Schema for Old UCSC Genes - Previous Version of UCSC Genes |
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Database: hg38 Primary Table: knownGeneOld9 Row Count: 195,178
Format description: Transcript from default gene set in UCSC browser
| field | example | SQL type | info | description |
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| name | uc031tla.1 | varchar(255) | values | Name of gene |
| chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
| strand | - | char(1) | values | + or - for strand |
| txStart | 17368 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
| txEnd | 17436 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
| cdsStart | 17368 | int(10) unsigned | range | Coding region start (or end position if for minus strand item) |
| cdsEnd | 17368 | int(10) unsigned | range | Coding region end (or start position if for minus strand item) |
| exonCount | 1 | int(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 | ENST00000619216.1 | varchar(255) | values | Unique identifier (GENCODE transcript ID for GENCODE Basic) |
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Sample Rows
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| name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds | proteinID | alignID |
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| uc031tla.1 | chr1 | - | 17368 | 17436 | 17368 | 17368 | 1 | 17368, | 17436, | | ENST00000619216.1 |
| uc057aty.1 | chr1 | + | 29553 | 31097 | 29553 | 29553 | 3 | 29553,30563,30975, | 30039,30667,31097, | | ENST00000473358.1 |
| uc057atz.1 | chr1 | + | 30266 | 31109 | 30266 | 30266 | 2 | 30266,30975, | 30667,31109, | | ENST00000469289.1 |
| uc031tlb.1 | chr1 | + | 30365 | 30503 | 30365 | 30365 | 1 | 30365, | 30503, | | ENST00000607096.1 |
| uc001aak.4 | chr1 | - | 34553 | 36081 | 34553 | 34553 | 3 | 34553,35276,35720, | 35174,35481,36081, | | ENST00000417324.1 |
| uc057aua.1 | chr1 | - | 35244 | 36073 | 35244 | 35244 | 2 | 35244,35720, | 35481,36073, | | ENST00000461467.1 |
| uc001aal.1 | chr1 | + | 69090 | 70008 | 69090 | 70008 | 1 | 69090, | 70008, | Q8NH21 | ENST00000335137.3 |
| uc057aub.1 | chr1 | - | 89294 | 120932 | 89294 | 89294 | 4 | 89294,92090,112699,120774, | 91629,92240,112804,120932, | | ENST00000466430.4 |
| uc057auc.1 | chr1 | - | 89550 | 91105 | 89550 | 89550 | 2 | 89550,90286, | 90050,91105, | | ENST00000495576.1 |
| uc057aud.1 | chr1 | - | 92229 | 129217 | 92229 | 92229 | 4 | 92229,112699,120720,129054, | 92240,112804,120932,129217, | | ENST00000477740.4 |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Old UCSC Genes (knownGeneOld9) Track Description
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Description
The Old UCSC Genes track shows genes from the previous version of
the UCSC Genes build, which was built with Gencode v22 models.
See the description page
for more information on how the new GENCODE track was built.
The new release has 197,782 total transcripts, compared with 195,178 in the previous version. The total number of canonical genes has increased from 49,534 to 49,948. Comparing the new gene set with the previous version:
- 193,647 transcripts did not change.
- 534 transcripts were not carried forward to the new version.
- 997 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.
- 406 transcripts overlap with those in the previous set, but do not show consistent splicing (i.e., they contain overlapping introns with differing splice sites)
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