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Database: hg18 Primary Table: orfeomeMrna Row Count: 34,179 Data last updated: 2018-10-16
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 | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| matches | 781 | int(10) unsigned | range | Number of bases that match that aren't repeats |
| misMatches | 9 | 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 | 1 | int(10) unsigned | range | Number of inserts in query |
| qBaseInsert | 1 | int(10) unsigned | range | Number of bases inserted in query |
| tNumInsert | 5 | int(10) unsigned | range | Number of inserts in target |
| tBaseInsert | 1821 | int(10) unsigned | range | Number of bases inserted in target |
| strand | - | char(2) | values | + or - for strand. First character query, second target (optional) |
| qName | KJ901026 | varchar(255) | values | Query sequence name |
| qSize | 924 | int(10) unsigned | range | Query sequence size |
| qStart | 65 | int(10) unsigned | range | Alignment start position in query |
| qEnd | 856 | int(10) unsigned | range | Alignment end position in query |
| tName | chr1 | varchar(255) | values | Target sequence name |
| tSize | 247249719 | int(10) unsigned | range | Target sequence size |
| tStart | 4562 | int(10) unsigned | range | Alignment start position in target |
| tEnd | 7173 | int(10) unsigned | range | Alignment end position in target |
| blockCount | 7 | int(10) unsigned | range | Number of blocks in alignment |
| blockSizes | 130,69,108,44,162,199,78, | longblob | | Size of each block |
| qStarts | 68,198,267,376,420,582,781, | longblob | | Start of each block in query. |
| tStarts | 4562,4832,5658,5766,6469,67... | 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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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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| 585 | 781 | 9 | 0 | 0 | 1 | 1 | 5 | 1821 | - | KJ901026 | 924 | 65 | 856 | chr1 | 247249719 | 4562 | 7173 | 7 | 130,69,108,44,162,199,78, | 68,198,267,376,420,582,781, | 4562,4832,5658,5766,6469,6719,7095, |
| 585 | 256 | 0 | 0 | 0 | 1 | 1 | 2 | 341 | - | KJ905121 | 391 | 68 | 325 | chr1 | 247249719 | 25002 | 25599 | 4 | 35,62,143,16, | 66,101,164,307, | 25002,25139,25201,25583, |
| 587 | 936 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | + | KJ899668 | 1071 | 68 | 1005 | chr1 | 247249719 | 357521 | 358458 | 1 | 937, | 68, | 357521, |
| 589 | 936 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | - | KJ899668 | 1071 | 68 | 1005 | chr1 | 247249719 | 610960 | 611897 | 1 | 937, | 66, | 610960, |
| 590 | 490 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | - | KJ901126 | 624 | 67 | 558 | chr1 | 247249719 | 751944 | 752435 | 1 | 491, | 66, | 751944, |
| 591 | 1491 | 1 | 0 | 0 | 5 | 5 | 7 | 3353 | + | KJ905008 | 1625 | 63 | 1560 | chr1 | 247249719 | 864550 | 869395 | 13 | 153,163,116,79,285,43,24,148,125,111,169,17,59, | 63,216,379,495,574,860,904,929,1077,1202,1313,1483,1501, | 864550,866386,867378,867652,867801,868086,868129,868153,868495,868940,869150,869319,869336, |
| 591 | 2246 | 4 | 0 | 0 | 0 | 0 | 18 | 12297 | - | KJ898602 | 2379 | 64 | 2314 | chr1 | 247249719 | 869937 | 884484 | 19 | 106,90,136,114,144,102,114,112,140,189,114,111,79,91,121,132,175,153,27, | 65,171,261,397,511,655,757,871,983,1123,1312,1426,1537,1616,1707,1828,1960,2135,2288, | 869937,870299,870760,871415,871644,873373,873732,876369,877242,877654,878417,879024,879246,881165,881337,882136,882341,884171,88 ... |
| 591 | 2197 | 7 | 44 | 0 | 0 | 0 | 18 | 12297 | - | AM393843 | 2289 | 19 | 2267 | chr1 | 247249719 | 869939 | 884484 | 19 | 104,90,136,114,144,102,114,112,140,189,114,111,79,91,121,132,175,153,27, | 22,126,216,352,466,610,712,826,938,1078,1267,1381,1492,1571,1662,1783,1915,2090,2243, | 869939,870299,870760,871415,871644,873373,873732,876369,877242,877654,878417,879024,879246,881165,881337,882136,882341,884171,88 ... |
| 591 | 1875 | 0 | 52 | 0 | 0 | 0 | 11 | 2569 | + | BC166618 | 1990 | 34 | 1961 | chr1 | 247249719 | 885936 | 890432 | 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, | 885936,886535,886871,887068,887597,887946,888351,888579,889162,889349,889591,890205, |
| 591 | 561 | 2 | 0 | 0 | 0 | 0 | 1 | 75 | + | KJ904192 | 693 | 65 | 628 | chr1 | 247249719 | 886876 | 887514 | 2 | 117,446, | 65,182, | 886876,887068, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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ORFeome Clones (orfeomeMrna) Track Description
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Description
This track show alignments of mouse clones from the
ORFeome Collaboration. The goal of the project is to be an
"unrestricted source of fully sequence-validated full-ORF human cDNA
clones in a format allowing easy transfer of the ORF sequences into
virtually any type of expression vector. A major goal is to provide
at least one fully-sequenced full-ORF clone for each human, mouse, and zebrafish gene.
This track is updated automatically as new clones become available.
Display Conventions and Configuration
The track follows the display conventions for
gene prediction
tracks.
Methods
ORFeome mouse clones were obtained from GenBank and aligned against the
genome using the blat program. When a single clone aligned in multiple
places, the alignment having the highest base identity was found. Only alignments
having a base identity level within 0.5% of the best and at least 96% base
identity with the genomic sequence were kept.
Credits and References
Visit the ORFeome Collaboration
members page for a list of credits and references.
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US Server