Schema for ncbiRefSeqHgmd
  Database: hg19    Primary Table: ncbiRefSeqHgmd    Row Count: 14,693   Data last updated: 2024-12-05
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 591smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_152486.4varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 861110int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 879954int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 861321int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 879533int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 14int(10) unsigned range Number of exons
exonStarts 861110,861301,865534,866418...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 861180,861393,865716,866469...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 SAMD11varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,0,0,2,2,1,1,1,2,1,2,1,0,0,longblob   Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region.

Connected Tables and Joining Fields
        hg19.ncbiRefSeq.name (via ncbiRefSeqHgmd.name)
      hg19.ncbiRefSeqCds.id (via ncbiRefSeqHgmd.name)
      hg19.ncbiRefSeqCurated.name (via ncbiRefSeqHgmd.name)
      hg19.ncbiRefSeqLink.id (via ncbiRefSeqHgmd.name)
      hg19.ncbiRefSeqPsl.qName (via ncbiRefSeqHgmd.name)
      hg19.ncbiRefSeqSelect.name (via ncbiRefSeqHgmd.name)
      hg19.seqNcbiRefSeq.acc (via ncbiRefSeqHgmd.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
591NM_152486.4chr1+86111087995486132187953314861110,861301,865534,866418,871151,874419,874654,876523,877515,877789,877938,878632,879077,879287,861180,861393,865716,866469,871276,874509,874840,876686,877631,877868,878438,878757,879188,879954,0SAMD11cmplcmpl-1,0,0,2,2,1,1,1,2,1,2,1,0,0,
591NM_015658.4chr1-87958289463688007389462019879582,880436,880897,881552,881781,883510,883869,886506,887379,887791,888554,889161,889383,891302,891474,892273,892478,894308,89 ...880180,880526,881033,881666,881925,883612,883983,886618,887519,887980,888668,889272,889462,891393,891595,892405,892653,894461,89 ...0NOC2Lcmplcmpl1,1,0,0,0,0,0,2,0,0,0,0,2,1,0,0,2,2,0,
591NM_198317.3chr1+89596390109989607390057112895963,896672,897008,897205,897734,898083,898488,898716,899299,899486,899728,900342,896180,896932,897130,897427,897851,898297,898633,898884,899388,899560,899910,901099,0KLHL17cmplcmpl0,2,1,0,0,0,1,2,2,1,0,2,
591NM_032129.3chr1+90186191124590191190995516901861,902083,905656,905900,906065,906258,906492,906703,907454,907667,908240,908565,908879,909212,909695,909821,901994,902183,905803,905981,906138,906386,906588,906784,907530,907804,908390,908706,909020,909431,909744,911245,0PLEKHN1cmplcmpl0,2,0,0,0,1,0,0,0,1,0,0,0,0,0,1,
591NM_001369898.1chr1-9105779165539115519164093910577,911878,914260,911649,911938,916553,0PERM1cmplcmpl1,1,0,
592NM_005101.4chr1+9488769499209489539498582948876,949363,948956,949920,0ISG15cmplcmpl0,0,
592NM_198576.4chr1+95549999149695555299036136955499,957580,970656,976044,976552,976857,977335,978618,978917,979202,979488,979713,980540,980738,981112,981343,981539,981776,98 ...955753,957842,970704,976260,976777,977082,977542,978837,979112,979403,979637,979819,980657,980903,981256,981468,981645,982115,98 ...0AGRNcmplcmpl0,0,1,1,1,1,1,1,1,1,1,0,1,1,1,1,0,1,1,1,0,1,1,1,2,2,1,1,2,2,0,0,1,2,2,1,
9NM_017891.5chr1-1017202105146910182721026923101017202,1019732,1019860,1021257,1022518,1022881,1025732,1026851,1027370,1051439,1018367,1019763,1019886,1021392,1022584,1022977,1025808,1026945,1027483,1051469,0C1orf159cmplcmpl1,0,1,1,1,1,0,0,-1,-1,
593NM_003327.4chr1-114671911495331146934114950771146719,1147083,1147321,1148017,1148371,1149042,1149362,1147005,1147212,1147518,1148084,1148473,1149165,1149533,0TNFRSF4cmplcmpl1,1,2,1,1,1,0,
593NM_016176.6chr1-115231011673811152891116415271152310,1153837,1154148,1158623,1159211,1163847,1167271,1153068,1154013,1154307,1158737,1159348,1164326,1167381,0SDF4cmplcmpl0,1,1,1,2,0,-1,

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