Schema for fRNAdb::piRNA - fRNAdb::piRNA track

Database: hg19 Primary Table: F_piRNA Row Count: 39,545

field	example	SQL type	info
`bin`	1959	`smallint(5) unsigned`	range
`matches`	26	`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`	FR331797	`varchar(255)`	values
`qSize`	26	`int(10) unsigned`	range
`qStart`	0	`int(10) unsigned`	range
`qEnd`	26	`int(10) unsigned`	range
`tName`	chr5	`varchar(255)`	values
`tSize`	180915260	`int(10) unsigned`	range
`tStart`	180113362	`int(10) unsigned`	range
`tEnd`	180113388	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	26,	`longblob`
`qStarts`	0,	`longblob`
`tStarts`	180113362,	`longblob`

bin	matches	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
1959	26	+	FR331797	26	26	chr5	180915260	180113362	180113388	1	26,	0,	180113362,
1062	29	+	FR047380	29	29	chr15	102531392	62560544	62560573	1	29,	0,	62560544,
725	27	+	FR027834	27	27	chr6	171115067	18368377	18368404	1	27,	0,	18368377,
719	29	+	FR016073	29	29	chr5	180915260	17584600	17584629	1	29,	0,	17584600,
719	29	+	FR016073	29	29	chr5	180915260	17596670	17596699	1	29,	0,	17596670,
719	29	+	FR016073	29	29	chr5	180915260	17589802	17589831	1	29,	0,	17589802,
719	29	+	FR016073	29	29	chr5	180915260	17584600	17584629	1	29,	0,	17584600,
718	29	-	FR016073	29	29	chr5	180915260	17523147	17523176	1	29,	0,	17523147,
719	29	+	FR016073	29	29	chr5	180915260	17593236	17593265	1	29,	0,	17593236,
718	29	-	FR016073	29	29	chr5	180915260	17530015	17530044	1	29,	0,	17530015,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

Description

This track shows Piwi-associated small RNAs (piRNAs) in the functional RNA database [1] v3.0.

Methods

Short sequences (shorter than 30nt) are aligned to genome by SeqMap [2] with 0 mismatch, no-gap and no-repeat.

Other sequences are aligned to genome by BLAT [3] with identity>=99, coverage>=90 and no-repeat.

References

  [1] 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.

  [2] 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.

  [3] Kent WJ.
      BLAT--the BLAST-like alignment tool.
      Genome Res. 2002 Apr;12(4):656-64.