| field | example | SQL type | info |
|---|---|---|---|
| bin | 1284 | smallint(5) unsigned | range |
| matches | 42 | int(10) unsigned | range |
| misMatches | 0 | int(10) unsigned | range |
| repMatches | 0 | int(10) unsigned | range |
| nCount | 0 | int(10) unsigned | range |
| qNumInsert | 0 | int(10) unsigned | range |
| qBaseInsert | 0 | int(10) unsigned | range |
| tNumInsert | 0 | int(10) unsigned | range |
| tBaseInsert | 0 | int(10) unsigned | range |
| strand | + | char(2) | values |
| qName | FR197792 | varchar(255) | values |
| qSize | 42 | int(10) unsigned | range |
| qStart | 0 | int(10) unsigned | range |
| qEnd | 42 | int(10) unsigned | range |
| tName | chr7 | varchar(255) | values |
| tSize | 159138663 | int(10) unsigned | range |
| tStart | 91739922 | int(10) unsigned | range |
| tEnd | 91739964 | int(10) unsigned | range |
| blockCount | 1 | int(10) unsigned | range |
| blockSizes | 42, | longblob | |
| qStarts | 0, | longblob | |
| tStarts | 91739922, | longblob |
| bin | matches | misMatches | repMatches | nCount | qNumInsert | qBaseInsert | tNumInsert | tBaseInsert | strand | qName | qSize | qStart | qEnd | tName | tSize | tStart | tEnd | blockCount | blockSizes | qStarts | tStarts |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1284 | 42 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | FR197792 | 42 | 0 | 42 | chr7 | 159138663 | 91739922 | 91739964 | 1 | 42, | 0, | 91739922, |
| 1961 | 45 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | FR399163 | 45 | 0 | 45 | chr3 | 198022430 | 180462296 | 180462341 | 1 | 45, | 0, | 180462296, |
| 944 | 24 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | FR190407 | 24 | 0 | 24 | chrX | 155270560 | 47072416 | 47072440 | 1 | 24, | 0, | 47072416, |
| 1116 | 25 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | FR297116 | 25 | 0 | 25 | chr16 | 90354753 | 69679173 | 69679198 | 1 | 25, | 0, | 69679173, |
| 1535 | 24 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | FR180550 | 24 | 0 | 24 | chr6 | 171115067 | 124639171 | 124639195 | 1 | 24, | 0, | 124639171, |
| 794 | 15 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | - | FR018873 | 15 | 0 | 15 | chr17 | 81195210 | 27423353 | 27423368 | 1 | 15, | 0, | 27423353, |
| 1358 | 18 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | FR061513 | 18 | 0 | 18 | chr7 | 159138663 | 101421482 | 101421500 | 1 | 18, | 0, | 101421482, |
| 788 | 34 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | FR341444 | 34 | 0 | 34 | chr7 | 159138663 | 26729341 | 26729375 | 1 | 34, | 0, | 26729341, |
| 966 | 29 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | FR238560 | 29 | 0 | 29 | chr10 | 135534747 | 49947118 | 49947147 | 1 | 29, | 0, | 49947118, |
| 1321 | 19 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | + | FR301340 | 19 | 0 | 19 | chr1 | 249250621 | 96475753 | 96475772 | 1 | 19, | 0, | 96475753, |
Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.
This track shows conserved non-coding regions predicted by EvoFold [1].
This track is prepared to give interoperability with the functional RNA database [2] v3.0.
Short sequences (shorter than 30nt) are aligned to genome by SeqMap [3] with 0 mismatch, no-gap and no-repeat.
Other sequences are aligned to genome by BLAT [4] with identity>=99, coverage>=90 and no-repeat.
And limit results to positions of EvoFold track in UCSC Genome Browser.
[1] Pedersen JS, Bejerano G, Siepel A, Rosenbloom K, Lindblad-Toh K, Lander ES, Kent J, Miller W, Haussler D.
Identification and classification of conserved RNA secondary structures in the human genome.
PLoS Comput Biol. 2006 Apr;2(4):e33.
[2] Kin T, Yamada K, Terai G, Okida H, Yoshinari Y, Ono Y, Kojima A, Kimura Y, Komori T, Asai K.
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences.
Nucleic Acids Res. 2007 Jan;35(Database issue):D145-8.
[3] Jiang H, Wong WH
SeqMap: mapping massive amount of oligonucleotides to the genome.
Bioinformatics. 2008 Oct 15;24(20):2395-6. Epub 2008 Aug 12.
[4] Kent WJ.
BLAT--the BLAST-like alignment tool.
Genome Res. 2002 Apr;12(4):656-64.