Schema for Transcriptome - TROMER Transcriptome database
  Database: mm9    Primary Table: transcriptome    Row Count: 143,241   Data last updated: 2008-04-15
Format description: A gene prediction with some additional info.
fieldexampleSQL type info description
bin 608smallint(5) unsigned range Indexing field to speed chromosome range queries.
name MTR061646.1.0.0varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 3042999int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 3045517int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 3043927int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 3044251int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 3042999,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 3045517,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 MTR061646varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,longblob   Exon frame {0,1,2}, or -1 if no frame for exon

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
608MTR061646.1.0.0chr1+304299930455173043927304425113042999,3045517,0MTR061646incmplincmpl0,
608MTR036582.1.1.0chr1+306333330644030013063333,3064403,0MTR036582nonenone-1,
609MTR063886.1.2.0chr1-319549832064253206102320642523195498,3203689,3197398,3206425,0MTR063886incmplincmpl-1,0,
609MTR063886.1.2.1chr1-319549832057133196524319661423195498,3203519,3197398,3205713,0MTR063886incmplincmpl0,-1,
76MTR062881.1.3.0chr1-320456236629093206102366142933204562,3411782,3660632,3207049,3411982,3662909,0MTR062881incmplincmpl1,2,0,
610MTR023928.1.13.0chr1-329944533011590013299445,3301159,0MTR023928nonenone-1,
610MTR027616.1.8.0chr1-335580933586303356452335662313355809,3358630,0MTR027616incmplincmpl0,
610MTR071605.1.11.0chr1-336561333678930013365613,3367893,0MTR071605nonenone-1,
611MTR027617.1.9.0chr1-342437434268423425133342522313424374,3426842,0MTR027617incmplincmpl0,
611MTR031882.1.10.0chr1-345505734573663456931345709313455057,3457366,0MTR031882incmplincmpl0,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Transcriptome (transcriptome) Track Description
 

Description

The transcriptome track shows gene predictions based on data from RefSeq and EMBL/GenBank. This is a moderately conservative set of predictions, requiring the support of either one GenBank full length RNA sequence, one RefSeq RNA, or one spliced EST. The track includes both protein-coding and non-coding transcripts. The CDS are predicted using ESTScan.

Display Conventions and Configuration

This track in general follows the display conventions for gene prediction tracks. The exons for putative noncoding genes and untranslated regions are represented by relatively thin blocks, while those for coding open reading frames are thicker.

This track contains an optional codon coloring feature that allows users to quickly validate and compare gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. Click here for more information about this feature.

Further information on the predicted transcripts can be found on the Transcriptome Web interface.

Methods

The transcriptome is built using a multi-step pipeline:

  1. RefSeq and GenBank RNAs and ESTs are aligned to the genome with SIBsim4, keeping only the best alignments for each RNA.

  2. Alignments are broken up at non-intronic gaps, with small isolated fragments thrown out.

  3. A splicing graph is created for each set of overlapping alignments. This graph has an edge for each exon or intron, and a vertex for each splice site, start, and end. Each RNA that contributes to an edge is kept as evidence for that edge.

  4. The graph is traversed to generate all unique transcripts. The traversal is guided by the initial RNAs to avoid a combinatorial explosion in alternative splicing.

  5. Protein predictions are generated.

Credits

The transcriptome track was produced on the Vital-IT high-performance computing platform using a computational pipeline developed by Christian Iseli with help from colleagues at the Ludwig institute for Cancer Research and the Swiss Institute of Bioinformatics. It is based on data from NCBI RefSeq and GenBank/ EMBL. Our thanks to the people running these databases and to the scientists worldwide who have made contributions to them.

References

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: PMC308779