Schema for Pfam in RefSeq - Pfam Domains in RefSeq Genes

Database: dm6 Primary Table: pfam_refseq_genes Row Count: 25,865 Data last updated: 2022-10-21

field	example	SQL type	info
`bin`	585	`smallint(5) unsigned`	range
`chrom`	chr2L	`varchar(255)`	values
`chromStart`	8730	`int(10) unsigned`	range
`chromEnd`	9258	`int(10) unsigned`	range
`name`	Peptidase_C48	`varchar(255)`	values
`score`	0	`int(10) unsigned`	range
`strand`	+	`char(1)`	values
`thickStart`	0	`int(10) unsigned`	range
`thickEnd`	0	`int(10) unsigned`	range
`reserved`	0	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	528,	`longblob`
`chromStarts`	0,	`longblob`

Sample Rows

bin	chrom	chromStart	chromEnd	name	strand	blockCount	blockSizes	chromStarts
585	chr2L	8730	9258	Peptidase_C48	+	1	528,	0,
585	chr2L	12127	12485	Lgl_C	-	2	94,200,	0,158,
585	chr2L	14651	14994	LLGL	-	2	223,62,	0,281,
585	chr2L	22386	23348	Lig_chan	-	3	301,193,355,	0,356,607,
585	chr2L	27348	28619	Polysacc_deac_1	-	3	142,203,209,	0,666,1062,
585	chr2L	39603	39756	CBM_14	-	1	153,	0,
585	chr2L	67645	67999	zf-AD	+	2	117,108,	0,246,
585	chr2L	74956	75372	Gal-bind_lectin	+	2	62,295,	0,121,
585	chr2L	75600	76026	Gal-bind_lectin	+	1	426,	0,
585	chr2L	76571	76931	Gal-bind_lectin	+	1	360,	0,

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

Pfam in RefSeq (pfam_refseq_genes) Track Description


	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 proteins associated with the RefSeq Genes transcripts. Methods The proteins associated with RefSeq genes were 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. 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, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016 Jan 4;44(D1):D279-85.

Description