Schema for Old UCSC Genes - Previous Version of UCSC Genes
  Database: hg19    Primary Table: knownGeneOld6    Row Count: 80,922   Data last updated: 2011-12-22
Format description: Transcript from default gene set in UCSC browser
fieldexampleSQL type info description
name uc001aaa.3varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 11873int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 14409int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 11873int(10) unsigned range Coding region start (or end position if for minus strand item)
cdsEnd 11873int(10) unsigned range Coding region end (or start position if for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 11873,12612,13220,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 12227,12721,14409,longblob   Exon end positions (or start positions for minus strand item)
proteinID  varchar(40) values UniProt display ID, UniProt accession, or RefSeq protein ID
alignID uc001aaa.3varchar(255) values Unique identifier (GENCODE transcript ID for GENCODE Basic)

Connected Tables and Joining Fields
        hg19.kg6ToKg7.oldId (via knownGeneOld6.name)
      hg19.kgXrefOld6.kgID (via knownGeneOld6.name)

Sample Rows
 
namechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsproteinIDalignID
uc001aaa.3chr1+11873144091187311873311873,12612,13220,12227,12721,14409,uc001aaa.3
uc010nxr.1chr1+11873144091187311873311873,12645,13220,12227,12697,14409,uc010nxr.1
uc010nxq.1chr1+11873144091218913639311873,12594,13402,12227,12721,14409,B7ZGX9uc010nxq.1
uc009vis.3chr1-14361167651436114361414361,14969,15795,16606,14829,15038,15942,16765,uc009vis.3
uc009vit.3chr1-14361197591436114361914361,14969,15795,16606,16857,17232,17914,18267,18912,14829,15038,15947,16765,17055,17742,18061,18366,19759,uc009vit.3
uc009viu.3chr1-143611975914361143611014361,14969,15795,16606,16857,17232,17914,18267,18500,18912,14829,15038,15947,16765,17055,17742,18061,18369,18554,19759,uc009viu.3
uc001aae.4chr1-143611975914361143611014361,14969,15795,16606,16857,17232,17605,17914,18267,18912,14829,15038,15947,16765,17055,17368,17742,18061,18366,19759,uc001aae.4
uc001aah.4chr1-143612937014361143611114361,14969,15795,16606,16857,17232,17605,17914,18267,24737,29320,14829,15038,15947,16765,17055,17368,17742,18061,18366,24891,29370,uc001aah.4
uc009vir.3chr1-143612937014361143611014361,14969,15795,16606,16857,17232,17914,18267,24737,29320,14829,15038,15947,16765,17055,17742,18061,18366,24891,29370,uc009vir.3
uc009viq.3chr1-14361293701436114361714361,15795,16606,16857,17605,24737,29320,14829,15947,16765,17055,18061,24891,29370,uc009viq.3

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

Old UCSC Genes (knownGeneOld6) Track Description
 

Description

The Old UCSC Genes track shows genes from the previous version of the UCSC Genes build. This is similar to the current version but without explicitly including Rfam or tRNA sequences.

The new release has 82,960 total transcripts, compared with 80,922 in the previous version. The total number of canonical genes has increased from 31,227 to 31,848. Comparing the new gene set with the previous version:

  • 74,657 transcripts did not change between versions.
  • 88 transcripts were not carried forward to the new version.
  • 5,556 transcripts are "compatible" with those in the previous set, meaning that the two transcripts show consistent splicing. In most cases, the old and new transcripts differ in the lengths of their UTRs.
  • 621 transcripts overlap with those in the previous set but do not show consistent splicing, i.e., they contain overlapping introns with differing splice sites.

Read the description of how the current version of the UCSC Genes track was built.