Database: hg19    Primary Table: mgcFullMrna    Row Count: 31,114
Format description: Summary info about a patSpace alignment

field	example	SQL type	info	description
bin	587	smallint(5) unsigned	range	Indexing field to speed chromosome range queries.
matches	995	int(10) unsigned	range	Number of bases that match that aren't repeats
misMatches	0	int(10) unsigned	range	Number of bases that don't match
repMatches	0	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	0	int(10) unsigned	range	Number of inserts in target
tBaseInsert	0	int(10) unsigned	range	Number of bases inserted in target
strand	+	char(2)	values	+ or - for strand. First character query, second target (optional)
qName	BC137547	varchar(255)	values	Query sequence name
qSize	995	int(10) unsigned	range	Query sequence size
qStart	0	int(10) unsigned	range	Alignment start position in query
qEnd	995	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	367639	int(10) unsigned	range	Alignment start position in target
tEnd	368634	int(10) unsigned	range	Alignment end position in target
blockCount	1	int(10) unsigned	range	Number of blocks in alignment
blockSizes	995,	longblob		Size of each block
qStarts	0,	longblob		Start of each block in query.
tStarts	367639,	longblob		Start of each block in target.

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

bin	matches	misMatches	repMatches	nCount	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
587	995	0	0	0	0	0	0	0	+	BC137547	995	0	995	chr1	249250621	367639	368634	1	995,	0,	367639,
587	994	1	0	0	0	0	0	0	+	BC137568	995	0	995	chr1	249250621	367639	368634	1	995,	0,	367639,
589	995	0	0	0	0	0	0	0	-	BC137547	995	0	995	chr1	249250621	621058	622053	1	995,	0,	621058,
589	994	1	0	0	0	0	0	0	-	BC137568	995	0	995	chr1	249250621	621058	622053	1	995,	0,	621058,
591	2096	3	20	0	0	0	10	6690	+	BC024295	2143	3	2122	chr1	249250621	871145	879954	11	86,44,90,138,163,116,79,500,125,111,667,	3,89,133,223,361,524,640,719,1219,1344,1455,	871145,871232,874419,874654,876523,877515,877789,877938,878632,879077,879287,
591	1896	3	20	0	0	0	7	3353	+	BC033213	1940	0	1919	chr1	249250621	874689	879961	8	151,163,116,79,500,125,111,674,	0,151,314,430,509,1009,1134,1245,	874689,876523,877515,877789,877938,878632,879077,879287,
591	2690	6	64	0	0	0	18	12297	-	BC003555	2801	0	2760	chr1	249250621	879595	894652	19	585,90,136,114,144,102,114,112,140,189,114,111,79,91,121,132,175,153,58,	41,626,716,852,966,1110,1212,1326,1438,1578,1767,1881,1992,2071,2162,2283,2415,2590,2743,	879595,880436,880897,881552,881781,883510,883869,886506,887379,887791,888554,889161,889383,891302,891474,892273,892478,894308,89 ...
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	2191	2	0	0	0	0	14	6313	+	BC101386	2194	0	2193	chr1	249250621	901881	910387	15	113,100,147,81,73,128,132,81,76,137,150,141,219,49,566,	0,113,213,360,441,514,642,774,855,931,1068,1218,1359,1578,1627,	901881,902083,905656,905900,906065,906258,906456,906703,907454,907667,908240,908879,909212,909695,909821,
591	2451	3	0	0	0	0	14	6052	+	BC101387	2455	0	2454	chr1	249250621	901881	910387	15	113,100,147,81,321,132,81,76,137,150,141,141,219,49,566,	0,113,213,360,441,762,894,975,1051,1188,1338,1479,1620,1839,1888,	901881,902083,905656,905900,906065,906456,906703,907454,907667,908240,908565,908879,909212,909695,909821,

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

Description

This track shows alignments of human mRNAs from the Mammalian Gene Collection (MGC) having full-length open reading frames (ORFs) to the genome. The goal of the Mammalian Gene Collection is to provide researchers with unrestricted access to sequence-validated full-length protein-coding cDNA clones for human, mouse, and rat genes.

Display Conventions and Configuration

The track follows the display conventions for gene prediction tracks.

An optional codon coloring feature is available for quick validation and comparison of gene predictions. To display codon colors, select the genomic codons option from the Color track by codons pull-down menu. Click here for more information about this feature.

Methods

GenBank human MGC mRNAs identified as having full-length ORFs were aligned against the genome using blat. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 1% of the best and at least 95% base identity with the genomic sequence were kept.

Credits

The human MGC full-length mRNA track was produced at UCSC from mRNA sequence data submitted to GenBank by the Mammalian Gene Collection project.

References

Mammalian Gene Collection project references.

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64.