The chromosome band track represents the approximate \ location of bands seen on Giemsa-stained chromosomes at\ an 800 band resolution.
\A full description of the method by which the chromosome \ band locations are estimated can be found in \ Furey, T.S., and Haussler, D.,Integration of the Cytogenetic Map with the\ Draft Human Genome Sequence, Hum. Mol. Gen., 12(9):1037-1044 (2003).\
\ \ Barbara Trask, Vivian Cheung, Norma Nowak and others in the BAC Resource\
Consortium used fluorescent in-situ\
hybridization (FISH) to determine a cytogenetic location for \
large genomic clones on the chromosomes.\
The results from these experiments are the primary source of information used\
in estimating the chromosome band locations.\
For more information about the BAC Resource Consortium, see
\ BAC clone placements in the human sequence are determined at UCSC using a combination of full BAC clone sequence,\ BAC end sequence, and STS marker information.\
\We would like to thank all of the labs that have contributed to this resource:\
This track shows locations of Sequence Tagged Site (STS) markers\ along the draft assembly. These markers have been mapped using \ either genetic mapping (Genethon, Marshfield, and deCODE maps),\ radiation hybridization mapping (Stanford, Whitehead RH, and GeneMap99 maps) or\ YAC mapping (the Whitehead YAC map) techniques. \ Prior to August 2001, this track also\ showed the approximate position of fluorescent in situ hybridization (FISH) mapped clones.\ In the August 2001 and later assemblies, the FISH clones are displayed in a separate track.
\Genetic map markers are shown in blue; radiation hybrid map markers are shown \ in black. When a marker maps to multiple positions in the genome, it is shown in a \ lighter color.
\ \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:\
When you have finished configuring the filter, click the Submit button.
\ \Many thanks to the researchers who worked on these\ maps, and to Greg Schuler, Arek Kasprzyk, Wonhee Jang,\ Terry Furey and Sanja Rogic for helping\ process the data. Additional data on the individual maps can be\ found at the following links:\
This track shows the location of fluorescent in situ hybridization (FISH) mapped clones along the \
draft assembly sequence. The locations of these clones were\
contributed as a part of The BAC Resource Consortium's paper "
More information about the BAC clones, including how they can be\ obtained, can be found at the \ Human BAC Resource\ and the Clone Registry\ web sites hosted by NCBI.\ To view Clone Registry information for a clone, click on the clone name at the top of the details page for that item.
\ \The track filter can be used to change the color or include/exclude the display of a dataset from an individual lab. 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:\
When you have finished configuring the filter, click the Submit button.
\ \We would like to thank all of the labs that have contributed to this resource:\
BAC clones from GenMapDB\ are placed on the draft sequence using BAC end sequence information\ and confirmed using STS markers by Vivian Cheung's lab at the\ Department of Pediatrics, University of Pennsylvania. Further\ information about each clone can be obtained by clicking on the clone\ name on the track detail page.\
The recombination rate track represents\ calculated sex-averaged rates of recombination based on either the\ deCODE, Marshfield, or Genethon genetic maps. By default, the deCODE\ map rates are displayed. Female and male specific recombination\ rates, and well as rates from the Marshfield and Genethon maps, can\ also be displayed by choosing the appropriate filter option on the track description page.\
\ \The deCODE genetic map was created at \ deCODE Genetics and is \ based on 5,136 microsatellite markers for 146 families with a total\ of 1,257 meiotic events. For more information on this map, see\ A. Kong et. al., "A high-resolution recombination map of the human genome", \ Nature Genetics, 31(3), pages 241-247 (2002).\
\ The Marshfield genetic map was created at the
The Genethon genetic map was created at
Each base is assigned the recombination rate calculated by\ assuming a linear genetic distance across the immediately flanking\ genetic markers. The recombination rate assigned to each 1Mb window\ is the average recombination rate of the bases contained within the\ window.\
\ \To view a particular map or gender-specific rate, select the corresponding\ option from the "Map Distances" pulldown list. By default, the browser \ displays the deCODE sex-averaged distances.
\ \This track is produced at UCSC and uses data that are freely available for\ the Genethon, Marshfield, and deCODE genetic maps (see above links). Thanks\ to all who have played a part in the creation of these maps.
\ \ map 1 ctgPos Map Contigs Physical Map Contigs 0 9 150 0 0 202 127 127 0 0 0\ From the August 2001 to the Nov 2002 freeze, this track was based on\ tiling path (TPF) maps curated by the sequencing centers responsible for\ each chromosome, which were integrated into an assembly done by NCBI.\ Beginning with the April 2003 freeze, the chromosome coordinators\ at the individual sequencing centers took over complete responsibility\ for preparing the assembly of their chromosomes in AGP format. The\ files provided by these centers are checked and validated at NCBI, and\ form the basis for the definition of the physical map contigs.\
\ map 0 gold Assembly bed 3 + Assembly from Fragments 0 10 150 100 30 230 170 40 0 0 0This track shows the draft assembly of the $organism genome.\ This assembly merges contigs from overlapping drafts and\ finished clones into longer sequence contigs. The sequence\ contigs are ordered and oriented when possible by mRNA, EST,\ paired plasmid reads (from the SNP Consortium) and BAC end\ sequence pairs.
\In dense mode, this track depicts the path through the draft and \ finished clones (aka the golden path) used to create the assembled sequence. \ Clone boundaries are distinguished by the use of alternating gold and brown \ coloration. Where gaps\ exist in the path, spaces are shown between the gold and brown\ blocks. If the relative order and orientation of the contigs\ between the two blocks is known, a line is drawn to bridge the\ blocks.
\\ Clone Type Key:\
\ 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. \
\There are four principal types of gaps:\
\ In dense display mode, this track shows the coverage level of \ the genome. Finished regions are depicted in black. Draft regions \ are shown in various shades of gray that correspond to the level of coverage. \
\ In full display mode, this track shows the position of each contig inside each \ draft or finished clone ("fragment") in the assembly. For some \ assemblies, clones in the sequencing center tiling path are displayed with\ blue rather than gray backgrounds.\
\ map 0 bacEndPairs BAC End Pairs bed 6 + BAC End Pairs 0 15 0 0 0 127 127 127 0 0 0Bacterial artificial chromosomes (BACs) are a key part of many large\ scale sequencing projects. A BAC typically consists of 50-300kb 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 50Kb but no more than 600Kb 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 "-".
\ \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\ fosEndPairs Fosmid End Pairs bed 6 + Fosmid End Pairs 0 18 0 0 0 127 127 127 0 0 0A valid pair of fosmid end sequences must be\ at least 32 kb but no more than 47 kb away from each other. \ The orientation of the first fosmid end sequence must be "+" and\ the orientation of the second fosmid end sequence must be "-".
\ \End sequences were trimmed at the NCBI using\ ssahaCLIP written by Jim Mullikin. Trimmed fosmid end sequences were\ placed on the assembled sequence using Jim Kent's \ blat \ program.
\ \Sequencing of the fosmid ends was done at the \ Eli & Edythe L. Broad Institute of MIT \ and Harvard University.\ Sequences and quality scores are available in the NCBI Trace Respository.\
\ map 1 exonArrows off\ gcPercent GC Percent bed 4 + Percentage GC in 20,000 Base Windows 0 23 0 0 0 127 127 127 1 0 0\ The GC percent track shows the percentage of G (guanine) and C (cytosine) bases\ in a 20,000 base window. Windows with high GC content are drawn more darkly \ than windows with low GC content. High GC content is typically associated with \ gene-rich areas.\
\\ This track was generated at UCSC.\ map 1 knownGene Known Genes genePred refPep refMrna Known Genes Based on SWISS-PROT, TrEMBL, mRNA, and RefSeq 3 34 12 12 120 133 133 187 0 0 0
\ The Known Genes track shows known protein coding genes based on \ proteins from SWISS-PROT, TrEMBL, and TrEMBL-NEW and their\ corresponding mRNAs from \ GenBank.\ Coding exons are displayed as thicker blocks than 5' and 3' \ untranslated regions (UTR). Connecting introns \ are one-pixel lines with hatch marks indicating direction of transcription.\ Entries which have corresponding entries in PDB are colored black.\ Entries which either have corresponding proteins in SWISS-PROT or mRNAs that are \ NCBI Reference Sequences with a "Reviewed" status are colored dark blue.\ Entries which have mRNAs that are \ NCBI Reference Sequences with a "Provisional" status are colored lighter blue.\ Everything else is colored with lightest blue.
\ \\ All mRNAs of a species are aligned against the genome using the blat\ program. When a single mRNA aligns in multiple places, only\ the best alignments are kept. The alignments must also have \ at least 98% sequence identity to be kept. \ This set of mRNA alignments is further reduced by keeping only those mRNAs that \ are referenced by a protein in SWISS-PROT, TrEMBL, or TrEMBL-NEW.
\\ Among multiple mRNAs referenced by a single protein, the best mRNA is chosen based on \ a quality score, which depends on its length, how good its translation matches \ the protein sequence, and its release date.\ The list of mRNA and protein pairs are further cleaned up by removing \ short invalid entries and consolidating entries with identical CDS regions.
\\ Finally, RefSeq entries which are derived from DNA sequences instead of \ mRNA sequences are added. Disease annotations are from SWISS-PROT.
\ \\ The Known Genes track is produced at UCSC based primarily on cross-references \ between proteins from \ SWISS-PROT \ (also including TrEMBL and TrEMBL-NEW) and mRNAs from GenBank\ generated by scientists worldwide. Part of \ NCBI RefSeq \ data are also included in this track.
\ \\ The SWISS-PROT entries in this annotation track are copyrighted. They are \ produced through a collaboration \ between the Swiss Institute of Bioinformatics and the EMBL Outstation - the \ European Bioinformatics Institute. There are no restrictions on their use by \ non-profit institutions as long as their content is in no way modified and this \ statement is not removed. Usage by and for commercial entities requires a \ license agreement (see \ http://www.isb-sib.ch/announce/ or send an email to \ license@isb-sib.ch).
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. (2004)\ GenBank: update. \ Nucleic Acids Res. 32 Database issue:D23-6.\ genes 1 hgGene off\ 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 mRNA \ reference sequences compiled at LocusLink. Coding exons are represented by \ blocks connected by horizontal lines representing introns. The 5' and 3' \ untranslated regions (UTRs) are displayed as thinner blocks on the leading \ and trailing ends of the aligning regions. In full display mode, arrowheads \ on the connecting intron lines indicate the direction of transcription.\ The color shading indicates the level of review the RefSeq record has \ undergone: predicted (light), provisional (medium), reviewed (dark). \
\\ Non-coding RNA genes have their own track in some assemblies.\
\\ Refseq mRNAs are aligned against the genome using the \ blat\ program. When a single mRNA aligns in multiple places, only\ the best alignments which also have at least 98% sequence identity are kept.\
\The track filter can be used to configure the labeling of the features within\ the track. By default, items are labeled by gene name. Click the \ appropriate Label option to display the accession name instead of the gene\ name, show both the gene and accession names, or turn off the label completely.\ After you have made your selection, click Submit to return to the tracks display\ page.\
\ The RefSeq Genes track is produced at UCSC from mRNA sequence data\ generated by scientists worldwide and curated by the \ NCBI RefSeq project. \
\ genes 1 vegaGene Vega Genes genePred vegaPep Vega Annotations from Sanger, Genoscope 0 37 0 100 180 127 177 217 0 0 3 chr14,chr20,chr22, http://vega.sanger.ac.uk/Homo_sapiens/geneview?transcript=$$\ Excerpted from the Vega \ main page:
\\ "The \ \ Vertebrate Genome Annotation (VEGA) \ database is designed to be a central repository for manual annotation\ of different vertebrate finished genome sequence.\ In collaboration with the genome sequencing centres Vega attempts to\ present consistent high-quality curation of the published chromosome\ sequences."
\\ "Finished genomic sequence is analysed on a clone by clone basis using\ a combination of similarity searches against DNA and protein databases\ as well as a series of ab initio gene predictions (GENSCAN, Fgenes)."
\\ "In addition, comparative analysis using vertebrate datasets such as\ the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores\ (Evolutionary Conserved Regions) are used for novel gene discovery."
\\ NOTE: VEGA annotations appear only on chromosomes 14, 20, and 22 in this assembly.\ \
\ Thanks to Steve Searle at the\ Sanger Institute \ for providing the GTF and FASTA files for the Vega annotations. Vega gene annotations are \ generated by manual annotation from the following groups:\
\
Chromosome 14: \
\ \
\ Genoscope
\
\ Relevant publication: Heilig et al., The DNA sequence and analysis of \
\ human chromosome 14. Nature 421:601-607 (2003).\
\
Chromosome 20: \
\ The HAVANA Group, \
\ Wellcome Trust Sanger Institute
\
\ Relevant publication: Deloukas et al., The DNA sequence and \
\ comparative analysis of human chromosome 20. Nature 414:865-871 (2001).\
\
Chromosome 22: Chromosome 22 Group,\
\ \
\ Wellcome Trust Sanger Institute
\
\ Relevant publications:
\
\ -- Collins et al., Reevaluating Human Gene Annotation: \
\ A Second-Generation Analysis of Chromosome 22. Genome Research 13(1):27-36 (2003).
\
\ -- Dawson et al., A \
\ first-generation linkage disequilibrium map of \
\ human chromosome 22. Nature 418:544-548 (2002).
\
\ -- Dunham et al., The DNA sequence of human chromosome 22. Nature 402:489-495 (1999).\
\
genes 1
vegaPseudoGene Vega Pseudogenes genePred Vega Annotated Pseudogenes and Immunoglobulin Segments 0 37.1 30 130 210 142 192 232 0 0 3 chr14,chr20,chr22, http://vega.sanger.ac.uk/Homo_sapiens/geneview?transcript=$$
\ Excerpted from the Vega \ main page:
\\ "The \ \ Vertebrate Genome Annotation (VEGA) \ database is designed to be a central repository for manual annotation\ of different vertebrate finished genome sequence.\ In collaboration with the genome sequencing centres Vega attempts to\ present consistent high-quality curation of the published chromosome\ sequences."
\\ "Finished genomic sequence is analysed on a clone by clone basis using\ a combination of similarity searches against DNA and protein databases\ as well as a series of ab initio gene predictions (GENSCAN, Fgenes)."
\\ "In addition, comparative analysis using vertebrate datasets such as\ the Riken mouse cDNAs and Genoscope Tetraodon nigroviridis Ecores\ (Evolutionary Conserved Regions) are used for novel gene discovery."
\\ NOTE: VEGA annotations appear only on chromosomes 14, 20, and 22 in this assembly.\ \
\ Thanks to Steve Searle at the\ Sanger Institute \ for providing the GTF and FASTA files for the Vega annotations. Vega gene annotations are \ generated by manual annotation from the following groups:\
\
Chromosome 14: \
\ \
\ Genoscope
\
\ Relevant publication: Heilig et al., The DNA sequence and analysis of \
\ human chromosome 14. Nature 421:601-607 (2003).\
\
Chromosome 20: \
\ The HAVANA Group, \
\ Wellcome Trust Sanger Institute
\
\ Relevant publication: Deloukas et al., The DNA sequence and \
\ comparative analysis of human chromosome 20. Nature 414:865-871 (2001).\
\
Chromosome 22: Chromosome 22 Group,\
\ \
\ Wellcome Trust Sanger Institute
\
\ Relevant publications:
\
\ -- Collins et al., Reevaluating Human Gene Annotation: \
\ A Second-Generation Analysis of Chromosome 22. Genome Research 13(1):27-36 (2003).
\
\ -- Dawson et al., A \
\ first-generation linkage disequilibrium map of \
\ human chromosome 22. Nature 418:544-548 (2002).
\
\ -- Dunham et al., The DNA sequence of human chromosome 22. Nature 402:489-495 (1999).\
\
genes 1
ensGene Ensembl Genes genePred ensPep Ensembl Gene Predictions 1 40 150 0 0 202 127 127 0 0 0 http://www.ensembl.org/perl/transview?transcript=$$
\ These gene predictions are from Ensembl.
\ \For a description of the methods used in Ensembl gene prediction, refer to \ "\ The Ensembl genome database project", Nucleic Acids Research, \ 2002, 30(1) 38-41.
\ \\ Thanks to Ensembl for providing this annotation.
\ \ genes 1 acembly Acembly Genes genePred acemblyPep acemblyMrna AceView Gene Models With Alt-Splicing 1 41 155 0 125 205 127 190 0 0 0 http://www.ncbi.nih.gov/IEB/Research/Acembly/av.cgi?db=human&l=$$This track shows gene models reconstructed solely from\ mRNA and EST evidence by Danielle and Jean Thierry-Mieg\ and Vahan Simonyan using the Acembly program.
\ \Acembly attempts to find the best alignment of each mRNA against the \ genome, and considers alternative splice models. If more than one gene \ model is produced that has statistical significance, all of these models \ are displayed.
\ \Thanks to Jean Thierry-Mieg at NIH for \ providing this track.
\ \ \ genes 1 twinscan Twinscan genePred twinscanPep Twinscan Gene Predictions Using Mouse/Human Homology 0 45 0 100 100 127 177 177 0 0 0\ The Twinscan program predicts genes in a manner similar to Genscan, except that\ Twinscan takes advantage of genome comparison to improve gene prediction\ accuracy. More information and a web server can be found at\ \ http://genes.cs.wustl.edu/.\
\\
The Twinscan algorithm is described in Korf I, Flicek P, Duan D, and Brent MR \
(2001), "
\ Thanks to Michael Brent's Computational Genomics Group at Washington University St. Louis for providing these data.\ genes 1 slamMouse Slam Mouse genePred Slam Gene Predictions Using Human/Mouse (Feb. 2002/mm2) Homology 0 45.5 100 50 0 175 150 128 0 0 0
\ Slam \ predicts coding exons and conserved noncoding regions in a pair of homologous DNA sequences, incorporating both statistical sequence properties and degree of conservation in making the predictions. This particular annotation uses the Feb. 2002 (mm2) assembly of the mouse genome. The model is symmetric and the same gene structure (with possibly different exon lengths) is predicted in both sequences.
\ \\ The symmetry of the model gives it a higher degree of accuracy for regions where the true underlying gene structures contain the same number of coding exons, in cases where this is not true, or when one of the sequences is of lower quality and contains in-frame stop codons, the resulting predictions tend to have lower accuracy.
\ \\ More information on the accuracy of the predictions can be found at http://bio.math.berkeley.edu/slam/mouse. A web server for individual requests is available at http://bio.math.berkeley.edu/slam.
\ \\ M. Alexandersson, S. Cawley, L. Pachter (2003). SLAM - Cross-species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model. Genome Research 13(3):496-502.
\\ L. Pachter, M. Alexandersson, S. Cawley (2001). \ Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems, \ Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB 2001).
\\ L. Pachter , M. Alexandersson, S. Cawley (2002). \ Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems, \ Journal of Computational Biology 9(2):389-400.
\ \ genes 1 slamRat Slam Rat genePred Slam Gene Predictions Using Human/Rat (Nov. 2002/rn1) Homology 0 45.6 100 50 0 175 150 128 0 0 0\ Slam \ predicts coding exons and conserved noncoding regions in a pair of homologous DNA sequences, incorporating both statistical sequence properties and degree of conservation in making the predictions. This particular annotation uses the Nov. 2002 (rn1) assembly of the rat genome. The model is symmetric and the same gene structure (with possibly different exon lengths) is predicted in both sequences.
\\ The symmetry of the model gives it a higher degree of accuracy for regions where the true underlying gene structures contain the same number of coding exons, in cases where this is not true, or when one of the sequences is of lower quality and contains in-frame stop codons, the resulting predictions tend to have lower accuracy.
\\ More information on the accuracy of the predictions can be found at http://bio.math.berkeley.edu/slam/rat. A web server for individual requests is available at http://bio.math.berkeley.edu/slam.
\ \\ M. Alexandersson, S. Cawley, L. Pachter (2003). SLAM - Cross-species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model. Genome Research 13(3):496-502.
\\ L. Pachter, M. Alexandersson, S. Cawley (2001). \ Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems, \ Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB 2001).
\\ L. Pachter , M. Alexandersson, S. Cawley (2002). \ Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems, \ Journal of Computational Biology 9(2):389-400.
\ \ genes 1 sgpGene SGP Genes genePred sgpPep SGP Gene Predictions Using Human/Mouse (Feb. 2002/mm2) Homology 0 47 0 90 100 127 172 177 0 0 0\ This track shows gene predictions from the SGP program, which is being developed at \ the Grup de Recerca en\ Informàtica Biomèdica (GRIB) at Institut Municipal d'Investigació Mèdica (IMIM) in \ Barcelona. To predict genes in a genomic\ query, SGP combines geneid predictions with tblastx comparisons of the \ genomic query against other genomic sequences. In this particular annotation, \ the Feb. 2002 (mm2) assembly of the mouse genome was used to find homology \ evidence between the two genomes.\
\\ Thanks to GRIB for providing these gene predictions.\
\ \ \ \ genes 1 softberryGene Fgenesh++ Genes genePred softberryPep Fgenesh++ Gene Predictions 0 48 0 100 0 127 177 127 0 0 0Fgenesh++ predictions are based on Softberry's gene finding software.
\ \The Fgenesh++ gene predictions were produced by \ Softberry Inc. \ Commercial use of these predictions is restricted to viewing in \ this browser. Please contact Softberry Inc. to make arrangements for further commercial access.\ \ 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 \ Grup de Recerca en\ Informàtica Biomèdica (GRIB) at Institut Municipal d'Investigació Mèdica (IMIM) 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 GRIB for providing these data.\
\ genes 1 genscan Genscan Genes genePred genscanPep Genscan Gene Predictions 1 50 170 100 0 212 177 127 0 0 0This track shows predictions from the \ Genscan program written by Chris Burge.\
\\ This track shows the location of non-protein coding RNA genes and\ pseudogenes. \
\ Feature types include:\
\ \
\
Eddy-tRNAscanSE (tRNA genes, Sean Eddy):
\
tRNAscan-SE 1.23 with default parameters.\
Score field contains tRNAscan-SE bit score; >20 is good, >50 is great.
\
Eddy-BLAST-tRNAlib (tRNA pseudogenes, Sean Eddy):
\
Wublast 2.0, with options "-kap wordmask=seg B=50000 W=8 cpus=1".\
Score field contains % identity in blast-aligned region.\
Used each of 602 tRNAs and pseudogenes predicted by tRNAscan-SE\
in the human oo27 assembly as queries. Kept all nonoverlapping\
regions that hit one or more of these with P <= 0.001.
\
Eddy-BLAST-snornalib (known snoRNAs and snoRNA pseudogenes, Steve Johnson):
\
Wublastn 2.0, with options "-V=25 -hspmax=5000 -kap wordmask=seg \
B=5000 W=8 cpus=1".\
Score field contains blast score.\
Used each of 104 unique snoRNAs in snorna.lib as a query.\
Any hit >=95% full length and >=90% identity is annotated as a\
"true gene".\
Any other hit with P <= 0.001 is annotated as a "related sequence" \
and interpreted as a putative pseudogene.
\
Eddy-BLAST-otherrnalib \
(non-tRNA, non-snoRNA noncoding RNAs with GenBank entries\
for the human gene.):
\
Wublastn 2.0 [15 Apr 2002]\
with options: "-kap -cpus=1 -wordmask=seg -W=8 -E=0.01 -hspmax=0\
-B=50000 -Z=3000000000". Exceptions to this are:\
\ The score field contains the blastn score. \ Used 41 unique miRNAs, and 29 other ncRNAs as queries.\ Any hit >=95% full length and >=95% identity is annotated as a \ "true gene".\ Any other hit with P <= 0.001 and >= 65% identity is annotated\ as a "related sequence". An exception to this is: all miRNAs consist \ \ of 16-26 bp sequences in GenBank \ and are only annotated if 100% full length and 100% identity. \ miRNAs consist of Let-7 from Pasquinelli et al., \ Nature (2000) 408:86; 40 from Mourelatos et al., Gene & Dev (2002) \ 16:720.
\\ These data were kindly provided by Sean Eddy at Washington University.
\ genes 1 superfamily Superfamily bed 4 + Superfamily/SCOP: Proteins Having Homologs with Known Structure/Function 0 53 150 0 0 202 127 127 0 0 0 http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/cgi-bin/gene.cgi?genome=\ The \ Superfamily \ track shows proteins having homologs with known structures or functions.
\\ Each entry on the track shows the coding region of a gene (based on Ensembl gene predictions).\ In full display mode, the label for an entry consists of the names of \ all known protein domains coded by this gene. This \ usually contains structural and/or function descriptions that provide valuable information to help users get a quick grasp of the biological significance of the gene.
\\ Data are downloaded from the Superfamily server.\ Using the cross-reference between Superfamily entries and Ensembl gene prediction entries\ and their alignment to the appropriate genome, the associated data are processed to generate \ a simple BED format track.
\\ Superfamily is developed by\ Julian\ Gough at the MRC Laboratory\ of Molecular Biology, Cambridge.
\\ Gough, J., Karplus, K., Hughey, R. and\ Chothia, C. (2001). "Assignment of Homology to Genome Sequences using a\ Library of Hidden Markov Models that Represent all Proteins of Known Structure". \ J. Mol. Biol., 313(4), 903-919.
\ \ genes 1 mrna $Organism mRNAs psl . $Organism mRNAs from GenBank 3 54 0 0 0 127 127 127 1 0 0\ The $Organism mRNA track shows alignments between $organism mRNAs\ in GenBank and the genome. Aligning regions (usually exons)\ are shown as black boxes connected by lines for gaps (spliced-out introns, \ usually). In full display, arrows on the introns\ indicate the direction of transcription.
\ \\ GenBank $organism mRNAs are aligned against the genome using the \ blat\ program. When a single mRNA aligns in multiple places, \ the alignment having the highest base identity is found. \ Only alignments that have a base identity level within 1% of\ the best are kept. Alignments must also have at least 95%\ base identity to be kept.
\ \The track filter can be used to change the color or include/exclude a subset of individual \ items within a 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:\
\ When you have finished configuring the filter, click the Submit button.
\ \\ The $Organism mRNA track is 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. (2004)\ GenBank: update. \ Nucleic Acids Res. 32 Database issue:D23-6.\ rna 1 cdsDrawOptions enabled\ intronEst Spliced ESTs psl est $Organism ESTs That Have Been Spliced 1 56 0 0 0 127 127 127 1 0 0
The Spliced EST track displays Expressed Sequence Tags \ (ESTs) from GenBank that show signs of splicing when\ aligned against the genome. To be considered spliced, an EST must show \ evidence of at least one cannonical intron, i.e. one that is at least\ 32 bases in length and has 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.
\ \Expressed sequence tags are single-read (typically\ approximately 500 base) sequences which usually\ represent fragments of transcribed genes. Aligning \ regions (usually exons) are shown as black boxes \ connected by lines for gaps (usually spliced-out introns). \ In full display mode, arrows on the introns\ indicate the direction of transcription. In the\ December 2001 assembly and later, this direction is\ taken by looking at the splice sites. In previous\ assemblies, the direction of transcription was taken from \ the Genbank annotations, which frequently were inaccurate.
\ \Strand information provided for ESTs (+/-) 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.\ \
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 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 are starting to hit transcription start\ reasonably well. Before the cap-selection techniques\ emerged, some projects used random rather than poly-A\ priming in an attempt to get 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. However, because the $organism 3' UTRs are quite\ long, the splicing requirement does eliminate many genuine 3'\ ESTs.
\ \To generate this track, $organism ESTs from Genbank are aligned \ against the genome using the \ blat program. Note that the maximum intron length\ allowed by blat is 500,000 bases, which may eliminate some ESTs with very \ long introns that might otherwise align. When a single \ EST aligns in multiple places, the alignment having the \ highest base identity is found. Only alignments that have \ a base identity level within 0.1% of the best are kept. \ Alignments must also have at least 98% base identity to be kept.
\ \The track filter can be used to change the color or include/exclude a subset of \ individual items within a 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:\
When you have finished configuring the filter, click the Submit button.
\ \\ The Spliced EST track is 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. (2004)\ GenBank: update. \ Nucleic Acids Res. 32 Database issue:D23-6.\ rna 1 intronGap 30\ 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.
\ \Expressed sequence tags are single-read (typically\ approximately 500 base) sequences which usually\ represent fragments of transcribed genes. Aligning \ regions (usually exons) are shown as black boxes \ connected by lines for gaps (usually spliced-out introns). \ In full display mode, arrows on the introns\ indicate the direction of transcription. In the\ December 2001 assembly and later, this direction is\ taken by looking at the splice sites. In previous\ assemblies, the direction of transcription was taken from \ the Genbank annotations, which frequently were inaccurate.
\ \Strand information provided for ESTs (+/-) 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.\ \
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 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 are starting to hit transcription start\ reasonably well. Before the cap-selection techniques\ emerged, some projects used random rather than poly-A\ priming in an attempt to get 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. However, because the $organism 3' UTRs are quite\ long, the splicing requirement does eliminate many genuine 3'\ ESTs.
\ \To generate this track, $organism ESTs from Genbank are aligned \ against the genome using the \ blat \ program. Note that the maximum intron length\ allowed by blat is 500,000 bases, which may eliminate some ESTs with very \ long introns that might otherwise align. When a single \ EST aligns in multiple places, the alignment having the \ highest base identity is found. Only alignments that have \ a base identity level within 0.1% of the best are kept. \ Alignments must also have at least 98% base identity to be kept.
\ \The track filter can be used to change the color or include/exclude a subset of \ individual items within a 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:\
When you have finished configuring the filter, click the Submit button.
\ \\ The $Organism EST track is produced at UCSC from EST sequence data\ submitted to the international public sequence databases by \ scientists worldwide.
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. (2004)\ GenBank: update. <\ em>Nucleic Acids Res. 32 Database issue:D23-6.\ rna 1 intronGap 30\ xenoMrna Non-$Organism mRNAs psl xeno Non-$Organism mRNAs from GenBank 0 63 0 0 0 127 127 127 1 0 0
\ This track displays translated \ blat\ alignments of\ non-$organism vertebrate and invertebrate mRNA from \ GenBank.
\ \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 alignments were passed through a near-best-in-genome filter.
\ \The track filter can be used to color, include, or exclude a subset of individual \ items within a 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:\
When you have finished configuring the filter, click the Submit button.
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. (2004)\ GenBank: update. \ Nucleic Acids Res. 32 Database issue:D23-6.\ rna 1 cdsDrawOptions enabled\ xenoEst Non-$Organism ESTs psl xeno Non-$Organism ESTs from GenBank 0 65 0 0 0 127 127 127 1 0 0 http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?form=4&db=n&term=$$
\ This track displays translated \ blat\ alignments of non-$organism vertebrate ESTs from \ GenBank.
\ \The strand information (+/-) for this track is in two parts. The\ first + or - indicates the orientation of the query sequence whose\ translated protein produced the match. The second + or - indicates the\ orientation of the matching translated genomic sequence. Because the two\ orientations of a DNA sequence give different predicted protein sequences,\ there are four combinations. ++ is not the same as --; nor is +- the same\ as -+.\ \
\ To generate this track, the ESTs are aligned against the genome using the blat\ program. The alignments are passed through a piecewise near-best-in-genome\ filter.
\ \The track filter can be used to change the color or include/exclude a subset of \ individual items within a track. This is helpful when many items are shown in the \ track display, especially when only some are relevant to the current task. To use the\ filter:\
When you have finished configuring the filter, click the Submit button.
\ \\ This track is produced at UCSC from EST sequence data submitted to the\ international public sequence databases by scientists worldwide.
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. (2004)\ GenBank: update. Nucleic Acids Res. 32 Database issue:D23-6.\ rna 1 tigrGeneIndex TIGR Gene Index genePred Alignment of TIGR Gene Index TCs Against the $Organism Genome 0 68 100 0 0 177 127 127 0 0 0 http://www.tigr.org/tigr-scripts/tgi/tc_report.pl?$$
This track displays alignments of the TIGR Gene Index (TGI)\ against the $organism genome. The TIGR Gene Index is based\ largely on assemblies of EST sequences in the public databases.\ See \ www.tigr.org for more information about TIGR and the Gene Index.
\Thanks to Foo Cheung and Razvan Sultana of the The Institute for Genomic Research, for converting these data into a track for the browser.
\ rna 1 uniGene_2 UniGene bed 12 UniGene Hs 159 Alignments and SAGEmap Info 0 69 0 0 0 127 127 127 1 0 0Description\\
Serial Analysis of Gene Expression (SAGE)\
is a quantative measurement gene expression. Data is presented for\
every cluster contained in the browser window and the selected cluster\
name is highlighted in red. All data are from the repository at the Methods\\ SAGE counts are produced by sequencing small "tags" of DNA believed to\ be associated with a gene. These tags are produced by attatching\ poly-A RNA to oligo-dT beads. After synthesis of double stranded cDNA\ transcripts are cleaved by an anchoring enzyme (usually NIaIII). Then\ small tags are produced by ligation with a linker containing a type\ IIS restriction enzyme site and cleavage with the tagging enzyme\ (usually BsmFI). The tags are then concatenated together and\ sequenced. The frequency of each tag is counted and used to infer\ expression level of transcripts that can be matched to that tag. \ \Credits\\
All\
SAGE data presented here was mapped to UniGene transcripts by the |
\ This track shows the boundaries of genes and the direction of\ transcription as deduced from clustering spliced ESTs and mRNAs\ against the genome. When there are many spliced variants\ of the same gene, this track shows the variant that\ spans the greatest distance in the genome.
\ \\ ESTs and mRNAs from \ GenBank are aligned against the genome with the \ blat\ program, and filtered to keep only those alignments\ that have at least 97.5% base identity within the \ aligning blocks. When multiple alignments occur, only the\ alignments with a percentage identity within 0.2% of the\ best alignment are kept. ESTs that align without any\ introns are discarded. Blocks that are less than 130 bases\ and are not next to an intron are discarded. Blocks smaller\ than 10 bases are discarded. The orientations of the \ ESTs and mRNAs are deduced from the GT/AG splice sites\ at the introns, and ESTs and mRNAs with overlapping blocks\ on the same strand are merged into clusters. Only the\ extent and orientation of the clusters are shown here.\
\\ This track -- which was originally developed by Jim Kent --\ was generated at UCSC and uses data submitted to GenBank by \ scientists worldwide.
\ \\ Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. (2004)\ GenBank: update. \ Nucleic Acids Res. 32 Database issue:D23-6.\ rna 1 affyTranscriptome Transcriptome sample Affymetrix Experimentally Derived Transcriptome 0 88 100 50 0 0 0 255 0 0 2 chr22,chr21,
\
Transcriptome data for chromosomes 21 and 22 from \
To present a more\
interpretable display when zoomed out, averages have been precalculated\
over the chromosome at two different resolutions in addition to the\
raw data. For example, when zoomed out, there may appear to be a peak at\
the center of a gene rather than a signal at every exon. Zooming in\
will reveal the "raw" data for that region.\
\
NOTE: Affymetrix transcriptome annotations appear only on chromosomes 21 and 22.\
\
\
Thanks to Affymetrix for providing these data. Questions/Comments? Email \
sugnet@soe.ucsc.edu. \
\
regulation 0
cpgIsland 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 C's 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 C's tend to turn into T's because of spontaneous\
deamination. The result is that CpG's 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 CpG's are present at\
significantly higher levels than is typical for the genome as a whole.\
\
CpG islands are 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 is then\
evaluated to determine GC content (roughly >= 50%), length (> 200), and ratio of\
observed number of CG dinucleotides to the expected number on\
the basis of the GC content of the segment (> 0.6). \
\
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.\
\
This track was generated \
using a\
modification of a program developed by G. Miklem and L. Hillier. \
The Stanford Human Promoters dataset was generated by\
Rick Myers' Lab\
at Stanford University and is described thoroughly in\
\
"Identification and Functional Analysis of Human\
Transcriptional Promoters."\
Briefly, Full-length human cDNAs were aligned to the human genome\
sequence to predict putative starts of transcription. Roughly 500 bp\
of putative promoter sequence was then cloned into a reporter\
construct for 150 random promoters. More than 90% of these fragments\
had significant promoter activity in at least one of the cell types\
we tested.\
The promoters highlighted in black have been experimentally confirmed as functional promoters, and the ones highlighted in gray are predicted and are in the process of being tested.\
\
Any questions or comments, email \
nathant@stanford.edu\
\
or\
shelleyj@stanford.edu. \
\
regulation 1
snpMap SNPs bed 4 . Simple Nucleotide Polymorphisms (SNPs) 0 144 0 0 0 127 127 127 0 0 0 \
This track consolidates all the Simple Nucleotide Polymorphisms\
into a single track. It is the union of the Overlap SNPs,\
Random SNPs, Affymetrix 120K SNP, and Affymetrix 10K SNP tracks that\
previously existed in the Genome Browser. \
The SNPs in this track include all known polymorphisms that\
can be mapped against the current assembly. These include known point\
mutations (Single Nucleotide Polymorphisms), insertions, deletions,\
and segmental mutations from the current build of \
dbSnp, which is \
shown in the Genome Browser release log.\
\
There are three major cases that are not mapped and/or annotated:\
Credits
\
Description
\
Method
\
Credits
\
Description
\
\
Description
\
\
\
\
\
Variant Types\
(These were previously located in \
the Random SNPs track.)\
(These were \
previously located in the Random SNPs track.)\
(These were previously located in \
the Overlap SNPs track.)\
(These were previously located\
in the Overlap SNPs track.)\
(These were \
previously located in the Affymetrix 10K SNP track.)\
(These were \
previously located in the Affymetrix 120K SNP track.)\
\
\
\
Filtering
\
\
\
The heuristics for the non-SNP variations (i.e. named elements and\ STRs) are quite conservative; therefore, some of these are probably lost. This\ approach was chosen to avoid false annotation of variation in\ inappropriate locations.
\ \\ Positional information can be found in the annotations section\ of the Genome Browser \ downloads page, \ which is organized by species and assembly. Non-positional information\ can be found in the \ shared\ data section of the same page, where it is split into tables by\ organism: \ dbSnpRsHg for Human, \ dbSnpRsMm for Mouse, and \ dbSnpRsRn for Rat.\ \
\ Thanks to the SNP\ Consortium and NIH for providing the public data, which are available from \ dbSnp at \ NCBI.
\\ Thanks to Perlegen Sciences, \ Inc. for providing additional SNPs from their database.\ Additional information about the Perlegen SNP discovery process can be\ found in Patil, N. (2001) \ \ Blocks of Limited Haplotype Diversity Revealed by High-Resolution\ Scanning of Human Chromosome 21. Science 294:1719-1723.\
\\ Thanks to Affymetrix, Inc. for developing the genotyping\ arrays. For more details on this genotyping assay, please see the\ supplemental information on the \ Affymetrix 10K SNP and \ Affymetrix 120K SNP products. Additional information, \ including genotyping data, is available from the details pages for the \ Affymetrix 120K SNP and Affymetrix 10K SNP tracks.
\ \Please see the Terms and Conditions page on the Affymetrix website for \ restrictions on the use of their data. \ \ \ \ varRep 1 perlegen Perlegen Haplotypes bed 12 Perlegen Common High-Resolution Haplotype Blocks 0 145.21 0 0 0 127 127 127 1 0 1 chr21, http://www.perlegen.com/haplotype/blk/$$.html
\ Haplotype blocks derived from common single nucleotide polymorphisms (SNPs) on Chromosome 21 by\ Perlegen Sciences, as described\ in Patil N et. al. (2001), \ "\ Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning", \ Science 294:1719-1723.\
\\ The location of each haplotype block is represented by\ a blue horizontal line with tall vertical blue bars at the first and\ last SNPs of the block. Blocks are displayed as starting at the first\ SNP and ending at the last SNP of the block. This is slightly\ different from the representation on the Perlegen web site in which blocks are \ stretched until they abut each other. The shade of the blue indicates the minimum\ number of SNPs required to discriminate between haplotype patterns\ that account for at least 80% of genotyped chromosomes. Darker colors\ indicate that fewer SNPs are necessary. Individual SNPs are denoted by\ smaller black vertical bars. At multi-megabase resolution in dense\ display mode, clusters of tall blue bars may indicate hotspots for\ recombination. \
\For more information on a particular block, click "Outside Link" \ on the item's details page. General information on the\ blocks is available from Perlegen's\ \ Chromosome 21 Haplotype Browser.\
\ NOTE: Perlegen annotations appear only on chromosome 21.\
\\ Haplotype blocks on Chromosome 22 from \ The University of Oxford and \ The Wellcome Trust Sanger Institute, \ as described in Dawson E. et. al. (2002), \ "A first-generation linkage disequilibrium map of human chromosome 22", Nature 418:544-8. \
\ The location of each haplotype block is represented by\ a blue horizontal line with tall vertical blue bars at the first and\ last SNPs of the block. Blocks are displayed as starting at the first\ SNP and ending at the last SNP of the block. Individual SNPs are denoted by\ smaller black vertical bars. At multi-megabase resolution in dense\ display mode, clusters of tall blue bars may indicate hotspots for\ recombination. \
\ NOTE: Haplotype block annotations appear only on chromosome 22.\ \
This region was detected as a putative genomic duplication within the golden path.\ Orange, yellow, dark-light gray represent similarities of >99\\%, 99-98\\% and 98-90% \ respectively. Duplications greater than 98% similarity that lack sufficient SDD \ evidence (likely missed overlaps) are shown as red. Cut off values were at least \ 1 kb of total sequence aligned (containing at least 500 bp non-RepeatMasked sequence) \ and at least 90% sequence identity. \ \
\
This track was created by using Arian Smit's \
In full display mode, this track displays nine different classes of repeats:\
\
For a discussion of repeats in mammalian genomes, see: \
\
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. \
\
\
This track displays simple tandem repeats (possibly imperfect) located\
by Tandem Repeats\
Finder, which is specialized to 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 Tandem Repeats Finder, see G. Benson, "Tandem repeats finder: a program to analyze DNA sequences", Nucleic Acids \
Research, 1999, 27(2) 573-580. \
Tandem Repeats Finder was written by Gary Benson. \
The Fugu v.3.0 (Aug. 2002) whole genome shotgun assembly was provided by the\
US \
DOE Joint Genome Institute (JGI). The assembly was constructed with the JGI\
assembler, JAZZ, from paired end sequencing reads produced at JGI, Myriad \
Genetics, and Celera Genomics, resulting in a sequence coverage of 5.7X. All reads are\
plasmid, cosmid, or BAC end-sequences, with the predominant coverage\
derived from 2 Kb insert plasmids. This assembly contains 20,379\
scaffolds totaling 319 million base pairs. The largest 679 scaffolds\
total 160 million base pairs.\
\
The strand information (+/-) for this track is in two parts. The\
first + or - indicates the orientation of the query sequence whose\
translated protein produced the match. 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 alignments were done \
with blat in translated protein mode requiring 2 nearby 4-mer matches\
to trigger a detailed alignment. The $organism\
genome was masked with RepeatMasker and Tandem Repeat Finder before \
running blat. The 3.0 draft from the\
\
JGI Fugu rubripes website was used in the\
UCSC Genome Browser Fugu blat alignments. These data have been provided freely by the JGI\
for use in this publication only. \
Slam \
predicts coding exons and conserved noncoding regions in a pair of\
homologous DNA sequences, incorporating both statistical sequence properties\
and degree of conservation into predictions. This particular annotation uses the Nov. 2002 (rn1) assembly of the rat genome. The model is symmetric and the\
same structure (with possibly different lengths) is predicted in both\
sequences. \
The CNS (conserved non-coding sequence) predictions are ab-initio\
predictions of conserved regions that do not fit in with a gene structure.\
Thus, slam is not simply trying to predict conserved regions to be coding,\
but is classifying such regions according to an overall probabilistic model\
of gene structure. The set of slam CNS predictions is therefore highly\
enriched for conserved non-coding regions. \
More information and a web server can be found at \
M. Alexandersson, S. Cawley, L. Pachter (2003). SLAM - Cross-species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model. Genome Research 13(3):496-502. \
L. Pachter, M. Alexandersson, S. Cawley (2001). \
Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems, \
Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB 2001). \
L. Pachter , M. Alexandersson, S. Cawley (2002). \
Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems, \
Journal of Computational Biology 9(2):389-400. \
This track shows syntenous (corresponding) regions between $organism and rat chromosomes. The Nov. 2002 (rn1) assembly of the rat genome was used to produce this annotation. \
We passed a 100k non-overlapping window over the genome and - using the blastz best in rat \
genome alignments - looked for high-scoring regions with at least 40% of the bases aligning \
with the same region in rat. 100k segments were joined together if they agreed in direction and\
were within 500kb of each other in the $Organism genome and within 4mb of each other in the rat. \
Gaps were joined between syntenic anchors if the bases between two flanking regions agreed with \
synteny (direction and rat location). Finally, we extended the syntenic block to include those \
areas. \
Contact Robert \
Baertsch at UCSC for more information about this track.\
Thanks to the Rat Genome Sequencing Consortium for providing the rat sequence \
data. For more information, see the Baylor College Human Genome Sequencing Center\
Rat Genome Project page. \
Slam \
predicts coding exons and conserved noncoding regions in a pair of\
homologous DNA sequences, incorporating both statistical sequence properties\
and degree of conservation into predictions. This particular annotation uses the Feb. 2002 (mm2) assembly of the mouse genome. The model is symmetric and the\
same structure (with possibly different lengths) is predicted in both\
sequences. \
The CNS (conserved non-coding sequence) predictions are ab-initio\
predictions of conserved regions that do not fit in with a gene structure.\
Thus, slam is not simply trying to predict conserved regions to be coding,\
but is classifying such regions according to an overall probabilistic model\
of gene structure. The set of slam CNS predictions is therefore highly\
enriched for conserved non-coding regions. \
More information and a web server can be found at \
M. Alexandersson, S. Cawley, L. Pachter (2003). SLAM - Cross-species Gene Finding and Alignment with a Generalized Pair Hidden Markov Model. Genome Research 13(3):496-502. \
L. Pachter, M. Alexandersson, S. Cawley (2001). \
Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems, \
Proceedings of the Fifth Annual International Conference on Computational Molecular Biology (RECOMB 2001). \
L. Pachter , M. Alexandersson, S. Cawley (2002). \
Applications of Generalized Pair Hidden Markov Models to Alignment and Gene Finding Problems, \
Journal of Computational Biology 9(2):389-400. \
This track displays the conservation between the human and mouse genomes for \
50bp windows in the human genome that have at least 15 bp aligned to\
mouse. The score for a window reflects the probability that the\
level of observed conservation in that 50bp region would occur by\
chance under neutral evolution. It is given on a logarithmic scale,\
and thus it is called the "L-score". An L-score of 1 means there is a\
1/10 probability that the observed conservation level would occur by\
chance, an L-score of 2 means a 1/100 probability, an L-score of 3\
means a 1/1000 probability, etc. The L-scores display as\
"mountain ranges". Clicking on a mountain range, a detail page is\
displayed from which you can access the base level alignments, both\
for the whole region and for the individual 50bp windows.\
\
Genome-wide alignments between human and mouse were produced by\
blastz.\
A set of 50bp windows in the human genome were determined\
by scanning the sequence, sliding 5 bases at a time, and only those\
windows with at least 15 aligned bases were kept. For each window,\
a conservation score defined by\
\
\
\
\
Methods
\
Credits
\
We'd like to thank Arian Smit and GIRI\
for providing the tools and repeat libraries used to generate this track.\
varRep 0
simpleRepeat Simple Repeats bed 4 + Simple Tandem Repeats by TRF 0 149.3 0 0 0 127 127 127 0 0 0 Description
\
Methods
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Credits
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Description
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Methods
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Description and Credits
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References
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Description
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Methods
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Description and Credits
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References
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Methods
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\
\
was calculated, where n is the number of aligning bases in the\
window, p is the percent identity between human and mouse for these\
aligning bases, and m is the average percent identity for aligned\
neutrally evolving bases in a larger region surrounding the 50bp\
window being scored. Neutral bases were taken from ancestral repeat\
sequences, which are relics of transposons that were inserted before\
the human-mouse split. To transform S into an L-score, the empirical\
cumulative distribution function CDF(S) = P(x < S)\
is computed from the scores of all windows genome-wide, and\
the L-score is defined as\
\
\
\
The L-score\
provides a frequentist confidence assessment. A Bayesian\
calculation of the probability that a window is under\
selection can also be made using a mixture decomposition of\
the empirical density of the scores for all windows\
genome-wide into a neutral and a selected component. Details\
are given in a manuscript in preparation. The results are\
summarized in the table below.\
\
\
L-score Frequentist probability Bayesian probability\
of this L-score or greater that window with this\
given neutral evolution L-score is under\
selection\
\
------------------------------------------------------------------\
\
1 0.1 0.32 \
2 0.01 0.75\
3 0.001 0.94\
4 0.0001 0.97\
5 0.00001 0.98\
6 0.000001 0.99\
7 0.0000001 >0.99 \
8 0.00000001 >0.99\
\
\
The track filter can be used to configure some of the display characteristics\ of the track. \
\ When you have finished configuring the filter, click the Submit button.
\ \\ \ Thanks to Webb Miller and Scott Schwartz for creating the blastz\ alignments, Jim Kent for post-processing them, and \ Mark Diekhans for scoring the windows and selecting out the ancestral repeats. \ Krishna Roskin created S-scores for these windows. Ryan Weber computed the CDF \ for these S-scores, \ and created the remaining track display functions. Mouse sequence data are provided by the Mouse Genome Sequencing Consortium.\
\ \ compGeno 0 blastzTightMouse Tight Mouse psl xeno mm3 $o_Organism ($o_date/$o_db) Blastz Tight Subset of Best Alignments 0 181 100 50 0 255 240 200 1 0 0\ This track displays blastz alignments of the Feb. 2003 mouse draft\ assembly to the human genome, filtered by axtBest and \ subsetAxt with very stringent constraints as described below.
\ \Each item in the display is identified by the chromosome, strand, and \ location of the match (in thousands). \ \
\ Blastz uses 12 of 19 seeds and this matrix: \
\
A C G T\
A 91 -114 -31 -123\
C -114 100 -125 -31\
G -31 -125 100 -114\
T -123 -31 -114 91\
\
O = 400, E = 30, K = 3000, L = 3000, M = 50\
\
\ A second pass is done at reduced stringency (7mer seeds and\ MSP threshold of K=2200) to attempt to fill in gaps of up to about 10K bp.\ Lineage specific repeats are abridged during this alignment.\ axtBest\ is used to select only the best alignment for any given region\ of the genome. subsetAxt is then run on axtBest-filtered alignments\ with this matrix:\
\
A C G T\
A 100 -200 -100 -200\
C -200 100 -200 -100\
G -100 -200 100 -200\
T -200 -100 -200 100\
\
\ with a gap open penalty of 2000 and a gap extension penalty of 50.\ The minimum score threshold was 3400.\
\ \The track filter can be used to turn on the chromosome color track or to \ filter the display output by chromosome.\
\ When you have finished configuring the filter, click the Submit button.
\ \\ The alignments are contributed by Scott Schwartz from the\ \ Penn State Bioinformatics Group. \ The best in genome filtering is done by UCSC's \ axtBest\ and subsetAxt programs. Mouse sequence data are provided by the \ Mouse Genome Sequencing Consortium.
\ \ compGeno 1 otherDb mm3\ blastzBestMouse Best Mouse psl xeno mm3 $o_Organism ($o_date/$o_db) Blastz Best-in-Genome Alignments 0 183 100 50 0 255 240 200 1 0 0This track displays blastz alignments of the Feb. 2003 mouse draft\ assembly to the human genome filtered to display only the best alignment for any\ given region of the human genome. The track has an optional\ feature that color codes alignments to indicate the chromosomes from which \ they are derived in the aligning assembly. To activate the color feature,\ click the on radio button next to "Color track based on chromosome".\
\\ For blastz, we use 12 of 19 seeds and then score using: \
\
A C G T\
A 91 -114 -31 -123\
C -114 100 -125 -31\
G -31 -125 100 -114\
T -123 -31 -114 91\
\
O = 400, E = 30, K = 3000, L = 3000, M = 50\
\
\ We then do a second pass at reduced stringency (7mer seeds and\ MSP threshold of K=2200) to attempt to fill in gaps of up to about 10K bp.\ Lineage specific repeats are abridged during this alignment.
\ \The track filter can be used to turn on the chromosome color track or to \ filter the display output by chromosome.\
\ When you have finished configuring the filter, click the Submit button.
\ \\ These alignments are contributed by Scott Schwartz from the Penn State Bioinformatics Group. The best in genome filtering\ is done by UCSC's \ axtBest\ program. Mouse sequence data are provided by the \ Mouse Genome Sequencing Consortium.
\ compGeno 1 otherDb mm3\ mouseChain Mouse Chain chain mm3 $o_Organism ($o_date/$o_db) Chained Blastz Alignments 0 186 100 50 0 255 240 200 1 0 0\ This track shows mouse/$organism genomic alignments using\ a gap scoring system that allows longer gaps than traditional\ affine gap scoring systems. It can also tolerate gaps\ in both mouse and $organism simultaneously. These "double-sided"\ gaps can be caused by local inversions and overlapping deletions\ in both species. The mouse sequence is from the Feb. 2003 (mm3)\ assembly.
\\ The chain track displays boxes joined together by either single or \ double lines. The boxes represent aligning regions. Single lines \ indicate gaps that are largely due to missing sequence in the \ non-$organism species. Double lines represent gaps in the chain where \ sequence is present in both species but they do not align. \ In cases where there are multiple \ chains over a particular portion of the $organism genome, chains with \ single-lined gaps often are due to processed pseudogenes, while chains \ with double-lined gaps are more often due to paralogs and unprocessed\ pseudogenes.\ \
The display indicates the chromosome, strand, and location of the match \ for each matching alignment (in thousands). \ \
\ Transposons that have been inserted since the mouse/$organism\ split are removed, and the resulting abbreviated genomes are\ aligned with blastz. The transposons are then put back into the\ alignments. The resulting alignments are converted into axt format\ and the resulting axts are fed into axtChain. AxtChain organizes all \ the alignments between a single mouse and a single $organism chromosome,\ into a group, and makes a kd-tree out of all the gapless subsections\ (blocks) of the alignments. Next, maximally scoring chains of these\ blocks are found by running a dynamic program over the kd-tree. Chains\ scoring below a threshold are discarded, and the remaining chains are\ displayed here.
\ \Blastz was developed at Pennsylvania State University by \ 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 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 made\ by Robert Baertsch and Jim Kent.
\ \\ Chiaromonte F, Yap VB, Miller W (2002). \ Scoring pairwise genomic sequence alignments. \ Pac Symp Biocomput 2002;:115-26.
\\ Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D (2003).\ Evolution's cauldron: \ Duplication, deletion, and rearrangement in the mouse and human genomes. \ Proc Natl Acad Sci USA 100(20):11484-11489 Sep 30 2003.\
\ Schwartz S, Kent WJ, Smit A, Zhang Z, Baertsch R, Hardison R, Haussler D, and \ Miller W (2003). \ Human-Mouse \ Alignments with BLASTZ. Genome Res. 13(1):103-7.
\ compGeno 1 otherDb mm3\ mouseNet Mouse Net netAlign mm3 mouseChain $o_Organism ($o_date/$o_db) Alignment Net 0 187 0 0 0 127 127 127 1 0 0This track shows the best mouse/$organism chain for \ every part of the $organism genome. It is useful for\ finding orthologous regions and for studying genome\ rearrangement. In full mode the top level (level 1)\ chains are the largest, highest scoring chains that\ span this region. In many cases there are gaps 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. The mouse sequence used in this annotation is from the Feb. 2003 (mm3) assembly.
\\ In the graphical display, the boxes represent ungapped \ alignments, while the lines represent gaps. Clicking\ on a box brings up detailed information about the chain\ as a whole, while clicking on a line brings up information\ on the gap. The detailed information is useful in determining\ the cause of the gap or, for lower level chains, the genomic\ rearrangement.
\ \First, chains are derived from blastz alignments as\ described in the details pages of the chain tracks\ and sorted so that the highest scoring chain in the\ genome is first. The program chainNet then places\ chains one at a time, trimming them as necessary to\ fit into section that is not already covered by \ a higher scoring chain. During this process, a\ natural hierarchy emerges where chains that fill gaps\ in a previous chain are considered underneath the\ previous chain. The program netSyntenic fills in\ information about the relationship between upper\ and lower level chains, including whether a lower level\ chain is syntenic with the higher level chain, whether\ it is inverted with respect to the higher level chain,\ and so forth. The program netClass then fills in \ how much of the gaps and chains are filled with N's\ (sequencing gaps) in one or both species, how much\ is filled with transposons inserted before and after\ mouse and $organism diverged, and so forth.
\ \The chainNet, netSyntenic, and netClass programs were\ developed at the University of California\ at Santa Cruz by Jim Kent.\ For more information, see \ Kent WJ, Baertsch R, Hinrichs A, Miller W, and Haussler D (2003). \ Evolution's cauldron: \ Duplication, deletion, and rearrangement in the mouse and human genomes. \ Proc Natl Acad Sci USA 100(20):11484-11489 Sep 30 2003.\ \
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.
\ \ compGeno 0 otherDb mm3\ syntenyMouse Mouse Synteny bed 4 . $o_Organism ($o_date/$o_db) Synteny Using Blastz Single Coverage (100k window) 0 188 0 100 0 255 240 200 0 0 0\ This track shows syntenous (corresponding) regions between human and mouse chromosomes. \ The Feb. 2003 (mm3) assembly of the mouse genome was used for this annotation.
\\ We passed a 100k non-overlapping window over the genome and - using the blastz best in mouse \ genome alignments - looked for high-scoring regions with at least 40% of the bases aligning \ with the same region in mouse. 100k segments were joined together if they agreed in direction and\ were within 500kb of each other in the human genome and within 4mb of each other in the mouse. \ Gaps were joined between syntenic anchors if the bases between two flanking regions agreed with \ synteny (direction and mouse location). Finally, we extended the syntenic block to include those \ areas.
\ \\ Contact Robert \ Baertsch at UCSC for more information about this track.\ Thanks to the Mouse Genome Sequencing Consortium for providing the mouse sequence data.
\ compGeno 1 otherDb mm3\