Schema for Old UCSC Genes - Previous Version of UCSC Genes
  Database: hg38    Primary Table: knownGeneOld11    Row Count: 226,811   Data last updated: 2019-09-03
Format description: Transcript from default gene set in UCSC browser
fieldexampleSQL type info description
name ENST00000619216.1varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 17368int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 17436int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 17368int(10) unsigned range Coding region start (or end position if for minus strand item)
cdsEnd 17368int(10) unsigned range Coding region end (or start position if for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 17368,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 17436,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 uc031tla.1varchar(255) values Unique identifier (GENCODE transcript ID for GENCODE Basic)

Connected Tables and Joining Fields
        hg38.kg10ToKg11.oldId (via knownGeneOld11.name)
      hg38.kgXrefOld11.kgID (via knownGeneOld11.name)

Sample Rows
 
namechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsproteinIDalignID
ENST00000619216.1chr1-17368174361736817368117368,17436,uc031tla.1
ENST00000473358.1chr1+29553310972955329553329553,30563,30975,30039,30667,31097,uc057aty.1
ENST00000469289.1chr1+30266311093026630266230266,30975,30667,31109,uc057atz.1
ENST00000607096.1chr1+30365305033036530365130365,30503,uc031tlb.1
ENST00000417324.1chr1-34553360813455334553334553,35276,35720,35174,35481,36081,uc001aak.4
ENST00000461467.1chr1-35244360733524435244235244,35720,35481,36073,uc057aua.1
ENST00000641515.2chr1+65418715856556470008365418,65519,69036,65433,65573,71585,A0A2U3U0J3uc001aal.2
ENST00000335137.4chr1+69054701086909070008169054,70108,Q8NH21uc285fxb.1
ENST00000466430.5chr1-892941209328929489294489294,92090,112699,120774,91629,92240,112804,120932,uc057aub.1
ENST00000495576.1chr1-89550911058955089550289550,90286,90050,91105,uc057auc.1

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

Old UCSC Genes (knownGeneOld11) Track Description
 

Description

The Old UCSC Genes track shows genes from the previous version of the UCSC Genes build, which was built with GENCODE v29 models. See the description page for more information on how the new GENCODE v32 track was built.

The new release has 247,541 total transcripts, compared with 226,811 in the previous version. The total number of canonical genes has increased from 64,792 to 66,622. Comparing the new gene set with the previous version:

  • 209,076 transcripts did not change.
  • 195 transcripts were not carried forward to the new version.
  • 16,798 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.
  • 751 transcripts overlap with those in the previous set, but do not show consistent splicing (i.e., they contain overlapping introns with differing splice sites)