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Database: bosTau4 Primary Table: mgcFullMrna Row Count: 9,734 Data last updated: 2020-01-27
Format description: Summary info about a patSpace alignment
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
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| bin | 587 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| matches | 2273 | 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 | 4 | int(10) unsigned | range | Number of inserts in target |
| tBaseInsert | 8929 | int(10) unsigned | range | Number of bases inserted in target |
| strand | + | char(2) | values | + or - for strand. First character query, second target (optional) |
| qName | BC103185 | varchar(255) | values | Query sequence name |
| qSize | 2342 | int(10) unsigned | range | Query sequence size |
| qStart | 1 | int(10) unsigned | range | Alignment start position in query |
| qEnd | 2274 | int(10) unsigned | range | Alignment end position in query |
| tName | chr1 | varchar(255) | values | Target sequence name |
| tSize | 161106243 | int(10) unsigned | range | Target sequence size |
| tStart | 327876 | int(10) unsigned | range | Alignment start position in target |
| tEnd | 339078 | int(10) unsigned | range | Alignment end position in target |
| blockCount | 5 | int(10) unsigned | range | Number of blocks in alignment |
| blockSizes | 167,174,160,1726,46, | longblob | | Size of each block |
| qStarts | 1,168,342,502,2228, | longblob | | Start of each block in query. |
| tStarts | 327876,331232,333962,337305... | longblob | | Start of each block in target. |
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To download this table in different text formats or to intersect or correlate it with other tables, use the Table Browser.
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Connected Tables and Joining Fields
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bosTau4.all_mrna.qName (via mgcFullMrna.qName)
bosTau4.mgcGenes.name (via mgcFullMrna.qName)
bosTau4.mrnaOrientInfo.name (via mgcFullMrna.qName)
hgFixed.gbCdnaInfo.acc (via mgcFullMrna.qName)
hgFixed.gbSeq.acc (via mgcFullMrna.qName)
hgFixed.imageClone.acc (via mgcFullMrna.qName)
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Sample Rows
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| bin | matches | misMatches | repMatches | nCount | qNumInsert | qBaseInsert | tNumInsert | tBaseInsert | strand | qName | qSize | qStart | qEnd | tName | tSize | tStart | tEnd | blockCount | blockSizes | qStarts | tStarts |
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| 587 | 2273 | 0 | 0 | 0 | 0 | 0 | 4 | 8929 | + | BC103185 | 2342 | 1 | 2274 | chr1 | 161106243 | 327876 | 339078 | 5 | 167,174,160,1726,46, | 1,168,342,502,2228, | 327876,331232,333962,337305,339032, |
| 587 | 775 | 1 | 20 | 0 | 0 | 0 | 2 | 5700 | + | BC112873 | 909 | 1 | 797 | chr1 | 161106243 | 377375 | 383871 | 3 | 72,95,629, | 1,73,168, | 377375,378426,383242, |
| 588 | 1012 | 7 | 0 | 1 | 0 | 0 | 0 | 0 | - | BC110185 | 1118 | 2 | 1022 | chr1 | 161106243 | 436007 | 437027 | 1 | 1020, | 96, | 436007, |
| 588 | 522 | 0 | 0 | 0 | 0 | 0 | 3 | 14912 | - | BC146134 | 539 | 1 | 523 | chr1 | 161106243 | 439762 | 455196 | 4 | 183,178,99,62, | 16,199,377,476, | 439762,442426,448986,455134, |
| 588 | 779 | 0 | 0 | 0 | 0 | 0 | 1 | 7029 | - | BC111662 | 794 | 1 | 780 | chr1 | 161106243 | 460824 | 468632 | 2 | 673,106, | 14,687, | 460824,468526, |
| 590 | 737 | 0 | 0 | 0 | 0 | 0 | 6 | 6619 | + | BC102204 | 806 | 2 | 739 | chr1 | 161106243 | 720700 | 728056 | 7 | 64,51,111,130,113,87,181, | 2,66,117,228,358,471,558, | 720700,722100,723097,725361,726173,727511,727875, |
| 592 | 1405 | 0 | 0 | 0 | 0 | 0 | 12 | 32307 | + | BC118422 | 1422 | 1 | 1406 | chr1 | 161106243 | 988441 | 1022153 | 13 | 56,72,78,73,45,69,134,112,99,122,106,46,393, | 1,57,129,207,280,325,394,528,640,739,861,967,1013, | 988441,997164,998806,999699,1001812,1003535,1012150,1013410,1015778,1017532,1018682,1021174,1021760, |
| 592 | 2126 | 0 | 236 | 0 | 0 | 0 | 9 | 7730 | + | BC133573 | 2380 | 2 | 2364 | chr1 | 161106243 | 1032567 | 1042659 | 10 | 314,81,204,179,179,82,105,199,213,806, | 2,316,397,601,780,959,1041,1146,1345,1558, | 1032567,1033632,1034646,1035752,1037144,1037946,1038136,1039087,1040465,1041853, |
| 593 | 3685 | 0 | 32 | 0 | 0 | 0 | 22 | 22572 | + | BC122573 | 3788 | 0 | 3717 | chr1 | 161106243 | 1074721 | 1101010 | 23 | 51,186,96,175,112,69,126,88,86,169,232,95,110,199,252,153,207,138,131,142,116,682,102, | 0,51,237,333,508,620,689,815,903,989,1158,1390,1485,1595,1794,2046,2199,2406,2544,2675,2817,2933,3615, | 1074721,1077457,1078725,1079298,1082717,1083798,1084369,1085572,1086149,1086399,1089540,1091651,1092040,1092492,1093733,1094277, ... |
| 593 | 2052 | 0 | 0 | 0 | 0 | 0 | 6 | 34787 | + | BC102794 | 2068 | 1 | 2053 | chr1 | 161106243 | 1135358 | 1172197 | 7 | 101,140,113,68,93,58,1479, | 1,102,242,355,423,516,574, | 1135358,1153790,1155902,1157299,1164351,1167219,1170718, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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MGC Genes (mgcFullMrna) Track Description
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Description
This track show alignments of mouse 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, rat, xenopus, and zerbrafish 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 mouse 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 mouse 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
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