Schema for Gene Bounds - Gene Boundaries as Defined by RNA and Spliced EST Clusters
  Database: hg19    Primary Table: rnaCluster    Row Count: 37,017   Data last updated: 2010-10-20
Format description: Browser extensible data
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
chromStart 10025int(10) unsigned range Start position in chromosome
chromEnd 12171int(10) unsigned range End position in chromosome
name chr1.1varchar(255) values Name of item
score 300int(10) unsigned range Optional score, nominal range 0-1000
strand -char(1) values + or -
thickStart 10025int(10) unsigned range Start of where display should be thick (start codon)
thickEnd 12171int(10) unsigned range End of where display should be thick (stop codon)
reserved 0int(10) unsigned range Used as itemRgb as of 2004-11-22
blockCount 2int(10) unsigned range Number of blocks
blockSizes 1,1,longblob   Comma separated list of block sizes
chromStarts 0,2145longblob   Start positions relative to chromStart

Sample Rows
 
binchromchromStartchromEndnamescorestrandthickStartthickEndreservedblockCountblockSizeschromStarts
585chr11002512171chr1.1300-1002512171021,1,0,2145
585chr11039714409chr1.21000+1039714409021,1,0,4011
585chr11435829985chr1.31000-1435829985021,1,0,15626
585chr13037931110chr1.4300+3037931110021,1,0,730
585chr13455336081chr1.51000-3455336081021,1,0,1527
585chr16909070008chr1.6300+6909070008021,1,0,917
585chr18752190896chr1.7300-8752190896021,1,0,3374
73chr189294762912chr1.81000-89294762912021,1,0,673617
585chr191433112785chr1.9300-91433112785021,1,0,21351
73chr1124239133566chr1.101000-124239133566021,1,0,9326

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

Gene Bounds (rnaCluster) Track Description
 

Description

This track shows the boundaries of genes and the direction of transcription as deduced from clustering spliced ESTs and mRNAs against the genome. When many spliced variants of the same gene exist, this track shows the variant that spans the greatest distance in the genome.

Method

ESTs and mRNAs from GenBank were aligned against the genome using BLAT. Alignments with less than 97.5% base identity within the aligning blocks were filtered out. When multiple alignments occurred, only those alignments with a percentage identity within 0.2% of the best alignment were kept. The following alignments were also discarded: ESTs that aligned without any introns, blocks smaller than 10 bases, and blocks smaller than 130 bases that were not located next to an intron. The orientations of the ESTs and mRNAs were deduced from the GT/AG splice sites at the introns; ESTs and mRNAs with overlapping blocks on the same strand were merged into clusters. Only the extent and orientation of the clusters are shown in this track.

Scores for individual gene boundaries were assigned based on the number of cDNA alignments used:

  • 300 — based on a single cDNA alignment
  • 600 — based on two alignments
  • 900 — based on three alignments
  • 1000 — based on four or more alignments

Credits

This track, which was originally developed by Jim Kent, was generated at UCSC and uses data submitted to GenBank by scientists worldwide.

References

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32:D23-6.

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.