Schema for mgcFullMrna
  Database: danRer7    Primary Table: mgcFullMrna    Row Count: 18,266   Data last updated: 2020-01-27
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
matches 1733int(10) unsigned range Number of bases that match that aren't repeats
misMatches 3int(10) unsigned range Number of bases that don't match
repMatches 4int(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 14int(10) unsigned range Number of inserts in target
tBaseInsert 20427int(10) unsigned range Number of bases inserted in target
strand +char(2) values + or - for strand. First character query, second target (optional)
qName BC157389varchar(255) values Query sequence name
qSize 3017int(10) unsigned range Query sequence size
qStart 34int(10) unsigned range Alignment start position in query
qEnd 1774int(10) unsigned range Alignment end position in query
tName Zv9_NA110varchar(255) values Target sequence name
tSize 25708int(10) unsigned range Target sequence size
tStart 3369int(10) unsigned range Alignment start position in target
tEnd 25536int(10) unsigned range Alignment end position in target
blockCount 15int(10) unsigned range Number of blocks in alignment
blockSizes 195,105,82,129,53,191,66,55...longblob   Size of each block
qStarts 34,229,334,416,545,598,789,...longblob   Start of each block in query.
tStarts 3369,4371,5127,7177,8049,11...longblob   Start of each block in target.

Connected Tables and Joining Fields
        danRer7.all_mrna.qName (via mgcFullMrna.qName)
      danRer7.mgcGenes.name (via mgcFullMrna.qName)
      danRer7.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
5851733340001420427+BC1573893017341774Zv9_NA1102570833692553615195,105,82,129,53,191,66,55,80,134,75,172,217,65,121,34,229,334,416,545,598,789,855,910,990,1124,1199,1371,1588,1653,3369,4371,5127,7177,8049,11127,13688,13992,14258,15888,16240,19924,20951,22766,25415,
58586130013031858-BC04887837767411635Zv9_NA1196288116138834551,116,129,68,2141,2692,2808,2967,1161,1983,3095,3815,
585210010000212718-BC165814140233253Zv9_NA12218352012938356,127,37,1149,1205,1332,0,6871,12901,
585467110000212718-BC04545119450478Zv9_NA12218352013196356,127,295,1467,1523,1650,0,6871,12901,
585472110000212718-BC06566119190483Zv9_NA12218352013201356,127,300,1436,1492,1619,0,6871,12901,
5851216627400024274-BC1428291572591555Zv9_NA12351610391504492031124,144,228,17,1141,1285,39150,41107,44692,
58515813000023004+BC10000712227196Zv9_NA15227301856421757338,69,82,7,45,114,18564,18608,21675,
58523828000029-BC154641241742394Zv9_NA154360972965732056373,127,2190,23,96,223,29657,29733,29866,
58522327000016-BC171687223902239Zv9_NA154360972980932054251,2188,0,51,29809,29866,
58522327000016-BC171691223902239Zv9_NA154360972980932054251,2188,0,51,29809,29866,

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