Database: hg19    Primary Table: orfeomeMrna    Row Count: 13,963
Format description: Summary info about a patSpace alignment

field	example	SQL type	info	description
bin	591	smallint(5) unsigned	range	Indexing field to speed chromosome range queries.
matches	2197	int(10) unsigned	range	Number of bases that match that aren't repeats
misMatches	7	int(10) unsigned	range	Number of bases that don't match
repMatches	44	int(10) unsigned	range	Number of bases that match but are part of repeats
nCount	0	int(10) unsigned	range	Number of 'N' bases
qNumInsert	0	int(10) unsigned	range	Number of inserts in query
qBaseInsert	0	int(10) unsigned	range	Number of bases inserted in query
tNumInsert	18	int(10) unsigned	range	Number of inserts in target
tBaseInsert	12297	int(10) unsigned	range	Number of bases inserted in target
strand	-	char(2)	values	+ or - for strand. First character query, second target (optional)
qName	AM393843	varchar(255)	values	Query sequence name
qSize	2289	int(10) unsigned	range	Query sequence size
qStart	19	int(10) unsigned	range	Alignment start position in query
qEnd	2267	int(10) unsigned	range	Alignment end position in query
tName	chr1	varchar(255)	values	Target sequence name
tSize	249250621	int(10) unsigned	range	Target sequence size
tStart	880076	int(10) unsigned	range	Alignment start position in target
tEnd	894621	int(10) unsigned	range	Alignment end position in target
blockCount	19	int(10) unsigned	range	Number of blocks in alignment
blockSizes	104,90,136,114,144,102,114,...	longblob		Size of each block
qStarts	22,126,216,352,466,610,712,...	longblob		Start of each block in query.
tStarts	880076,880436,880897,881552...	longblob		Start of each block in target.

      hg19.all_mrna.qName (via orfeomeMrna.qName)
      hg19.gbCdnaInfo.acc (via orfeomeMrna.qName)
      hg19.gbSeq.acc (via orfeomeMrna.qName)
      hg19.gbStatus.acc (via orfeomeMrna.qName)
      hg19.imageClone.acc (via orfeomeMrna.qName)
      hg19.mrnaOrientInfo.name (via orfeomeMrna.qName)
      hg19.orfeomeGenes.name (via orfeomeMrna.qName)
      hg19.seq.acc (via orfeomeMrna.qName)
      hg19.spMrna.mrnaID (via orfeomeMrna.qName)

bin	matches	misMatches	repMatches	nCount	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
591	2197	7	44	0	0	0	18	12297	-	AM393843	2289	19	2267	chr1	249250621	880076	894621	19	104,90,136,114,144,102,114,112,140,189,114,111,79,91,121,132,175,153,27,	22,126,216,352,466,610,712,826,938,1078,1267,1381,1492,1571,1662,1783,1915,2090,2243,	880076,880436,880897,881552,881781,883510,883869,886506,887379,887791,888554,889161,889383,891302,891474,892273,892478,894308,89 ...
591	1875	0	52	0	0	0	11	2569	+	BC166618	1990	34	1961	chr1	249250621	896073	900569	12	107,260,122,222,117,214,145,168,89,74,182,227,	34,141,401,523,745,862,1076,1221,1389,1478,1552,1734,	896073,896672,897008,897205,897734,898083,898488,898716,899299,899486,899728,900342,
591	1832	3	0	0	0	0	15	6208	+	AM393848	1875	18	1853	chr1	249250621	901909	909952	16	85,100,147,81,73,128,96,81,76,137,150,141,141,219,49,131,	18,103,203,350,431,504,632,728,809,885,1022,1172,1313,1454,1673,1722,	901909,902083,905656,905900,906065,906258,906492,906703,907454,907667,908240,908565,908879,909212,909695,909821,
591	1832	3	0	0	0	0	15	6208	+	BC141658	1873	17	1852	chr1	249250621	901909	909952	16	85,100,147,81,73,128,96,81,76,137,150,141,141,219,49,131,	17,102,202,349,430,503,631,727,808,884,1021,1171,1312,1453,1672,1721,	901909,902083,905656,905900,906065,906258,906492,906703,907454,907667,908240,908565,908879,909212,909695,909821,
592	622	0	46	0	0	0	3	249	-	DQ895490	706	18	686	chr1	249250621	934440	935357	4	372,88,96,112,	20,392,480,576,	934440,934905,935071,935245,
592	492	2	0	0	0	0	0	0	+	EU176738	538	24	518	chr1	249250621	949362	949856	1	494,	24,	949362,
592	493	2	0	0	0	0	0	0	+	DQ892714	538	24	519	chr1	249250621	949362	949857	1	495,	24,	949362,
593	768	0	0	0	0	0	3	2213	-	BC156964	829	33	801	chr1	249250621	1138971	1141952	4	369,88,123,188,	28,397,485,608,	1138971,1139778,1140749,1141764,
593	767	0	0	0	0	0	3	2213	-	BC156102	829	33	800	chr1	249250621	1138972	1141952	4	368,88,123,188,	29,397,485,608,	1138972,1139778,1140749,1141764,
593	789	0	201	0	0	0	0	0	+	BC160034	1051	32	1022	chr1	249250621	1167656	1168646	1	990,	32,	1167656,

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

Description

This track shows alignments of human clones from the ORFeome Collaboration. The project goal is to be an "unrestricted source of fully sequence-validated full-ORF human cDNA clones in a format allowing easy transfer of the ORF sequences into virtually any type of expression vector. A major goal is to provide at least one fully sequenced full-ORF clone for each human gene." This track is updated automatically as new clones become available.

Display Conventions and Configuration

The track follows the display conventions for gene prediction tracks.

Methods

ORFeome human clones were obtained from GenBank and aligned against the genome using the blat program. When a single clone aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept.

Credits and references

Visit the ORFeome Collaboration members page for a list of credits and references.