Schema for Pfam in UCSC Gene - Pfam Domains in UCSC Genes |
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Database: hg38 Primary Table: ucscGenePfam Row Count: 62,551
Format description: Browser extensible data
| field | example | SQL type | info | description |
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| bin | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
| chromStart | 69168 | int(10) unsigned | range | Start position in chromosome |
| chromEnd | 69972 | int(10) unsigned | range | End position in chromosome |
| name | 7tm_4 | varchar(255) | values | Name of item |
| score | 0 | int(10) unsigned | range | Score from 0-1000 |
| strand | + | char(1) | values | + or - |
| thickStart | 0 | int(10) unsigned | range | Start of where display should be thick (start codon) |
| thickEnd | 0 | int(10) unsigned | range | End of where display should be thick (stop codon) |
| reserved | 0 | int(10) unsigned | range | Used as itemRgb as of 2004-11-22 |
| blockCount | 1 | int(10) unsigned | range | Number of blocks |
| blockSizes | 804, | longblob | | Comma separated list of block sizes |
| chromStarts | 0, | longblob | | Start positions relative to chromStart |
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Sample Rows
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| bin | chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts |
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| 585 | chr1 | 69168 | 69972 | 7tm_4 | 0 | + | 0 | 0 | 0 | 1 | 804, | 0, |
| 585 | chr1 | 69183 | 69816 | 7TM_GPCR_Srsx | 0 | + | 0 | 0 | 0 | 1 | 633, | 0, |
| 585 | chr1 | 69189 | 69930 | 7tm_1 | 0 | + | 0 | 0 | 0 | 1 | 741, | 0, |
| 586 | chr1 | 187279 | 195375 | WASH_WAHD | 0 | - | 0 | 0 | 0 | 10 | 8,202,132,7,4,141,48,96,112,117, | 0,96,475,742,822,846,1159,1209,1511,7979, |
| 588 | chr1 | 450772 | 451585 | 7tm_4 | 0 | - | 0 | 0 | 0 | 1 | 813, | 0, |
| 588 | chr1 | 450973 | 451558 | 7tm_1 | 0 | - | 0 | 0 | 0 | 1 | 585, | 0, |
| 590 | chr1 | 685748 | 686561 | 7tm_4 | 0 | - | 0 | 0 | 0 | 1 | 813, | 0, |
| 590 | chr1 | 685949 | 686534 | 7tm_1 | 0 | - | 0 | 0 | 0 | 1 | 585, | 0, |
| 592 | chr1 | 943311 | 943910 | SAM_1 | 0 | + | 0 | 0 | 0 | 3 | 66,111,3, | 0,386,596, |
| 592 | chr1 | 943314 | 943799 | SAM_2 | 0 | + | 0 | 0 | 0 | 2 | 63,102, | 0,383, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Pfam in UCSC Gene (ucscGenePfam) Track Description
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Description
Most proteins are composed of one or more conserved functional regions called
domains. This track shows the high-quality, manually-curated
Pfam-A
domains found in transcripts located in the UCSC Genes track.
Display Conventions and Configuration
This track follows the display conventions for
gene
tracks.
Methods
The sequences from the knownGenePep table (see
UCSC Genes description page)
are submitted to the set of Pfam-A HMMs which annotate regions within the
predicted peptide that are recognizable as Pfam protein domains. These regions
are then mapped to the transcripts themselves using the
pslMap utility.
Credits
pslMap was written by Mark Diekhans at UCSC.
References
Finn RD, Mistry J, Tate J, Coggill P, Heger A, Pollington JE, Gavin OL, Gunasekaran P, Ceric G,
Forslund K et al.
The Pfam protein families database.
Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22.
PMID: 19920124; PMC: PMC2808889
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