Schema for altGraphX
  Database: hg16    Primary Table: altGraphX    Row Count: 21,413   Data last updated: 2004-05-19
Format description: An alternatively spliced gene graph.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
tName chr1varchar(255) values name of target sequence, often a chrom.
tStart 1731int(11) range First bac touched by graph.
tEnd 4121int(11) range Start position in first bac.
name chr1.0varchar(255) values Human readable name.
id 1int(10) unsigned range Unique ID.
strand +char(2) values + or - strand.
vertexCount 6int(10) unsigned range Number of vertices in graph.
vTypes 0,3,1,3,1,2,longblob   Type for each vertex.
vPositions 1731,2090,2475,2584,3083,4121,longblob   Position in target for each vertex.
edgeCount 5int(10) unsigned range Number of edges in graph.
edgeStarts 0,1,2,3,4,longblob   Array with start vertex of edges.
edgeEnds 1,2,3,4,5,longblob   Array with end vertex of edges.
evidence {2,{1,0,},},{2,{1,0,},},{2,...longblob   array of evidence tables containing references to mRNAs that support a particular edge.
edgeTypes 0,2,0,2,0,longblob   Type for each edge, ggExon, ggIntron, etc.
mrnaRefCount 2int(11) range Number of supporting mRNAs.
mrnaRefs BM920887,BC032353,longblob   Ids of mrnas supporting this.
mrnaTissues 0,164,longblob   Ids of tissues that mrnas come from, indexes into tissue table
mrnaLibs 118,108,longblob   Ids of libraries that mrnas come from, indexes into library table

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.library (via altGraphX.mrnaLibs)
      hgFixed.library.id (via altGraphX.mrnaLibs)
      hg16.all_est.qName (via altGraphX.mrnaRefs)
      hg16.all_mrna.qName (via altGraphX.mrnaRefs)
      hg16.dupSpMrna.dupMrnaID (via altGraphX.mrnaRefs)
      hg16.dupSpMrna.mrnaID (via altGraphX.mrnaRefs)
      hg16.est.qName (via altGraphX.mrnaRefs)
      hg16.estOrientInfo.name (via altGraphX.mrnaRefs)
      hg16.intronEst.qName (via altGraphX.mrnaRefs)
      hg16.kgXref.refseq (via altGraphX.mrnaRefs)
      hg16.knownToRefSeq.value (via altGraphX.mrnaRefs)
      hg16.mgcFullMrna.qName (via altGraphX.mrnaRefs)
      hg16.mgcGenes.name (via altGraphX.mrnaRefs)
      hg16.mrnaOrientInfo.name (via altGraphX.mrnaRefs)
      hg16.mrnaRefseq.mrna (via altGraphX.mrnaRefs)
      hg16.mrnaRefseq.refseq (via altGraphX.mrnaRefs)
      hg16.refFlat.name (via altGraphX.mrnaRefs)
      hg16.refGene.name (via altGraphX.mrnaRefs)
      hg16.refSeqAli.qName (via altGraphX.mrnaRefs)
      hg16.spMrna.mrnaID (via altGraphX.mrnaRefs)
      hg16.xenoEst.qName (via altGraphX.mrnaRefs)
      hg16.xenoMrna.qName (via altGraphX.mrnaRefs)
      hg16.xenoRefFlat.name (via altGraphX.mrnaRefs)
      hg16.xenoRefGene.name (via altGraphX.mrnaRefs)
      hg16.xenoRefSeqAli.qName (via altGraphX.mrnaRefs)
      hgFixed.gbCdnaInfo.acc (via altGraphX.mrnaRefs)
      hgFixed.gbSeq.acc (via altGraphX.mrnaRefs)
      hgFixed.imageClone.acc (via altGraphX.mrnaRefs)
      hgFixed.refLink.mrnaAcc (via altGraphX.mrnaRefs)
      hgFixed.refSeqStatus.mrnaAcc (via altGraphX.mrnaRefs)
      hgFixed.refSeqSummary.mrnaAcc (via altGraphX.mrnaRefs)
      knownGeneV39.kgXref.refseq (via altGraphX.mrnaRefs)
      knownGeneV39.knownToRefSeq.value (via altGraphX.mrnaRefs)
      hgFixed.gbCdnaInfo.tissue (via altGraphX.mrnaTissues)
      hgFixed.tissue.id (via altGraphX.mrnaTissues)

Sample Rows
 
bintNametStarttEndnameidstrandvertexCountvTypesvPositionsedgeCountedgeStartsedgeEndsevidenceedgeTypesmrnaRefCountmrnaRefsmrnaTissuesmrnaLibs
585chr117314121chr1.01+60,3,1,3,1,2,1731,2090,2475,2584,3083,4121,50,1,2,3,4,1,2,3,4,5,{2,{1,0,},},{2,{1,0,},},{2,{1,0,},},{2,{1,0,},},{2,{0,1,},},0,2,0,2,0,2BM920887,BC032353,0,164,118,108,
585chr1426619211chr1.12-390,0,3,1,3,2,1,3,2,1,3,1,1,3,2,1,1,3,1,1,3,2,1,3,1,3,3,3,2,1,3,1,3,2,0,1,3,1,2,4266,4269,4692,4832,4901,4933,5658,5810,6145,6469,6628,6716,6720,6918,6919,7095,7121,7231,7388,7468,7605,7614,7777,7924,8130,822 ...510,1,2,3,3,4,6,6,7,9,10,10,11,12,13,13,13,13,15,15,16,17,17,18,19,19,20,22,23,23,23,24,24,24,24,25,25,26,26,26,27,27,29,30,31,31, ...2,10,3,4,5,6,7,8,9,10,11,12,14,13,15,16,19,22,17,20,17,18,19,21,20,23,22,23,24,35,37,25,26,27,28,31,35,29,31,35,31,35,30,31,32,3 ...{50,{52,53,50,49,48,46,47,40,41,42,43,44,45,39,56,33,37,38,25,26,27,28,29,30,31,24,22,23,8,5,6,7,4,3,1,2,0,11,21,20,19,18,17,16, ...0,0,2,0,0,2,0,0,2,0,2,2,0,0,2,2,2,2,0,0,0,2,2,0,0,0,2,0,2,2,2,0,0,0,0,2,2,2,2,2,2,2,0,2,0,0,2,0,0,2,0,239AK095183,BC063682,CA426220,AI591352,BU191946,BU685032,AI805743,AI811673,AA478024,AL137714,BM980743,BM975519,BQ015518,BQ447519,CA ...950,153,5883,2857,5700,5880,2998,5346,2624,17,5880,5880,2839,3002,3002,5880,3169,2839,5883,5883,5376,2592,3169,3064,5112,164,163 ...3363,95,16767,3617,78,16756,5040,3616,4382,4100,16756,16756,16790,17077,17077,16756,16269,16790,16767,16767,8524,3136,16269,5057 ...
585chr12447525940chr1.33-70,3,0,1,3,1,2,24475,25037,25107,25139,25344,25583,25940,60,1,2,3,4,5,1,3,4,4,5,6,{12,{12,11,10,9,7,8,1,2,0,6,5,4,},},{12,{12,11,10,9,8,7,6,5,4,2,1,0,},},{2,{14,13,},},{13,{16,11,10,7,8,1,2,12,9,6,5,4,0,},},{10 ...0,2,0,0,2,0,17AF346307,BM704543,BM671686,AA074495,AY341953,AY341952,AY341950,BM690710,BM686056,AY341949,BQ638680,BQ640021,BQ637109,BU732746,BM ...0,4925,4925,0,0,0,0,5869,5869,0,78,78,78,4925,4925,26,0,0,16662,16662,4375,0,0,0,16663,16663,0,17164,17164,17164,16662,16662,13971,4375,
585chr1118943123429chr1.64-40,3,1,2,118943,119086,123236,123429,30,1,2,1,2,3,{4,{3,2,1,0,},},{4,{3,2,1,0,},},{4,{3,2,1,0,},},0,2,0,4BE155728,AW383060,AL844298,AW383003,0,0,0,0,10551,10540,9355,10540,
585chr1129178130219chr1.95-90,2,0,3,1,3,1,2,2,129178,129267,129299,129559,129652,129710,129937,130033,130219,80,1,2,3,4,4,5,6,1,2,3,4,5,7,6,8,{3,{2,1,0,},},{3,{2,1,0,},},{18,{17,16,15,14,13,12,11,10,9,8,6,7,5,4,3,2,1,0,},},{18,{17,16,15,14,13,12,11,10,9,8,7,6,5,4,3,2,1, ...0,2,0,2,0,0,2,0,21BE827177,BE827130,BQ345523,BF851028,BE827146,BQ330234,BQ330178,BQ330236,BE827282,BE827084,BF902235,BF881759,BG961470,BF892694,BF ...0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,13165,13165,17019,14573,13165,13165,13165,13165,13165,13165,14784,14699,14107,14757,14905,13165,14309,15923,15716,14780,14841,
586chr1148445154248chr1.106-40,3,1,2,148445,148537,154125,154248,30,1,2,1,2,3,{3,{2,1,0,},},{3,{2,1,0,},},{3,{2,1,0,},},0,2,0,3AW850063,AW850014,BF926381,0,0,0,11301,11301,14880,
587chr1360743364561chr1.137+91,3,1,2,0,1,3,1,2,360743,360801,360894,361111,364061,364150,364208,364301,364561,70,1,2,4,5,6,7,1,2,3,6,6,7,8,{6,{4,5,6,3,1,0,},},{6,{7,6,5,4,3,0,},},{4,{6,3,0,4,},},{3,{13,12,11,},},{20,{7,28,25,5,27,24,20,21,22,23,19,15,16,17,18,10,9,8, ...0,2,0,0,0,2,0,30BF803398,BF768973,BF844141,AA808688,BE827084,BE827145,BE827129,AA077350,BF881759,BF897311,BI022719,BG001968,BF995345,BF990288,BQ ...0,0,0,2592,0,0,0,20,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,20,14309,14213,10539,3136,13165,13165,13165,7425,14699,14784,15928,15091,15094,15094,17019,14788,14754,15920,15920,15957,13165,1316 ...
587chr1369646374134chr1.148+40,3,1,2,369646,369839,373991,374134,30,1,2,1,2,3,{7,{6,5,4,3,2,1,0,},},{7,{6,5,4,3,2,1,0,},},{7,{5,6,4,3,2,1,0,},},0,2,0,7BE155728,AW383060,AW383021,AW383003,BE154573,AL844300,AL844298,0,0,0,0,0,0,0,10551,10540,10540,10540,10540,9356,9355,
588chr1460067461702chr1.169+60,3,1,3,1,2,460067,460159,460854,461121,461258,461702,50,1,2,3,4,1,2,3,4,5,{2,{1,0,},},{2,{1,0,},},{2,{1,0,},},{2,{1,0,},},{2,{0,1,},},0,2,0,2,0,2BI464772,BC036251,0,17,94,94,
588chr1493046493811chr1.1710+40,3,1,2,493046,493181,493507,493811,30,1,2,1,2,3,{3,{3,2,1,},},{3,{3,2,1,},},{4,{1,0,3,2,},},0,2,0,4AW172999,AI147429,BX119452,AI262738,5340,0,0,0,3623,3206,3206,3206,

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