Schema for UniGene - UniGene Alignments |
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Database: hg19 Primary Table: uniGene_3 Row Count: 124,338 Data last updated: 2011-02-22
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 | 1631 | int(10) unsigned | range | Number of bases that match that aren't repeats |
| misMatches | 8 | 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 | 897 | int(10) unsigned | range | Number of bases inserted in target |
| strand | + | char(2) | values | + or - for strand. First character query, second target (optional) |
| qName | Hs.714157 | varchar(255) | values | Query sequence name |
| qSize | 1673 | int(10) unsigned | range | Query sequence size |
| qStart | 0 | int(10) unsigned | range | Alignment start position in query |
| qEnd | 1639 | int(10) unsigned | range | Alignment end position in query |
| tName | chr1 | varchar(255) | values | Target sequence name |
| tSize | 249250621 | int(10) unsigned | range | Target sequence size |
| tStart | 11873 | int(10) unsigned | range | Alignment start position in target |
| tEnd | 14409 | int(10) unsigned | range | Alignment end position in target |
| blockCount | 5 | int(10) unsigned | range | Number of blocks in alignment |
| blockSizes | 354,109,741,296,139, | longblob | | Size of each block |
| qStarts | 0,354,463,1204,1500, | longblob | | Start of each block in query. |
| tStarts | 11873,12612,13220,13962,14270, | longblob | | Start of each block in target. |
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Connected Tables and Joining Fields
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hg19.seq.acc (via uniGene_3.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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| 585 | 1631 | 8 | 0 | 0 | 0 | 0 | 4 | 897 | + | Hs.714157 | 1673 | 0 | 1639 | chr1 | 249250621 | 11873 | 14409 | 5 | 354,109,741,296,139, | 0,354,463,1204,1500, | 11873,12612,13220,13962,14270, |
| 585 | 1648 | 4 | 0 | 0 | 0 | 0 | 2 | 884 | + | Hs.644359 | 1652 | 0 | 1652 | chr1 | 249250621 | 11873 | 14409 | 3 | 354,109,1189, | 0,354,463, | 11873,12612,13220, |
| 585 | 2372 | 19 | 172 | 0 | 1 | 1 | 10 | 2754 | - | Hs.709408 | 2580 | 0 | 2564 | chr1 | 249250621 | 14403 | 19720 | 12 | 108,316,69,108,44,159,198,131,376,147,99,808, | 16,124,440,509,618,662,821,1019,1150,1526,1673,1772, | 14403,14513,14969,15795,15903,16606,16857,17232,17366,17914,18267,18912, |
| 585 | 2987 | 19 | 127 | 0 | 2 | 7 | 6 | 7355 | - | Hs.459573 | 3161 | 21 | 3161 | chr1 | 249250621 | 14406 | 24894 | 8 | 53,1446,859,198,136,137,147,157, | 0,58,1506,2365,2563,2699,2836,2983, | 14406,14459,15906,16857,17232,17605,17914,24737, |
| 585 | 4086 | 21 | 127 | 0 | 1 | 2 | 2 | 93 | - | Hs.461200 | 4236 | 0 | 4236 | chr1 | 249250621 | 14406 | 18733 | 3 | 1499,859,1876, | 0,1501,2360, | 14406,15906,16857, |
| 585 | 899 | 20 | 36 | 7 | 4 | 17 | 12 | 1653 | + | Hs.528770 | 1003 | 17 | 996 | chr1 | 249250621 | 14436 | 17051 | 15 | 19,374,69,57,51,41,138,24,113,9,20,15,3,22,7, | 17,41,415,484,542,595,636,783,807,920,929,949,964,967,989, | 14436,14455,14969,15795,15854,15906,16606,16744,16856,16970,16980,17001,17017,17021,17044, |
| 585 | 91 | 0 | 0 | 0 | 0 | 0 | 1 | 7 | + | Hs.649999 | 220 | 39 | 130 | chr1 | 249250621 | 14452 | 14550 | 2 | 7,84, | 39,46, | 14452,14466, |
| 585 | 699 | 7 | 64 | 0 | 3 | 13 | 7 | 15 | - | Hs.572592 | 811 | 0 | 783 | chr1 | 249250621 | 18970 | 19755 | 9 | 29,39,58,34,53,31,296,12,218, | 28,57,106,165,201,254,285,581,593, | 18970,19000,19048,19106,19141,19195,19227,19524,19537, |
| 585 | 115 | 0 | 0 | 0 | 1 | 1 | 1 | 1 | + | Hs.641059 | 125 | 0 | 116 | chr1 | 249250621 | 20690 | 20806 | 3 | 5,8,102, | 0,6,14, | 20690,20695,20704, |
| 585 | 131 | 12 | 279 | 0 | 1 | 2 | 2 | 309 | + | Hs.569413 | 427 | 3 | 427 | chr1 | 249250621 | 30379 | 31110 | 3 | 11,276,135, | 3,16,292, | 30379,30391,30975, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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UniGene (uniGene_3) Track Description
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Description
This track shows the UniGene genes from NCBI. Each UniGene entry is a set of transcript sequences
that appear to come from the same transcription locus (gene or expressed pseudogene), together with
information on protein similarities, gene expression, cDNA clone reagents, and genomic location.
Coding exons are represented by blocks connected by horizontal lines representing introns. In full
display mode, arrowheads on the connecting intron lines indicate the direction of transcription.
Methods
The UniGene sequence file, Hs.seq.uniq.gz, is downloaded from NCBI. Sequences are aligned to base
genome using BLAT to create this track.
When a single UniGene gene aligned in multiple places, the alignment having the highest base
identity was found. Only alignments having a base identity level within 0.2% of the best and
at least 96.5% base identity with the genomic sequence were kept.
Credits
Thanks to UniGene
for providing this annotation.
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US Server