkin in particular, for coordinating with UCSC on this annotation.
\ \ regulation 1 gnfAtlas2 GNF Atlas 2 expRatio GNF Expression Atlas 2 0 81 0 0 0 127 127 127 0 0 0This track shows expression data from the GNF Gene Expression\ Atlas 2. This contains two replicates each of 61 mouse \ tissues run over Affymetrix microarrays. In full mode all tissues are\ displayed. In packed or dense mode averages of related tissues are shown.\ As is standard with microarray data red indicates overexpression in the \ tissue, and green indicates underexpression. You may want to view gene\ expression with the Gene Sorter as well as the Genome Browser.
\ \\ Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, \ Soden R, Hayakawa M, Kreiman G, et al.\ A\ gene atlas of the mouse and human protein-encoding transcriptomes.\ Proc Natl Acad Sci U S A. 2004 Apr 20;101(16):6062-7. Epub 2004 Apr 9. \
\ \ regulation 1 expScale 4.0\ expStep 0.5\ expTable gnfMouseAtlas2MedianExps\ groupings gnfMouseAtlas2Groups\ rinnSex Rinn Sex Exp expRatio Rinn et al. Sex Gene Expression Data on MOE430A Chip 0 81.1 0 0 0 127 127 127 0 0 0\ This track shows gene expression differences between adult male \ and female tissues, as described in Rinn, J.L. et al. (2004) \ in the References section below.
\ \\ In full display mode, the medians of all replicates (technical and biological)\ for each sex's tissue are shown. To view the individual replicates, use the \ UCSC Gene Sorter. In packed and squished \ display modes, the average over all tissues is shown for each sex. Dense \ display mode shows the placement of the Affy MOE430A target sequences \ colored by overall expression level in both sexes, with darker colors \ representing higher levels of expression.
\ \\ Five adult mouse tissues (liver, kidney, hypothalamus, ovary and testis) \ were studied. For each somatic tissue, triple selected poly-A mRNA was \ prepared from six independent pools (biological replicates), three male and \ three female. Likewise, three pools were prepared from the ovary and three \ pools from the testis. Each pool of RNA was derived from ten individuals. \ For each biological replicate, two cDNAs (technical replicates) \ were prepared and independently hybridized to Affymetrix MOE430A chips.
\ \Thanks to John Rinn for providing these data.
\ \\ Rinn, J.L. et al. \ Major molecular differences between mammalian sexes are involved\ in drug metabolism and renal function, Developmental Cell \ 6, 791-800 (2004).
\ regulation 1 expScale 8.0\ expStep 1.0\ expTable mouseRinnSexMedianExps\ groupings rinnSexGroups\ affyGnfU74A GNF U74A expRatio GNF Expression Atlas on Mouse Affymetrix U74A Chip 0 82 0 0 0 127 127 127 0 0 0\ This track shows expression data from GNF (The Genomics Institute of the Novartis Research \ Foundation) using the Affymetrix U74A chip.
\ \\ For detailed information about the experiments, see Su et al. (2002)\ in the References section below. Alignments displayed on the track correspond \ to the consensus sequences used by Affymetrix to choose probes.
\\ In dense mode, the track color denotes the average signal over all\ experiments on a log base 2 scale. Lighter colors correspond to lower signals;\ darker colors correspond to higher signals. In full\ mode, the color of each item represents the log base 2 ratio of the signal of\ that particular experiment to the median signal of all experiments for that \ probe.
\\ More information about individual probes and probe sets is available at\ Affymetrix's netaffx.com website.
\ \\ Thanks to GNF for providing these data.
\ \\ Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T, \ Orth AP, Vega RG, Sapinoso LM, Moqrich A, et al. \ Large-scale analysis of the human and mouse transcriptomes. \ Proc Natl Acad Sci USA. 2002 Apr 2;99(7):4465-70. Epub 2002 Mar 19.\
\ regulation 1 expScale 4.0\ expStep 0.5\ expTable gnfMouseU74aAllExps\ groupings gnfMouseU74aGroups\ affyGnfU74B GNF U74B expRatio GNF Expression Atlas on Mouse Affymetrix U74B Chip 0 82.1 0 0 0 127 127 127 0 0 0\ This track shows expression data from GNF (The Genomics Institute of the Novartis Research \ Foundation) using the Affymetrix U74B chip.
\ \\ For detailed information about the experiments, see Su et al. (2002)\ in the References section below. Alignments displayed on the track\ correspond to the consensus sequences used by Affymetrix to choose probes.
\ \\ In dense mode, the track color denotes the average signal over all\ experiments on a log base 2 scale. Lighter colors correspond to lower signals;\ darker colors correspond to higher signals. In full\ mode, the color of each item represents the log base 2 ratio of the signal of\ that particular experiment to the median signal of all experiments for that \ probe.
\\ More information about individual probes and probe sets is available at\ Affymetrix's netaffx.com website.
\ \\ Thanks to GNF for providing these data.
\ \\ Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T,\ Orth AP, Vega RG, Sapinoso LM, Moqrich A, et al.\ Large-scale analysis of the human and mouse transcriptomes.\ Proc Natl Acad Sci USA. 2002 Apr 2;99(7):4465-70. Epub 2002 Mar 19. \
\ regulation 1 expScale 4.0\ expStep 0.5\ expTable gnfMouseU74bAllExps\ groupings gnfMouseU74bGroups\ affyGnfU74C GNF U74C expRatio GNF Expression Atlas on Mouse Affymetrix U74C Chip 0 82.2 0 0 0 127 127 127 0 0 0\ This track shows expression data from GNF (The Genomics Institute of the Novartis Research \ Foundation) using the Affymetrix U74C chip.
\ \\ For detailed information about the experiments, see Su et al. (2002)\ in the References section below. Alignments displayed on the track correspond \ to the consensus sequences used by Affymetrix to choose probes.
\\ In dense mode, the track color denotes the average signal over all\ experiments on a log base 2 scale. Lighter colors correspond to lower signals \ and darker colors correspond to higher signals. In full\ mode, the color of each item represents the log base 2 ratio of the signal of\ that particular experiment to the median signal of all experiments for that \ probe.
\\ More information about individual probes and probe sets is available at\ Affymetrix's netaffx.com website.
\ \\ Thanks to GNF for providing these data.
\ \\ Su AI, Cooke MP, Ching KA, Hakak Y, Walker JR, Wiltshire T,\ Orth AP, Vega RG, Sapinoso LM, Moqrich A, et al.\ Large-scale analysis of the human and mouse transcriptomes.\ Proc Natl Acad Sci USA. 2002 Apr 2;99(7):4465-70. Epub 2002 Mar 19. \
\ regulation 1 expScale 4.0\ expStep 0.5\ expTable gnfMouseU74cAllExps\ groupings gnfMouseU74cGroups\ affyGnf1m Affy GNF1M psl . Alignments of Probes from Affymetrix GNF1M Chip 0 85 0 0 0 127 127 127 0 0 0\ This track shows the location of the sequences used for the selection of \ probes on the Affymetrix GNF1M chips. The annotation contains 31,000 \ non-overlapping mouse genes and gene predictions.
\ \\ The sequences were mapped to the genome with blat followed by pslReps \ using the parameters -minCover=0.3, -minAli=0.95 and \ -nearTop=0.005.
\ \\ Thanks to the \ Genomics Institute of the Novartis\ Research Foundation (GNF) for the data underlying this track.
\ regulation 1 affyU74 Affy U74 psl . Alignments of Affymetrix Consensus Sequences from MG-U74 v2 (A,B, and C) 0 86 0 0 0 127 127 127 0 0 0\ This track shows the location of the consensus sequences used for the \ selection of probes on the Affymetrix MG-U74v2 set (A,B and C) of chips.
\ \\ Consensus sequences were downloaded from the\ Affymetrix Product Support\ and mapped to the genome with blat followed by pslReps using the parameters\ -minCover=0.3, -minAli=0.95 and -nearTop=0.005.
\ \\ Thanks to Affymetrix \ for the data underlying this track.
\ regulation 1 affyMOE430 Affy MOE430 psl . Alignments of Affymetrix Consensus Sequences from Mouse MOE430 (A and B) 0 87 0 0 0 127 127 127 0 0 0\ This track shows the location of the consensus sequences used for the \ selection of probes on the Affymetrix Mouse MOE430 set (A and B) of chips.
\ \\ Consensus sequences were downloaded from the\ Affymetrix Product Support\ and mapped to the genome with blat followed by pslReps using the parameters\ -minCover=0.3, -minAli=0.95 and -nearTop=0.005.
\ \\ Thanks to Affymetrix \ for the data underlying this track.
\ \ regulation 1 cpgIslandExt CpG Islands bed 4 + CpG Islands (Islands < 300 Bases are Light Green) 0 90 0 100 0 128 228 128 0 0 0\ CpG islands are associated with genes, particularly housekeeping\ genes, in vertebrates. CpG islands are typically common near\ transcription start sites, and may be associated with promoter\ regions. Normally a C (cytosine) base followed immediately by a \ G (guanine) base (a CpG) is rare in\ vertebrate DNA because the Cs in such an arrangement tend to be\ methylated. This methylation helps distinguish the newly synthesized\ DNA strand from the parent strand, which aids in the final stages of\ DNA proofreading after duplication. However, over evolutionary time\ methylated Cs tend to turn into Ts because of spontaneous\ deamination. The result is that CpGs are relatively rare unless\ there is selective pressure to keep them or a region is not methylated\ for some reason, perhaps having to do with the regulation of gene\ expression. CpG islands are regions where CpGs are present at\ significantly higher levels than is typical for the genome as a whole.\
\ \\ CpG islands were predicted by searching the sequence one base at a\ time, scoring each dinucleotide (+17 for CG and -1 for others) and\ identifying maximally scoring segments. Each segment was then\ evaluated for the following criteria:\
\ The CpG count is the number of CG dinucleotides in the island. \ The Percentage CpG is the ratio of CpG nucleotide bases\ (twice the CpG count) to the length. The ratio of observed to expected \ CpG is calculated according to the formula cited in \ Gardiner-Garden et al. (1987) in the References section below: \
\
Obs/Exp CpG = Number of CpG * N / (Number of C * Number of G)\
\
where N = length of sequence.\
\
\
\ This track was generated using a\ modification of a program developed by G. Miklem and L. Hillier.
\ \\ Gardiner-Garden M, Frommer M. \ CpG islands in vertebrate genomes.\ J. Mol. Biol. 1987 Jul 20;196(2):261-82.
\ regulation 1 multiz10way Conservation wigMaf 0.0 1.0 10-Way Vertebrate Multiz Alignment & Conservation 2 104 0 10 100 0 90 10 0 0 0\ This track shows a measure of evolutionary conservation in $organism, rat, human, \ dog, cow, opossum, chicken, frog, zebrafish, and Tetraodon based on a phylogenetic hidden Markov model (phastCons).\ Multiz alignments of the following assemblies were used to generate this\ annotation: \
\
\ In full display mode, this track shows the overall conservation score across \ all species, as well as pairwise alignments \ of rat, human, dog, cow, opossum, chicken, zebrafish and Tetraodon, each \ aligned to the $organism genome. The pairwise alignments are\ shown in dense display mode using a grayscale \ density gradient. The checkboxes in the track configuration section allow\ the exclusion of species from the pairwise display; however, this does not\ remove them from the conservation score display.
\\ When zoomed-in to the base-display level, the track shows the base \ composition of each alignment. The numbers and symbols on the Gaps\ line indicate the lengths of gaps in the $organism sequence at those \ alignment positions relative to the longest non-$organism sequence. \ If there is sufficient space in the display, the size of the gap is shown; \ if not, and if the gap size is a multiple of 3, a "*" is displayed, \ otherwise "+" is shown. \ To view detailed information about the alignments at a specific position,\ zoom in the display to 30,000 or fewer bases, then click on the alignment.
\\ This track may be configured in a variety of ways to highlight different \ aspects of the displayed information. Click \ here\ for an explanation of the configuration options.
\ \\ Best-in-genome blastz pairwise alignments \ were multiply aligned using multiz, beginning with $organism-rat alignments\ and subsequently adding in the other species, as diagrammed above.\ The resulting multiple alignments were then assigned \ conservation scores by phastCons.
\\ The phastCons program computes conservation scores based on a phylo-HMM, a\ type of probabilistic model that describes both the process of DNA\ substitution at each site in a genome and the way this process changes from\ one site to the next (Felsenstein and Churchill 1996, Yang 1995, Siepel and\ Haussler 2005). PhastCons uses a two-state phylo-HMM, with a state for\ conserved regions and a state for non-conserved regions. The value plotted\ at each site is the posterior probability that the corresponding alignment\ column was "generated" by the conserved state of the phylo-HMM. These\ scores reflect the phylogeny (including branch lengths) of the species in\ question, a continuous-time Markov model of the nucleotide substitution\ process, and a tendency for conservation levels to be autocorrelated along\ the genome (i.e., to be similar at adjacent sites). The general reversible\ (REV) substitution model was used. Note that, unlike many\ conservation-scoring programs, phastCons does not rely on a sliding window\ of fixed size, so short highly-conserved regions and long moderately\ conserved regions can both obtain high scores. More information about\ phastCons can be found in Siepel et al. (2005).
\\ PhastCons currently treats alignment gaps as missing data, which\ sometimes has the effect of producing undesirably high conservation scores\ in gappy regions of the alignment. We are looking at several possible ways\ of improving the handling of alignment gaps.
\ \\ This track was created at UCSC using the following programs:\
The phylogenetic tree is based on Murphy et al. (2001) and general\ consensus in the vertebrate phylogeny community.\
\ \\ Felsenstein J and Churchill GA (1996). \ A hidden Markov model approach to \ variation among sites in rate of evolution.\ Mol Biol Evol 13:93-104.
\\ Siepel A and Haussler D (2005). Phylogenetic hidden Markov models.\ In R. Nielsen, ed., Statistical Methods in Molecular Evolution,\ pp. 325-351, Springer, New York.
\\ Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M., Rosenbloom, \ K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., Weinstock, G.M., \ Wilson, R. K., Gibbs, R.A., Kent, W.J., Miller, W., and Haussler, D. \ Evolutionarily conserved elements in vertebrate, insect, worm, \ and yeast genomes.\ Genome Res. 15, 1034-1050 (2005).
\\ Yang Z (1995). \ A space-time process model for the evolution of DNA\ sequences. Genetics, 139:993-1005.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\ \\ Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F.A.,\ Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D.,\ Haussler, D., Miller, W.\ Aligning multiple genomic sequences with the threaded blockset\ aligner.\ Genome Res. 14(4), 708-15 (2004).
\ \\ Chiaromonte, F., Yap, V.B., Miller, W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \\ Murphy, W.J., et al.\ Resolution of the early placental mammal radiation using Bayesian phylogenetics.\ Science 294(5550), 2348-51 (2001).
\ compGeno 1 autoScaleDefault Off\ maxHeightPixels 100:40:11\ sGroup_mammal rn3 hg17 canFam2 bosTau1 monDom1\ sGroup_vertebrate galGal2 xenTro1 danRer3 tetNig1\ spanList 1\ speciesGroups mammal vertebrate\ summary multiz10waySummary\ treeImage phylo/mm6_10way.gif\ wiggle phastCons10\ windowingFunction mean\ yLineOnOff Off\ phastConsElements Most Conserved bed 5 . PhastCons Conserved Elements 0 105 0 0 0 127 127 127 0 0 0\ This track shows predictions of conserved elements produced by the phastCons\ program. PhastCons is part of the PHAST (PHylogenetic Analysis with \ Space/Time models) package. The predictions are based on a phylogenetic hidden \ Markov model (phylo-HMM), a type of probabilistic model that describes both \ the process of DNA substitution at each site in a genome and the way this \ process changes from one site to the next.
\ \\ Best-in-genome pairwise alignments were generated for\ each species using blastz, followed by chaining and netting. A multiple\ alignment was then constructed from these pairwise alignments using multiz.\ Predictions of conserved elements were then obtained by running phastCons\ on the multiple alignments with the --most-conserved option.
\\ PhastCons constructs a two-state phylo-HMM with a state for conserved\ regions and a state for non-conserved regions. The two states share a\ single phylogenetic model, except that the branch lengths of the tree\ associated with the conserved state are multiplied by a constant scaling\ factor rho (0 <= rho <= 1). The free parameters of the\ phylo-HMM, including the scaling factor rho, are estimated from\ the data by maximum likelihood using an EM algorithm. This procedure is\ subject to certain constraints on the "coverage" of the genome by conserved\ elements and the "smoothness" of the conservation scores. Details can be\ found in Siepel et al. (2005).
\\ The predicted conserved elements are segments of the alignment that are\ likely to have been "generated" by the conserved state of the phylo-HMM.\ Each element is assigned a log-odds score equal to its log probability\ under the conserved model minus its log probability under the non-conserved\ model. The "score" field associated with this track contains transformed\ log-odds scores, taking values between 0 and 1000. (The scores are\ transformed using a monotonic function of the form a * log(x) + b.) The\ raw log odds scores are retained in the "name" field and can be seen on the\ details page or in the browser when the track's display mode is set to\ "pack" or "full".
\ \\ This track was created at UCSC using the following programs:\
\ Siepel, A., Bejerano, G., Pedersen, J.S., Hinrichs, A., Hou, M., Rosenbloom, \ K., Clawson, H., Spieth, J., Hillier, L.W., Richards, S., Weinstock, G.M., \ Wilson, R. K., Gibbs, R.A., Kent, W.J., Miller, W., and Haussler, D. \ Evolutionarily conserved elements in vertebrate, insect, worm, \ and yeast genomes.\ Genome Res. 15, 1034-1050 (2005).
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\ \\ Blanchette, M., Kent, W.J., Riemer, C., Elnitski, L., Smit, A.F.A., \ Roskin, K.M., Baertsch, R., Rosenbloom, K., Clawson, H., Green, E.D., \ Haussler, D., Miller, W. \ Aligning multiple genomic sequences with the threaded blockset\ aligner.\ Genome Res. 14(4), 708-15 (2004).
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., \ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ. \ Genome Res. 13(1), 103-7 (2003).
\ compGeno 1 exonArrows off\ showTopScorers 200\ chainFr1 $o_Organism Chain chain fr1 $o_Organism ($o_date/$o_db) Chained Alignments 0 140 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_Organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_Organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_Organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ Transposons that have been inserted since the $o_Organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz, and the transposons were then added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single $o_Organism chromosome and a single\ $organism chromosome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks. \ \ $matrix\ \ Chains scoring below a threshold were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., \ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ. \ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 1 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\ matrixHeader A, C, G, T\ otherDb fr1\ netFr1 $o_Organism Net netAlign fr1 chainFr1 $o_Organism ($o_date/$o_db) Alignment Net 0 140.1 0 0 0 127 127 127 1 0 0\ This track shows the best $o_Organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_Organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 0 otherDb fr1\ rmsk RepeatMasker rmsk Repeating Elements by RepeatMasker 1 149.1 0 0 0 127 127 127 1 0 0\
This track was created by using Arian Smit's
\ In full display mode, this track displays up to ten different classes of repeats:\
\ The level of color shading in the graphical display reflects the amount of \ base mismatch, base deletion, and base insertion associated with a repeat \ element. The higher the combined number of these, the lighter the shading.
\ \\ UCSC has used the most current versions of the RepeatMasker software \ and repeat libraries available to generate these data. Note that these \ versions may be newer than those that are publicly available on the Internet. \
\\ Data are generated using the RepeatMasker -s flag. Additional flags\ may be used for certain organisms. Repeats are soft-masked. Alignments may \ extend through repeats, but are not permitted to initiate in them. \ See the \ FAQ for \ more information.
\ \\ Thanks to Arian Smit and GIRI\ for providing the tools and repeat libraries used to generate this track.
\ \\ Smit, AFA, Hubley, R and Green, P. RepeatMasker Open-3.0.\ http://www.repeatmasker.org. 1996-2007.\
\\ RepBase is described in \ Jurka J. \ Repbase update: a database and an electronic journal of \ repetitive elements. \ Trends Genet. 2000 Sep;16(9):418-420.
\\ For a discussion of repeats in mammalian genomes, see: \
\ Smit AF. Interspersed repeats and other mementos of transposable \ elements in mammalian genomes. Curr Opin Genet Dev. 1999 Dec;9(6):\ 657-63.
\\ Smit AF. The origin of interspersed repeats in the human genome. \ Curr Opin Genet Dev. 1996 Dec;6(6):743-8.\
\ varRep 0 simpleRepeat Simple Repeats bed 4 + Simple Tandem Repeats by TRF 0 149.3 0 0 0 127 127 127 0 0 0\ This track displays simple tandem repeats (possibly imperfect) located\ by Tandem Repeats\ Finder (TRF), which is specialized for this purpose. These repeats can\ occur within coding regions of genes and may be quite\ polymorphic. Repeat expansions are sometimes associated with specific\ diseases.
\ \\ For more information about the TRF program, see Benson (1999).\
\ \\ TRF was written by \ Gary Benson.
\ \\ Benson G. \ Tandem repeats finder: a program to analyze DNA sequences.\ Nucleic Acids Res. 1999 Jan 15;27(2):573-80.
\ varRep 1 chainTetNig1 $o_Organism Chain chain tetNig1 $o_Organism ($o_date/$o_db) Chained Alignments 0 150 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_Organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_Organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_Organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ Transposons that have been inserted since the $o_Organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz, and the transposons were then added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single $o_Organism chromosome and a single\ $organism chromosome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks. \ \ $matrix\ \ Chains scoring below a threshold were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte F, Yap VB, Miller W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput. 2002;:115-26.
\\ Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.
\\ Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\ Haussler D, Miller W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 2003 Jan;13(1):103-7.
\ \ compGeno 1 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\ matrixHeader A, C, G, T\ otherDb tetNig1\ netTetNig1 $o_Organism Net netAlign tetNig1 chainTetNig1 $o_Organism ($o_date/$o_db) Alignment Net 0 150.1 0 0 0 127 127 127 1 0 0\ This track shows the best $o_Organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_Organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\ \\ Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9.
\\ Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison RC,\ Haussler D, Miller W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 2003 Jan;13(1):103-7.
\ compGeno 0 otherDb tetNig1\ chainDanRer2 $o_Organism Chain chain danRer2 $o_Organism ($o_date/$o_db) Chained Alignments 0 160 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz, and the transposons were then added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single $o_organism chromosome and a single\ $organism chromosome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks. \ \ $matrix\ \ Chains scoring below a threshold were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., \ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ. \ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 1 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\ matrixHeader A, C, G, T\ otherDb danRer2\ netDanRer2 $o_Organism Net netAlign danRer2 chainDanRer2 $o_Organism ($o_date/$o_db) Alignment Net 0 160.1 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 0 otherDb danRer2\ chainXenTro1 $o_Organism Chain chain xenTro1 $o_Organism ($o_date/$o_db) Chained Alignments 0 170 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_Organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_Organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_Organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the scaffold, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ Transposons that have been inserted since the \ $o_Organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz, and the transposons were then added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single $o_Organism scaffold and a single\ $organism chromosome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks. \ \ $matrix\ \ Chains scoring below a threshold were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., \ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ. \ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 1 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\ matrixHeader A, C, G, T\ otherDb xenTro1\ netXenTro1 $o_Organism Net netAlign xenTro1 chainXenTro1 $o_Organism ($o_date/$o_db) Alignment Net 0 170.3 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is \ from the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \ \ compGeno 0 otherDb xenTro1\ chainGalGal2 $o_Organism Chain chain galGal2 $o_Organism ($o_date/$o_db) Chained Alignments 0 180 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz, and the transposons were then added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single $o_organism chromosome and a single\ $organism chromosome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks. \ \ $matrix\ \ Chains scoring below a threshold were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., \ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ. \ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 1 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91\ matrixHeader A, C, G, T\ otherDb galGal2\ netGalGal2 $o_Organism Net netAlign galGal2 chainGalGal2 $o_Organism ($o_date/$o_db) Alignment Net 0 180.1 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \ \ compGeno 0 otherDb galGal2\ chainMonDom1 $o_Organism Chain chain monDom1 $o_Organism ($o_date/$o_db) Chained Alignments 0 190 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the scaffold, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz, and the transposons were then added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single $o_organism scaffold and a single\ $organism chromosome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks. Chains scoring below a threshold were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., \ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ. \ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 1 otherDb monDom1\ netMonDom1 $o_Organism Net netAlign monDom1 chainMonDom1 $o_Organism ($o_date/$o_db) Alignment Net 0 190.1 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 0 otherDb monDom1\ chainCanFam1 $o_Organism Chain chain canFam1 $o_Organism ($o_date/$o_db) Chained Alignments 0 220.3 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz, and the transposons were then added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single $o_organism chromosome and a single\ $organism chromosome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks. Chains scoring below a threshold were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., \ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ. \ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 1 otherDb canFam1\ netCanFam1 $o_Organism Net netAlign canFam1 chainCanFam1 $o_Organism ($o_date/$o_db) Alignment Net 0 220.4 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 0 otherDb canFam1\ chainBosTau1 $o_Organism Chain chain bosTau1 $o_Organism ($o_date/$o_db) Chained Alignments 0 256.7 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the scaffold, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz, and the transposons were then added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single $o_organism scaffold and a single\ $organism chromosome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks. Chains scoring below a threshold were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., \ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ. \ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 1 otherDb bosTau1\ netBosTau1 $o_Organism Net netAlign bosTau1 chainBosTau1 $o_Organism ($o_date/$o_db) Alignment Net 0 256.8 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 0 otherDb bosTau1\ chainPanTro1 $o_Organism Chain chain panTro1 $o_Organism ($o_date/$o_db) Chained Alignments 0 278.5 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. The $o_organism genomic sequence is\ from the 13 Nov. 2003 Arachne draft assembly.\
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz, and the transposons were added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single $o_organism chromosome and a single\ $organism chromosome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks.\ \ $matrix\ \ Chains scoring below a threshold were discarded; the remaining\ chains are displayed in this track.
\ \\ The $o_organism sequence used in this track was obtained from the 13 Nov. \ 2003 Arachne assembly. We'd like to thank the National Human Genome Research \ Institute (NHGRI), the Broad Institute at MIT/Harvard, and Washington \ University St. Louis School of Medicine for providing this sequence.
\\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., \ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ. \ Genome Res. 13(1), 103-7 (2003).
\ compGeno 1 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\ matrixHeader A, C, G, T\ otherDb panTro1\ netPanTro1 $o_Organism Net netAlign panTro1 chainPanTro1 $o_Organism ($o_date/$o_db) Alignment Net 0 278.6 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \ \ compGeno 0 otherDb panTro1\ chainHg17 $o_Organism Chain chain hg17 $o_Organism ($o_date/$o_db) Chained Alignments 0 279.6 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz, and the transposons were added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single $o_organism chromosome and a single\ $organism chromosome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks. Chains scoring below a threshold were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., \ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ. \ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 1 otherDb hg17\ netHg17 $o_Organism Net netAlign hg17 chainHg17 $o_Organism ($o_date/$o_db) Alignment Net 0 279.7 0 0 0 127 127 127 1 0 0\ This track shows the best $o_Organism/$Organism chain for \ every part of the $Organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his program \ RepeatMasker.
\\ The browser display and database storage of the nets were made\ by Robert Baertsch and Jim Kent.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \ \ \ compGeno 0 otherDb hg17\ chainRn3 $o_Organism Chain chain rn3 $o_Organism ($o_date/$o_db) Chained Alignments 0 286.2 100 50 0 255 240 200 1 0 0\ This track shows alignments of $o_organism ($o_db, $o_date) to the\ $organism genome using a gap scoring system that allows longer gaps \ than traditional affine gap scoring systems. It can also tolerate gaps in both\ $o_organism and $organism simultaneously. These \ "double-sided" gaps can be caused by local inversions and \ overlapping deletions in both species. \
\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions.\ Single lines indicate gaps that are largely due to a deletion in the\ $o_organism assembly or an insertion in the $organism \ assembly. Double lines represent more complex gaps that involve substantial\ sequence in both species. This may result from inversions, overlapping\ deletions, an abundance of local mutation, or an unsequenced gap in one\ species. In cases where multiple chains align over a particular region of\ the $organism genome, the chains with single-lined gaps are often \ due to processed pseudogenes, while chains with double-lined gaps are more \ often due to paralogs and unprocessed pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ Transposons that have been inserted since the $o_organism/$organism\ split were removed from the assemblies. The abbreviated genomes were\ aligned with blastz, and the transposons were then added back in.\ The resulting alignments were converted into axt format using the lavToAxt\ program. The axt alignments were fed into axtChain, which organizes all\ alignments between a single $o_organism chromosome and a single\ $organism chromosome into a group and creates a kd-tree out\ of the gapless subsections (blocks) of the alignments. A dynamic program\ was then run over the kd-trees to find the maximally scoring chains of these\ blocks. \ \ $matrix\ \ Chains scoring below a threshold were discarded; the remaining\ chains are displayed in this track.
\ \\ Blastz was developed at Pennsylvania State University by \ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his \ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California at \ Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W. \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R., \ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ. \ Genome Res. 13(1), 103-7 (2003).
\ \ compGeno 1 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91\ matrixHeader A, C, G, T\ otherDb rn3\ netRn3 $o_Organism Net netAlign rn3 chainRn3 $o_Organism ($o_date/$o_db) Alignment Net 0 286.3 0 0 0 127 127 127 1 0 0\ This track shows the best $o_organism/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. The $o_organism sequence used in this annotation is from\ the $o_date ($o_db) assembly.
\ \\ In full display mode, the top-level (level 1)\ chains are the largest, highest-scoring chains that\ span this region. In many cases gaps exist in the\ top-level chain. When possible, these are filled in by\ other chains that are displayed at level 2. The gaps in \ level 2 chains may be filled by level 3 chains and so\ forth.
\\ In the graphical display, the boxes represent ungapped \ alignments; the lines represent gaps. Click\ on a box to view detailed information about the chain\ as a whole; click on a line to display information\ about the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\\ Individual items in the display are categorized as one of four types\ (other than gap):
\\ Chains were derived from blastz alignments, using the methods\ described on the chain tracks description pages, and sorted with the \ highest-scoring chains in the genome ranked first. The program\ chainNet was then used to place the chains one at a time, trimming them as \ necessary to fit into sections not already covered by a higher-scoring chain. \ During this process, a natural hierarchy emerged in which a chain that filled \ a gap in a higher-scoring chain was placed underneath that chain. The program \ netSyntenic was used to fill in information about the relationship between \ higher- and lower-level chains, such as whether a lower-level\ chain was syntenic or inverted relative to the higher-level chain. \ The program netClass was then used to fill in how much of the gaps and chains \ contained Ns (sequencing gaps) in one or both species and how much\ was filled with transposons inserted before and after the two organisms \ diverged.
\ \\ The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ Santa Cruz by Jim Kent.
\\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his\ program RepeatMasker.\
\\ The browser display and database storage of the nets were made\ by Robert Baertsch and Jim Kent.
\ \\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \ \ compGeno 0 otherDb rn3\ chainSelf Self Chain chain mm6 Self Chained Alignments 0 400 100 50 0 255 240 200 1 0 0\ This track shows alignments of the $organism genome with itself, using\ a gap scoring system that allows longer gaps than traditional\ affine gap scoring systems. The system can also tolerate gaps\ in both sets of sequence simultaneously. After filtering out the \ "trivial" alignments produced when identical locations of the \ genome map to one another (e.g. chrN mapping to chrN), \ the remaining alignments point out areas of duplication within the \ $organism genome.
\\ The chain track displays boxes joined together by either single or\ double lines. The boxes represent aligning regions. Single lines indicate \ gaps that are largely due to a deletion in the query assembly or an \ insertion in the target assembly. Double lines represent more complex gaps \ that involve substantial sequence in both the query and target assemblies. \ This may result from inversions, overlapping deletions, an abundance of local \ mutation, or an unsequenced gap in one of the assemblies. In cases where \ multiple chains align over a particular region of the $organism genome, the \ chains with single-lined gaps are often due to processed pseudogenes, while \ chains with double-lined gaps are more often due to paralogs and unprocessed \ pseudogenes.
\\ In the "pack" and "full" display\ modes, the individual feature names indicate the chromosome, strand, and\ location (in thousands) of the match for each matching alignment.
\ \\ The genome was aligned to itself using blastz. Trivial alignments were \ filtered out, and the remaining alignments were converted into axt format\ using the lavToAxt program. The axt alignments were fed into axtChain, which \ organizes all alignments between a single target chromosome and a single\ query chromosome into a group and creates a kd-tree out of the gapless \ subsections (blocks) of the alignments. A dynamic program was then run over \ the kd-trees to find the maximally scoring chains of these blocks. Chains \ scoring below a threshold were discarded; the remaining chains are displayed \ in this track.
\ \\ Blastz was developed at Pennsylvania State University by\ Minmei Hou, Scott Schwartz, Zheng Zhang, and Webb Miller with advice from\ Ross Hardison.
\\ Lineage-specific repeats were identified by Arian Smit and his\ RepeatMasker\ program.
\\ The axtChain program was developed at the University of California\ at Santa Cruz by Jim Kent with advice from Webb Miller and David Haussler.\
\\ The browser display and database storage of the chains were generated\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte, F., Yap, V.B., Miller, W.\ Scoring pairwise genomic sequence alignments.\ Pac Symp Biocomput 2002, 115-26 (2002).
\\ Kent, W.J., Baertsch, R., Hinrichs, A., Miller, W., and Haussler, D.\ Evolution's cauldron: Duplication, deletion, and rearrangement\ in the mouse and human genomes.\ Proc Natl Acad Sci USA 100(20), 11484-11489 (2003).
\\ Schwartz, S., Kent, W.J., Smit, A., Zhang, Z., Baertsch, R., Hardison, R.,\ Haussler, D., and Miller, W.\ Human-Mouse Alignments with BLASTZ.\ Genome Res. 13(1), 103-7 (2003).
\ \ varRep 1 chainColor Normalized Score\ otherDb mm6\