Schema for MGC Genes - Mammalian Gene Collection Full ORF mRNAs
  Database: hg38    Primary Table: mgcFullMrna    Row Count: 36,640   Data last updated: 2020-01-27
Format description: Summary info about a patSpace alignment
fieldexampleSQL type info description
bin 588smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 995int(10) unsigned range Number of bases that match that aren't repeats
misMatches 0int(10) unsigned range Number of bases that don't match
repMatches 0int(10) unsigned range Number of bases that match but are part of repeats
nCount 0int(10) unsigned range Number of 'N' bases
qNumInsert 0int(10) unsigned range Number of inserts in query
qBaseInsert 0int(10) unsigned range Number of bases inserted in query
tNumInsert 0int(10) unsigned range Number of inserts in target
tBaseInsert 0int(10) unsigned range Number of bases inserted in target
strand -char(2) values + or - for strand. First character query, second target (optional)
qName BC137547varchar(255) values Query sequence name
qSize 995int(10) unsigned range Query sequence size
qStart 0int(10) unsigned range Alignment start position in query
qEnd 995int(10) unsigned range Alignment end position in query
tName chr1varchar(255) values Target sequence name
tSize 248956422int(10) unsigned range Target sequence size
tStart 450702int(10) unsigned range Alignment start position in target
tEnd 451697int(10) unsigned range Alignment end position in target
blockCount 1int(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 450702,longblob   Start of each block in target.

Connected Tables and Joining Fields
        hg38.all_mrna.qName (via mgcFullMrna.qName)
      hg38.mgcGenes.name (via mgcFullMrna.qName)
      hg38.mrnaOrientInfo.name (via mgcFullMrna.qName)
      hgFixed.gbCdnaInfo.acc (via mgcFullMrna.qName)
      hgFixed.gbSeq.acc (via mgcFullMrna.qName)
      hgFixed.imageClone.acc (via mgcFullMrna.qName)

Sample Rows
 
binmatchesmisMatchesrepMatchesnCountqNumInsertqBaseInserttNumInserttBaseInsertstrandqNameqSizeqStartqEndtNametSizetStarttEndblockCountblockSizesqStartstStarts
5889950000000-BC1375479950995chr12489564224507024516971995,0,450702,
5889941000000-BC1375689950995chr12489564224507024516971995,0,450702,
5909950000000-BC1375479950995chr12489564226856786866731995,0,685678,
5909941000000-BC1375689950995chr12489564226856786866731995,0,685678,
592211630000106690+BC024295214332122chr12489564229357659445741186,44,90,138,163,116,79,500,125,111,667,3,89,133,223,361,524,640,719,1219,1344,1455,935765,935852,939039,939274,941143,942135,942409,942558,943252,943697,943907,
59219163000073353+BC033213194001919chr12489564229393099445818151,163,116,79,500,125,111,674,0,151,314,430,509,1009,1134,1245,939309,941143,942135,942409,942558,943252,943697,943907,
5922754600001812297-BC003555280102760chr124895642294421595927219585,90,136,114,144,102,114,112,140,189,114,111,79,91,121,132,175,153,58,41,626,716,852,966,1110,1212,1326,1438,1578,1767,1881,1992,2071,2162,2283,2415,2590,2743,944215,945056,945517,946172,946401,948130,948489,951126,951999,952411,953174,953781,954003,955922,956094,956893,957098,958928,95 ...
592192700000112569+BC1666181990341961chr124895642296069396518912107,260,122,222,117,214,145,168,89,74,182,227,34,141,401,523,745,862,1076,1221,1389,1478,1552,1734,960693,961292,961628,961825,962354,962703,963108,963336,963919,964106,964348,964962,
592219220000146313+BC101386219402194chr124895642296650197500815113,100,147,81,73,128,132,81,76,137,150,141,219,49,567,0,113,213,360,441,514,642,774,855,931,1068,1218,1359,1578,1627,966501,966703,970276,970520,970685,970878,971076,971323,972074,972287,972860,973499,973832,974315,974441,
592245230000146052+BC101387245502455chr124895642296650197500815113,100,147,81,321,132,81,76,137,150,141,141,219,49,567,0,113,213,360,441,762,894,975,1051,1188,1338,1479,1620,1839,1888,966501,966703,970276,970520,970685,971076,971323,972074,972287,972860,973185,973499,973832,974315,974441,

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 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. For more information about this feature, go to the Coloring Gene Predictions and Annotations by Codon page.

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. PMID: 11932250; PMC: PMC187518