Schema for rgdGene2
  Database: rn4    Primary Table: rgdGene2    Row Count: 17,487   Data last updated: 2011-12-07
Format description: A gene prediction.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
name RGD:1565877varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 98271int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 142335int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 98949int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 142335int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 98271,122723,127935,129576,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 99351,122826,128045,129679,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        rn4.affyExonTissuesGsMedianDistRgdGene2.query (via rgdGene2.name)
      rn4.affyExonTissuesGsMedianDistRgdGene2.target (via rgdGene2.name)
      rn4.affyExonTissuesGsMedianRgdGene2.name (via rgdGene2.name)
      rn4.affyExonTissuesGsRgdGene2.name (via rgdGene2.name)
      rn4.ceBlastTab.query (via rgdGene2.name)
      rn4.dmBlastTab.query (via rgdGene2.name)
      rn4.drBlastTab.query (via rgdGene2.name)
      rn4.gnfAtlas2RgdGene2Distance.query (via rgdGene2.name)
      rn4.gnfAtlas2RgdGene2Distance.target (via rgdGene2.name)
      rn4.hgBlastTab.query (via rgdGene2.name)
      rn4.mmBlastTab.query (via rgdGene2.name)
      rn4.rgdGene2BlastTab.query (via rgdGene2.name)
      rn4.rgdGene2BlastTab.target (via rgdGene2.name)
      rn4.rgdGene2Canonical.transcript (via rgdGene2.name)
      rn4.rgdGene2Isoforms.transcript (via rgdGene2.name)
      rn4.rgdGene2KeggPathway.rgdId (via rgdGene2.name)
      rn4.rgdGene2Pep.name (via rgdGene2.name)
      rn4.rgdGene2ToDescription.name (via rgdGene2.name)
      rn4.rgdGene2ToDisplayId.name (via rgdGene2.name)
      rn4.rgdGene2ToEnsembl.name (via rgdGene2.name)
      rn4.rgdGene2ToGenbank.name (via rgdGene2.name)
      rn4.rgdGene2ToGenbankAll.name (via rgdGene2.name)
      rn4.rgdGene2ToGnfAtlas2.name (via rgdGene2.name)
      rn4.rgdGene2ToKeggEntrez.name (via rgdGene2.name)
      rn4.rgdGene2ToLocusLink.name (via rgdGene2.name)
      rn4.rgdGene2ToPDB.name (via rgdGene2.name)
      rn4.rgdGene2ToPfam.name (via rgdGene2.name)
      rn4.rgdGene2ToRAE230.name (via rgdGene2.name)
      rn4.rgdGene2ToRefSeq.name (via rgdGene2.name)
      rn4.rgdGene2ToSymbol.rgdId (via rgdGene2.name)
      rn4.rgdGene2ToU34A.name (via rgdGene2.name)
      rn4.rgdGene2ToUniProt.name (via rgdGene2.name)
      rn4.rgdGene2Xref.rgdGeneId (via rgdGene2.name)
      rn4.rgdGenePathway.geneId (via rgdGene2.name)
      rn4.scBlastTab.query (via rgdGene2.name)

Sample Rows
 
namechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
RGD:1565877chr1-9827114233598949142335698271,122723,127935,129576,139688,142173,99351,122826,128045,129679,139737,142335,
RGD:1596944chr1-2458872670112458872670117245887,256156,257489,258566,259804,260546,266805,246774,256280,257714,259370,260077,260562,267011,
RGD:1561757chr1+7606577659147607537659144760657,762313,763741,765030,761461,762538,763865,765914,
RGD:1565892chr1+100941110219231009411102192361009411,1015935,1016643,1018297,1019750,1021039,1009617,1016218,1017447,1018522,1019874,1021923,
RGD:1564110chr1-113479711498651134797114986561134797,1136833,1144442,1145623,1146814,1149659,1135681,1136957,1144667,1146427,1147097,1149865,
RGD:1585898chr1+123490712435611234907124356161234907,1237683,1238354,1240008,1241408,1242674,1235113,1237966,1239158,1240233,1241532,1243561,
RGD:1562697chr1+128708512957561287085129575661287085,1289852,1290535,1292186,1293585,1294872,1287291,1290135,1291339,1292411,1293709,1295756,
RGD:2321865chr1-134044913471521340449134715251340449,1344407,1345112,1345642,1347061,1340586,1344556,1345380,1345903,1347152,
RGD:1584760chr1-138486114030431384861140304381384861,1386239,1390853,1400500,1400823,1401076,1401608,1402952,1385032,1386377,1391070,1400592,1400933,1401343,1401842,1403043,
RGD:1583663chr1-141417614193341414176141933461414176,1414894,1415621,1416333,1416859,1419018,1414243,1415036,1415774,1416597,1417120,1419334,

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