Schema for refFlat
  Database: felCat4    Primary Table: refFlat    Row Count: 493   Data last updated: 2020-08-21
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName TLR4varchar(255) values Name of gene as it appears in genome browser.
name NM_001009223varchar(255) values Name of gene
chrom chrD4varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 75394845int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 75407269int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 75394848int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 75406677int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 75394845,75401016,75404435,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 75394941,75401183,75407269,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      felCat4.mrnaOrientInfo.name (via refFlat.name)
      felCat4.refGene.name (via refFlat.name)
      felCat4.refSeqAli.qName (via refFlat.name)
      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)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
TLR4NM_001009223chrD4+75394845754072697539484875406677375394845,75401016,75404435,75394941,75401183,75407269,
MAN2B1NM_001009222chrA2-119139241193038911914035119303561711913924,11914618,11914660,11914667,11917677,11917944,11918211,11918403,11924512,11924650,11926248,11927271,11927676,11928472,11 ...11914145,11914659,11914666,11914675,11917761,11918032,11918313,11918524,11924547,11924736,11926365,11927417,11927809,11928666,11 ...
SMYHCNM_001009221chrE3+5182034526008151860935256418465182034,5186083,5188968,5190601,5191379,5191617,5191656,5192494,5193592,5194264,5195986,5196887,5197392,5199301,5201141,5202967, ...5182061,5186303,5189112,5190758,5191407,5191654,5191677,5192587,5193656,5194363,5196090,5197026,5197661,5199472,5201321,5203094, ...
EDN1NM_001009386chrB2-18154963181625901815541718160661518154963,18157147,18157418,18160489,18162324,18155520,18157261,18157577,18160661,18162590,
EGFNM_001009381chrB1-13321307913331789713321307913331789720133213079,133215259,133229920,133234891,133235661,133240366,133244686,133245702,133250844,133256106,133258164,133259362,13326101 ...133213330,133215366,133230043,133235017,133235753,133240492,133244802,133245870,133251068,133256256,133258301,133259388,13326114 ...
DPEP1NM_001043356chrUn_ACBE01451251+7767466881726610776,4715,5095,5376,5700,6109,6389,6554,6884,7098,985,4848,5228,5527,5770,6286,6474,6630,7020,7466,
UTS2RNM_001048011chrB4+1386309071386319841386309071386319842138630907,138631618,138631608,138631984,
CYP2E2NM_001048010chrUn_ACBE01551026+339813583339813583103398,3480,4515,7710,8247,8852,10043,11761,12382,13392,3480,3574,4675,7860,8408,9029,10185,11949,12524,13583,
CFTRNM_001048009chrA2+19593986719612659419597020519612563427195939867,195970205,195971237,195994589,195999460,196000401,196001408,196006406,196013129,196020417,196043834,196046718,19604672 ...195939993,195970327,195971250,195994806,195999550,196000565,196001534,196006654,196013314,196020609,196043929,196046723,19604714 ...
ISG15NM_001130843chrUn_ACBE01248948+306441813142410823064,3637,3145,4181,

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