Schema for Pfam in GENCODE - Pfam Domains in GENCODE Genes |
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Database: hg38 Primary Table: ucscGenePfam Row Count: 71,171 Data last updated: 2023-08-23
Format description: Browser extensible data
On download server: MariaDB table dump directory
| 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 | 69969 | int(10) unsigned | range | End position in chromosome |
| name | 7tm_4 | varchar(255) | values | Name of item |
| score | 0 | int(10) unsigned | range | Optional score, nominal range 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 | 801, | 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 | 69969 | 7tm_4 | 0 | + | 0 | 0 | 0 | 1 | 801, | 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, |
| 588 | chr1 | 450772 | 451585 | 7tm_4 | 0 | - | 0 | 0 | 0 | 1 | 813, | 0, |
| 588 | chr1 | 450817 | 451558 | 7tm_1 | 0 | - | 0 | 0 | 0 | 1 | 741, | 0, |
| 590 | chr1 | 685748 | 686561 | 7tm_4 | 0 | - | 0 | 0 | 0 | 1 | 813, | 0, |
| 590 | chr1 | 685793 | 686534 | 7tm_1 | 0 | - | 0 | 0 | 0 | 1 | 741, | 0, |
| 592 | chr1 | 924764 | 925959 | SAND | 0 | + | 0 | 0 | 0 | 2 | 184,38, | 0,1157, |
| 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 GENCODE (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 GENCODE Genes track by the software HMMER3.
Display Conventions and Configuration
This track follows the display conventions for
gene
tracks.
Methods
The sequences from the knownGenePep table (see
GENCODE 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. A complete shell script log for every version of UCSC genes can be found in
our GitHub repository under
hg/makeDb/doc/ucscGenes, e.g.
mm10.knownGenes17.csh is for the database mm10 and version 17 of UCSC known genes.
Of the several options for filtering out false positives, the "Trusted cutoff (TC)"
threshold method is used in this track to determine significance. For more information regarding
thresholds and scores, see the HMMER
documentation and
results interpretation pages.
Note: There is currently an undocumented but known HMMER problem which results in lessened
sensitivity and possible missed searches for some zinc finger domains. Until a fix is released for
HMMER /PFAM thresholds, please also consult the "UniProt Domains" subtrack of the UniProt
track for more comprehensive zinc finger annotations.
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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