Schema for Old UCSC Genes - Previous Version of UCSC Genes |
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Database: hg38 Primary Table: knownGeneOld12 Row Count: 247,541 Data last updated: 2021-02-03
Format description: Transcript from default gene set in UCSC browser
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
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| name | ENST00000619216.1 | 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 | uc031tla.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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| ENST00000619216.1 | chr1 | - | 17368 | 17436 | 17368 | 17368 | 1 | 17368, | 17436, | | uc031tla.1 |
| ENST00000473358.1 | chr1 | + | 29553 | 31097 | 29553 | 29553 | 3 | 29553,30563,30975, | 30039,30667,31097, | | uc057aty.1 |
| ENST00000469289.1 | chr1 | + | 30266 | 31109 | 30266 | 30266 | 2 | 30266,30975, | 30667,31109, | | uc057atz.1 |
| ENST00000607096.1 | chr1 | + | 30365 | 30503 | 30365 | 30365 | 1 | 30365, | 30503, | | uc031tlb.1 |
| ENST00000417324.1 | chr1 | - | 34553 | 36081 | 34553 | 34553 | 3 | 34553,35276,35720, | 35174,35481,36081, | | uc001aak.4 |
| ENST00000461467.1 | chr1 | - | 35244 | 36073 | 35244 | 35244 | 2 | 35244,35720, | 35481,36073, | | uc057aua.1 |
| ENST00000641515.2 | chr1 | + | 65418 | 71585 | 65564 | 70008 | 3 | 65418,65519,69036, | 65433,65573,71585, | A0A2U3U0J3 | uc001aal.2 |
| ENST00000335137.4 | chr1 | + | 69054 | 70108 | 69090 | 70008 | 1 | 69054, | 70108, | Q8NH21 | uc285fxb.1 |
| ENST00000466430.5 | chr1 | - | 89294 | 120932 | 89294 | 89294 | 4 | 89294,92090,112699,120774, | 91629,92240,112804,120932, | | uc057aub.1 |
| ENST00000495576.1 | chr1 | - | 89550 | 91105 | 89550 | 89550 | 2 | 89550,90286, | 90050,91105, | | uc057auc.1 |
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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 (knownGeneOld12) 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 v32 models.
See the description page
for more information on how the new GENCODE v36 track was built.
The new release has 232,184 total transcripts, compared with 247,541 in the previous version. The
total number of canonical genes has decreased from 66,622 to 60,675 . Comparing the new gene set with
the previous version:
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221,698 transcripts did not change.
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20,017 transcripts were not carried forward to the new version.
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4,860 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.
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966 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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