Schema for refFlat

Database: ornAna2 Primary Table: refFlat Row Count: 705 Data last updated: 2020-08-20
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory

field	example	SQL type	info	description
`geneName`	ORNANAV1R3238	`varchar(255)`	values	Name of gene as it appears in genome browser.
`name`	NM_001253630	`varchar(255)`	values	Name of gene
`chrom`	chrUn_DS181027v1	`varchar(255)`	values	Reference sequence chromosome or scaffold
`strand`	+	`char(1)`	values	+ or - for strand
`txStart`	80782	`int(10) unsigned`	range	Transcription start position (or end position for minus strand item)
`txEnd`	81709	`int(10) unsigned`	range	Transcription end position (or start position for minus strand item)
`cdsStart`	80782	`int(10) unsigned`	range	Coding region start (or end position for minus strand item)
`cdsEnd`	81709	`int(10) unsigned`	range	Coding region end (or start position for minus strand item)
`exonCount`	1	`int(10) unsigned`	range	Number of exons
`exonStarts`	80782,	`longblob`		Exon start positions (or end positions for minus strand item)
`exonEnds`	81709,	`longblob`		Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields


	hgFixed.refLink.name (via refFlat.geneName) hgFixed.gbCdnaInfo.acc (via refFlat.name) hgFixed.gbSeq.acc (via refFlat.name) hgFixed.imageClone.acc (via refFlat.name) hgFixed.refLink.mrnaAcc (via refFlat.name) hgFixed.refSeqStatus.mrnaAcc (via refFlat.name) hgFixed.refSeqSummary.mrnaAcc (via refFlat.name) knownGeneV39.kgXref.refseq (via refFlat.name) knownGeneV39.knownToRefSeq.value (via refFlat.name) ornAna2.mrnaOrientInfo.name (via refFlat.name) ornAna2.refGene.name (via refFlat.name) ornAna2.refSeqAli.qName (via refFlat.name)

Sample Rows

geneName	name	chrom	strand	txStart	txEnd	cdsStart	cdsEnd	exonCount	exonStarts	exonEnds
ORNANAV1R3238	NM_001253630	chrUn_DS181027v1	+	80782	81709	80782	81709	1	80782,	81709,
ORNANAV1R3237	NM_001253629	chrUn_DS181027v1	+	65280	66210	65280	66210	1	65280,	66210,
ORNANAV1R3235	NM_001253627	chrUn_DS181027v1	-	23124	24054	23124	24054	1	23124,	24054,
ORNANAV1R3234	NM_001253626	chrUn_DS181027v1	+	10157	11114	10157	11114	1	10157,	11114,
MIR142	NR_034731	chrUn_DS198477v1	-	1361	1471	1471	1471	1	1361,	1471,
MIR1421J	NR_034730	chrUn_DS197957v1	-	9646	9760	9760	9760	1	9646,	9760,
MIR1421H	NR_034728	chrUn_DS197957v1	-	6873	6963	6963	6963	1	6873,	6963,
MIR1421G-1	NR_034727	chrUn_DS197957v1	-	6128	6240	6240	6240	1	6128,	6240,
MIR1421F	NR_034726	chrUn_DS197957v1	-	5018	5107	5107	5107	1	5018,	5107,
MIR1421E	NR_034725	chrUn_DS197957v1	-	3935	4040	4040	4040	1	3935,	4040,

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