Schema for MGC Genes - Mammalian Gene Collection Full ORF mRNAs

Schema for MGC Genes - Mammalian Gene Collection Full ORF mRNAs

Database: bosTau4 Primary Table: mgcFullMrna Row Count: 9,701
Format description: Summary info about a patSpace alignment

field	example	SQL type	info	description
`bin`	1066	`smallint unsigned`	range	Indexing field to speed chromosome range queries.
`matches`	2064	`int unsigned`	range	Number of bases that match that aren't repeats
`misMatches`	0	`int unsigned`	range	Number of bases that don't match
`repMatches`	0	`int unsigned`	range	Number of bases that match but are part of repeats
`nCount`	0	`int unsigned`	range	Number of 'N' bases
`qNumInsert`	0	`int unsigned`	range	Number of inserts in query
`qBaseInsert`	0	`int unsigned`	range	Number of bases inserted in query
`tNumInsert`	14	`int unsigned`	range	Number of inserts in target
`tBaseInsert`	78664	`int unsigned`	range	Number of bases inserted in target
`strand`	-	`char(2)`	values	+ or - for strand. First character query, second target (optional)
`qName`	BC122682	`varchar(255)`	values	Query sequence name
`qSize`	2127	`int unsigned`	range	Query sequence size
`qStart`	0	`int unsigned`	range	Alignment start position in query
`qEnd`	2064	`int unsigned`	range	Alignment end position in query
`tName`	chrX	`varchar(255)`	values	Target sequence name
`tSize`	88516663	`int unsigned`	range	Target sequence size
`tStart`	63061134	`int unsigned`	range	Alignment start position in target
`tEnd`	63141862	`int unsigned`	range	Alignment end position in target
`blockCount`	15	`int unsigned`	range	Number of blocks in alignment
`blockSizes`	414,63,112,98,58,54,97,160,...	`longblob`		Size of each block
`qStarts`	63,477,540,652,750,808,862,...	`longblob`		Start of each block in query.
`tStarts`	63061134,63061734,63062042,...	`longblob`		Start of each block in target.

Connected Tables and Joining Fields


	bosTau4.all_mrna.qName (via mgcFullMrna.qName) bosTau4.gbCdnaInfo.acc (via mgcFullMrna.qName) bosTau4.gbSeq.acc (via mgcFullMrna.qName) bosTau4.gbStatus.acc (via mgcFullMrna.qName) bosTau4.imageClone.acc (via mgcFullMrna.qName) bosTau4.mgcGenes.name (via mgcFullMrna.qName) bosTau4.mrnaOrientInfo.name (via mgcFullMrna.qName)

Sample Rows

bin	matches	misMatches	repMatches	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qStart	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
1066	2064	0	0	0	0	14	78664	-	BC122682	2127	0	2064	chrX	88516663	63061134	63141862	15	414,63,112,98,58,54,97,160,150,142,92,105,138,95,286,	63,477,540,652,750,808,862,959,1119,1269,1411,1503,1608,1746,1841,	63061134,63061734,63062042,63064275,63065575,63071776,63076754,63077728,63078504,63084747,63088371,63089752,63112252,63124265,63 ...
127	1317	0	485	0	0	4	10335	+	BC123893	1826	0	1802	chrX	88516663	57135822	57147959	5	670,148,506,151,327,	0,670,818,1324,1475,	57135822,57136846,57142316,57145582,57147632,
1025	2046	0	18	0	0	4	75899	+	BC123715	2088	0	2064	chrX	88516663	57692089	57770052	5	113,172,173,163,1443,	0,113,285,458,621,	57692089,57742154,57744180,57745173,57768609,
1037	944	0	0	0	0	5	1373	+	BC110264	962	0	944	chrX	88516663	59274591	59276908	6	44,165,165,129,109,332,	0,44,209,374,503,612,	59274591,59274982,59275775,59276060,59276268,59276576,
1037	1462	1	0	0	0	7	12384	-	BC120408	1565	0	1463	chrX	88516663	59277069	59290916	8	237,395,119,345,82,117,72,96,	102,339,734,853,1198,1280,1397,1469,	59277069,59277413,59278197,59282580,59283130,59284288,59290404,59290820,
1039	1450	0	0	0	0	0	0	-	BC133466	1464	0	1450	chrX	88516663	59590905	59592355	1	1450,	14,	59590905,
16	809	0	0	0	0	0	0	-	BC140569	4042	0	809	chrX	88516663	59768792	59769601	1	809,	3233,	59768792,
1041	1970	16	177	6	33	1	3	+	BC118088	2486	3	2199	chrX	88516663	59792288	59794454	7	126,100,973,54,43,635,232,	3,130,241,1216,1271,1328,1967,	59792288,59792417,59792517,59793490,59793544,59793587,59794222,
1041	1987	0	0	0	0	15	26320	+	BC102363	2002	1	1988	chrX	88516663	59799917	59828224	16	83,68,41,108,117,84,136,104,145,88,175,143,137,128,220,210,	1,84,152,193,301,418,502,638,742,887,975,1150,1293,1430,1558,1778,	59799917,59802306,59809460,59810416,59811663,59812511,59812757,59813807,59816480,59819043,59819627,59819883,59820669,59822937,59 ...
1043	1948	0	193	0	0	11	4713	+	BC118289	2172	0	2141	chrX	88516663	60061929	60068783	12	276,474,309,64,80,95,80,43,63,115,407,135,	0,276,750,1059,1123,1203,1298,1378,1421,1484,1599,2006,	60061929,60062566,60063637,60064066,60064390,60065007,60065795,60065969,60066346,60067511,60068057,60068648,

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

MGC Genes (mgcFullMrna) Track Description

Description

This track shows alignments of cow 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 cow 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 cow 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.