\ The RefSeq Genes track shows known C. intestinalis protein-coding and \ non-protein-coding genes taken from the NCBI RNA reference sequences \ collection (RefSeq). The data underlying this track are updated weekly.
\ \\ Please visit the Feedback for Gene and Reference Sequences (RefSeq) page to\ make suggestions, submit additions and corrections, or ask for help concerning\ RefSeq records.\
\ \\ 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).
\\ 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 RNAs were aligned against the C. intestinalis genome using blat; \ those with an alignment of less than 15% were discarded. When a single RNA \ 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 RNA 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\ color 12,12,120\ group genes\ idXref hgFixed.refLink mrnaAcc name\ longLabel RefSeq Genes\ priority 35\ shortLabel RefSeq Genes\ track refGene\ type genePred refPep refMrna\ visibility hide\ jgiGene JGI Genes genePred jgiPep JGI Gene Predictions 1 49 0 0 0 127 127 127 0 0 0\ This track contains alignments of predicted transcripts from the \ DOE Joint Genome \ Institute (JGI) to the C. intestinalis genome.
\ \\ This track follows the display conventions for \ gene prediction \ tracks.
\\ The track description page offers the following filter and configuration\ options:\
\ Predicted peptides from JGI were aligned to their predicted transcripts using \ the blat program to establish the coding portion of the transcript. The \ transcripts were then aligned to the C. intestinalis genome using blat.\ For more information about this assembly and an analysis of the euchromatic\ regions of the genome, see Dehal, P. et al. (2002) in the References \ section below.
\ \\ The C. intestinalis predicted transcripts and peptides were provided by \ JGI.\ Blat was written by Jim Kent.
\ \\ Dehal P. et al.\ The Draft Genome of Ciona intestinalis: Insights into Chordate \ and Vertebrate Origins.\ Science. 298(5601):2157-67 (2002).\ PMID: 12481130\
\ \\
Kent WJ.\
BLAT - the BLAST-like alignment tool.\
Genome Res. 12(4), 656-664 (2002).\
PMID: 11932250; PMC:
\ This track shows gene predictions determined by the Semi-HMM-based Nucleic \ Acid Parser (SNAP), a general purpose gene-finding program written by Ian \ Korf. SNAP is suitable for both eukaryotic and prokaryotic genomes. For this \ set of predictions, the gene-finder was trained on gene annotations from the\ DOE Joint Genome \ Institute (JGI).
\ \\ This track follows the display conventions for \ gene prediction \ tracks.
\\ The track description page offers the following filter and configuration\ options:\
\ Thanks to \ Colin Dewey for providing these gene predictions.
\ genes 1 group genes\ longLabel SNAP Gene Predictions\ priority 49\ shortLabel SNAP Genes\ track snapGene\ type genePred\ visibility dense\ intronEst Spliced ESTs psl est C. intestinalis ESTs That Have Been Spliced 1 56 0 0 0 127 127 127 1 0 0\ This track shows alignments between C. intestinalis 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. 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 \ C. intestinalis 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.\
\ \\ 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, C. intestinalis 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\ group rna\ indelDoubleInsert on\ indelQueryInsert on\ intronGap 30\ longLabel C. intestinalis ESTs That Have Been Spliced\ priority 56\ shortLabel Spliced ESTs\ showDiffBasesAllScales .\ spectrum on\ track intronEst\ type psl est\ visibility dense\ est C. intestinalis ESTs psl est C. intestinalis ESTs Including Unspliced 0 100 0 0 0 127 127 127 1 0 0\ This track shows alignments between C. intestinalis 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,\ go to the\ \ Base Coloring for Alignment Tracks page.\ Several types of alignment gap may also be colored;\ for more information, go to the\ \ Alignment Insertion/Deletion Display Options page.\
\ \\ 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, C. intestinalis 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, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.\
\
GenBank.\
Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42.\
PMID: 23193287; PMC:
\
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\
GenBank: update.\
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.\
PMID: 14681350; PMC:
\
Kent WJ.\
BLAT - the BLAST-like alignment tool.\
Genome Res. 2002 Apr;12(4):656-64.\
PMID: 11932250; PMC:
\ The mRNA track shows alignments between C. intestinalis 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, go to the\ \ Codon and Base Coloring for Alignment Tracks page.\ Several types of alignment gap may also be colored;\ for more information, go to the\ \ Alignment Insertion/Deletion Display Options page.\
\ \\ GenBank C. intestinalis 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, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW.\
\
GenBank.\
Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42.\
PMID: 23193287; PMC:
\
Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL.\
GenBank: update.\
Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6.\
PMID: 14681350; PMC:
\
Kent WJ.\
BLAT - the BLAST-like alignment tool.\
Genome Res. 2002 Apr;12(4):656-64.\
PMID: 11932250; PMC:
\ This track shows the position of gaps — represented by Ns — within \ the C. intestinalis assembly. Gaps of 50 or more bases were most \ likely introduced by the JGI JAZZ assembler.
\\ For a discussion of gaps and the JAZZ assembler see \ Dehal, P. et al. (2002) in the References section below.
\ \\ Gaps are represented by boxes. If the relative order and orientation of \ the contigs on either side of the gap is known from mRNA, ESTs, or paired BAC \ end reads, it is a bridged gap, indicated by a white line drawn \ through the box. The display must be sufficiently zoomed in to view this \ feature. In full display mode, the item label indicates the type of gap and \ whether the gap is bridged.
\ \\ Murphy WJ, Eizirik E, O'Brien SJ, Madsen O, Scally M, Douady CJ, Teeling E, Ryder OA, Stanhope MJ,\ de Jong WW et al.\ The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins.\ Science. 2002 Dec 13;298(5601):2157-67.\ PMID: 12481130\
\ map 1 group map\ longLabel Gap Locations\ shortLabel Gap\ track gap\ type bed 3 +\ visibility dense\ gc5Base GC Percent wig 0 100 GC Percent in 5-Base Windows 0 100 0 0 0 128 128 128 0 0 0\ The GC percent track shows the percentage of G (guanine) and C (cytosine) bases\ in 5-base windows. High GC content is typically associated with\ gene-rich areas.\
\\ This track may be configured in a variety of ways to highlight different\ apsects 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 altColor 128,128,128\ autoScale Off\ color 0,0,0\ graphTypeDefault Bar\ gridDefault OFF\ group map\ longLabel GC Percent in 5-Base Windows\ maxHeightPixels 128:36:16\ shortLabel GC Percent\ spanList 5\ track gc5Base\ type wig 0 100\ viewLimits 30:70\ visibility hide\ windowingFunction Mean\ blastHg16KG Human Proteins psl protein Human Proteins (hg16) Mapped by Chained tBLASTn 3 100 0 0 0 127 127 127 0 0 0\ This track contains tBLASTn alignments of the peptides from the predicted \ and known genes identified in the hg16 Known Genes track.\
\ \\ First, the predicted proteins from the human Known Genes track were aligned \ with the human genome using the Blat program to discover exon boundaries. \ Next, the amino acid sequences that make up each exon were aligned with the \ C. intestinalis sequence using the tBLASTn program.\ Finally, the putative C. intestinalis exons were chained together using an \ organism-specific maximum gap size but no gap penalty. The single best exon \ chains extending over more than 60% of the query protein were included. Exon \ chains that extended over 60% of the query and matched at least 60% of the \ protein's amino acids were also included.
\ \\ tBLASTn is part of the NCBI BLAST tool set. For more information on BLAST, see\ Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ.\ Basic local alignment search tool.\ J Mol Biol. 1990 Oct 5;215(3):403-410.
\\ Blat was written by Jim Kent. The remaining utilities \ used to produce this track were written by Jim Kent or Brian Raney.
\ genes 1 blastRef hg16.blastKGRef00\ colorChromDefault off\ group genes\ longLabel Human Proteins (hg16) Mapped by Chained tBLASTn\ pred hg16.blastKGPep00\ shortLabel Human Proteins\ track blastHg16KG\ type psl protein\ visibility pack\ microsat Microsatellite bed 4 Microsatellites - Di-nucleotide and Tri-nucleotide Repeats 0 100 0 0 0 127 127 127 0 0 0\ This track displays regions that are likely to be useful as microsatellite\ markers. These are sequences of at least 15 perfect di-nucleotide and \ tri-nucleotide repeats and tend to be highly polymorphic in the\ population.\
\ \\ The data shown in this track are a subset of the Simple Repeats track, \ selecting only those \ repeats of period 2 and 3, with 100% identity and no indels and with\ at least 15 copies of the repeat. The Simple Repeats track is\ created using the \ Tandem Repeats Finder. For more information about this \ program, see Benson (1999).
\ \\ Tandem Repeats Finder 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.\
PMID: 9862982; PMC:
\ This track displays translated blat alignments of vertebrate and\ invertebrate mRNA in \ GenBank from organisms other than C. intestinalis.\ \
\ 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.\
\ \\ The mRNAs were aligned against the C. intestinalis 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\ group rna\ indelDoubleInsert on\ indelQueryInsert on\ longLabel Non-C. intestinalis mRNAs from GenBank\ shortLabel Other mRNAs\ showDiffBasesAllScales .\ spectrum on\ track xenoMrna\ type psl xeno\ visibility dense\ xenoRefGene Other RefSeq genePred xenoRefPep xenoRefMrna Non-C. intestinalis RefSeq Genes 1 100 12 12 120 133 133 187 0 0 0\ This track shows known protein-coding and non-protein-coding genes \ for organisms other than C. intestinalis, taken from the NCBI RNA reference\ sequences collection (RefSeq). The data underlying this track are \ updated weekly.
\ \\ 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).
\\ 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. \
\ The RNAs were aligned against the C. intestinalis genome using blat; those\ with an alignment of less than 15% were discarded. When a single RNA 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 25% base identity with the genomic sequence were kept.\
\ \\ This track was produced at UCSC from RNA 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.
\ genes 1 color 12,12,120\ group genes\ longLabel Non-C. intestinalis RefSeq Genes\ shortLabel Other RefSeq\ track xenoRefGene\ type genePred xenoRefPep xenoRefMrna\ visibility dense\ simpleRepeat Simple Repeats bed 4 + Simple Tandem Repeats by TRF 0 100 0 0 0 127 127 127 0 0 0\ This track displays simple tandem repeats (possibly imperfect repeats) 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.\
PMID: 9862982; PMC:
\ This track shows blat alignments of C. savignyi to the \ C. intestinalis genome. The C. savignyi genome was \ provided by the Broad Institute at MIT and Harvard.
\\ 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 -+.
\ \\ This track follows the display conventions for \ PSL alignment \ tracks.
\ \\ The alignments were made with blat in translated protein mode, requiring \ two nearby 4-mer matches to trigger a detailed alignment. The \ C. intestinalis genome was masked with RepeatMasker and Tandem Repeat \ Finder before running blat.
\ \\ Thanks to the Broad \ Institute for providing the C. savignyi sequence.
\ \\
Kent WJ.\
BLAT - the BLAST-like alignment tool.\
Genome Res. 12(4), 656-664 (2002).\
PMID: 11932250; PMC:
\
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.
\ \\ Jurka J.\ Repbase update: a database and an electronic journal of repetitive elements.\ Trends Genet. 2000 Sep;16(9):418-20.\ PMID: 10973072\
\ varRep 0 canPack off\ group varRep\ longLabel Repeating Elements by RepeatMasker\ priority 149.1\ shortLabel RepeatMasker\ spectrum on\ track rmsk\ type rmsk\ visibility dense\