Schema for SIB Alt-Splicing - Alternative Splicing Graph from Swiss Institute of Bioinformatics
  Database: hg38    Primary Table: sibTxGraph    Row Count: 47,817   Data last updated: 2014-08-27
Format description: An alternatively spliced gene graph.
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 11873int(11) range First bac touched by graph.
tEnd 14409int(11) range Start position in first bac.
name NC_000001_1varchar(255) values Human readable name.
id 1int(10) unsigned range Unique ID.
strand +char(2) values + or - strand.
vertexCount 8int(10) unsigned range Number of vertices in graph.
vTypes 0,3,1,1,3,3,1,2,longblob   Type for each vertex.
vPositions 11873,12227,12612,12645,126...longblob   Position in target for each vertex.
edgeCount 8int(10) unsigned range Number of edges in graph.
edgeStarts 0,1,1,2,3,4,5,6,longblob   Array with start vertex of edges.
edgeEnds 1,2,3,5,4,6,6,7,longblob   Array with end vertex of edges.
evidence {5,{0,1,3,4,5,},},{4,{0,1,4...longblob   array of evidence tables containing references to mRNAs that support a particular edge.
edgeTypes 0,1,1,0,0,1,1,0,longblob   Type for each edge, ggExon, ggIntron, etc.
mrnaRefCount 6int(11) range Number of supporting mRNAs.
mrnaRefs AM992871,AM992872,AM992873,...longblob   Ids of mrnas supporting this.
mrnaTissues 0,0,0,0,0,0,longblob   Ids of tissues that mrnas come from, indexes into tissue table
mrnaLibs 0,0,0,0,0,0,longblob   Ids of libraries that mrnas come from, indexes into library table

Sample Rows
 
bintNametStarttEndnameidstrandvertexCountvTypesvPositionsedgeCountedgeStartsedgeEndsevidenceedgeTypesmrnaRefCountmrnaRefsmrnaTissuesmrnaLibs
585chr11187314409NC_000001_11+80,3,1,1,3,3,1,2,11873,12227,12612,12645,12697,12721,13220,14409,80,1,1,2,3,4,5,6,1,2,3,5,4,6,6,7,{5,{0,1,3,4,5,},},{4,{0,1,4,5,},},{1,{3,},},{5,{0,1,2,4,5,},},{1,{3,},},{1,{3,},},{5,{0,1,2,4,5,},},{6,{0,1,2,3,4,5,},},0,1,1,0,0,1,1,0,6AM992871,AM992872,AM992873,AM992878,AM992879,NR_046018,0,0,0,0,0,0,0,0,0,0,0,0,
585chr11341930054NC_000001_02-592,1,1,0,2,1,3,3,1,1,3,3,0,3,0,2,1,3,3,3,1,2,0,3,1,3,3,3,1,3,3,1,2,3,1,3,1,1,3,3,1,3,1,1,3,1,1,3,3,0,2,0,3,1,0,3,1,3,0,30054,29823,29320,28045,28043,27542,25008,24891,24824,24737,24525,24439,24214,23618,23129,22471,22427,20286,19139,19075,18912,18 ...832,3,1,7,26,6,29,27,7,5,7,9,28,12,8,9,30,11,10,13,17,18,23,29,19,26,27,14,12,14,16,25,22,20,20,20,23,27,43,24,27,28,31,28,28,29,3 ...0,0,0,1,2,2,2,2,2,4,5,6,7,7,7,7,8,9,9,9,9,9,9,9,9,9,9,10,11,13,15,16,17,17,18,19,20,20,21,23,24,25,26,26,27,28,29,29,30,31,31,31 ...{81,{89,90,91,92,156,158,160,161,172,173,174,177,178,181,191,192,203,204,208,240,242,263,276,277,278,279,283,291,294,297,298,300 ...0,0,0,1,1,1,1,1,1,0,1,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,1,0,0,0,0,1,0,0,0,0,1,1,0,0,1,0,0,0,0,1,0,0,0,1,1,1,0,0,0,0,1,0,1,1,1,0,0,1, ...480AA057211,AA215404,AA215405,AA278412,AA291826,AA293308,AA310626,AA321532,AA411542,AA459408,AA486450,AA652404,AA766713,AA782158,AA ...0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, ...0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, ...
585chr12823431000NC_000001_33+60,3,1,3,1,2,28234,29206,30563,30667,30975,31000,50,1,2,3,4,1,2,3,4,5,{1,{0,},},{1,{0,},},{1,{0,},},{1,{0,},},{1,{0,},},0,1,0,1,0,1XR_433199,0,0,
585chr13455336081NC_000001_24-62,1,3,1,3,0,36081,35720,35481,35276,35174,34553,51,2,3,4,5,0,1,2,3,4,{17,{1,2,4,12,13,17,19,20,23,25,27,28,29,30,31,32,33,},},{13,{1,4,13,20,23,25,27,28,29,30,31,32,33,},},{17,{1,4,7,10,13,14,15,20 ...0,1,0,1,0,34AA063068,AA063097,AA074494,AL711883,BF726774,BM663738,BM671686,BM686056,BM688247,BM690270,BM690710,BM704543,BM707669,BQ637109,BQ ...0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
585chr16903370008NC_000001_45+20,2,69033,70008,10,1,{2,{0,1,},},0,2AY972819,NM_001005484,0,0,0,0,
585chr18752190896NC_000001_56-42,1,3,0,90896,90725,87727,87521,31,2,3,0,1,2,{1,{0,},},{1,{0,},},{1,{0,},},0,1,0,1AA846777,0,0,
585chr1108869120950NC_000001_307-72,1,3,1,0,3,0,120950,120774,112804,112699,112614,108962,108869,61,2,3,4,5,6,0,1,2,2,3,5,{2,{0,1,},},{2,{0,1,},},{1,{1,},},{1,{0,},},{1,{1,},},{1,{1,},},0,1,0,0,1,0,2XR_426573,XR_431105,0,0,0,0,
585chr1115049116054NC_000001_368+20,2,115049,116054,10,1,{2,{0,2,},},0,3BG105495,4422069,BC028185,0,0,0,0,0,0,
73chr1120711133748NC_000001_189-62,1,3,1,3,0,133748,133373,129223,129054,120932,120711,51,2,3,4,5,0,1,2,3,4,{1,{0,},},{1,{0,},},{1,{0,},},{1,{0,},},{1,{0,},},0,1,0,1,0,1XR_426563,0,0,
586chr1134772181130NC_000001_1110-622,1,2,3,1,3,0,2,3,1,3,1,3,1,2,1,3,1,3,1,3,1,3,1,2,3,1,1,0,2,3,1,0,3,0,3,0,3,0,2,1,1,1,2,1,3,1,0,2,3,3,1,3,1,3,0,2,1,3,0,2,0,181130,181036,178198,177730,177681,177588,177181,174392,173862,173752,172688,172556,169264,169048,168767,168609,168165,168099,16 ...691,3,8,4,6,5,6,9,9,10,16,11,12,13,16,15,16,17,18,19,20,23,21,22,23,30,25,27,28,27,26,30,45,30,31,32,31,33,35,37,45,34,36,38,40,42 ...0,1,1,2,3,4,5,7,8,9,9,10,11,12,13,14,15,16,17,18,19,20,20,21,22,23,23,24,25,25,25,26,26,27,29,30,30,31,31,31,31,33,35,37,39,39,3 ...{3,{213,223,304,},},{1,{304,},},{2,{213,223,},},{3,{320,321,322,},},{3,{34,304,305,},},{3,{320,321,322,},},{3,{320,321,322,},},{ ...0,1,1,0,0,1,0,0,0,1,1,0,1,0,1,0,1,0,1,0,1,0,0,1,0,1,1,0,0,0,0,1,1,1,0,0,0,1,1,1,1,0,0,0,0,0,0,1,1,1,0,1,0,0,1,1,0,0,0,0,1,0,1,0, ...349AA076680,AA077226,AA077241,AA077771,AA317624,AA393354,AA400447,AA429543,AA436413,AA481357,AA570077,AA603184,AA658860,AA658879,AA ...0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, ...0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0, ...

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

SIB Alt-Splicing (sibTxGraph) Track Description
 

Description

This track shows the graphs constructed by analyzing experimental RNA transcripts and serves as basis for the predicted alternative splicing transcripts shown in the SIB Genes track. The blocks represent exons; lines indicate introns. The graphical display is drawn such that no exons overlap, making alternative events easier to view when the track is in full display mode and the resolution is set to approximately gene-level.

Further information on the graphs can be found on the Transcriptome Web interface.

Methods

The splicing graphs were generated using a multi-step pipeline:

  1. RefSeq and GenBank RNAs and ESTs are aligned to the genome with SIBsim4, keeping only the best alignments for each RNA.
  2. Alignments are broken up at non-intronic gaps, with small isolated fragments thrown out.
  3. A splicing graph is created for each set of overlapping alignments. This graph has an edge for each exon or intron, and a vertex for each splice site, start, and end. Each RNA that contributes to an edge is kept as evidence for that edge.
  4. Graphs consisting solely of unspliced ESTs are discarded.

Credits

The SIB Alternative Splicing Graphs track was produced on the Vital-IT high-performance computing platform using a computational pipeline developed by Christian Iseli with help from colleagues at the Ludwig Institute for Cancer Research and the Swiss Institute of Bioinformatics. It is based on data from NCBI RefSeq and GenBank/EMBL. Our thanks to the people running these databases and to the scientists worldwide who have made contributions to them.