Schema for fRNAdb::pre-miRNA - fRNAdb::pre-miRNA track

Database: hg19 Primary Table: F_pre_miRNA Row Count: 744

field	example	SQL type	info
`bin`	921	`smallint(5) unsigned`	range
`matches`	99	`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`	FR057497	`varchar(255)`	values
`qSize`	99	`int(10) unsigned`	range
`qStart`	0	`int(10) unsigned`	range
`qEnd`	99	`int(10) unsigned`	range
`tName`	chr3	`varchar(255)`	values
`tSize`	198022430	`int(10) unsigned`	range
`tStart`	44155703	`int(10) unsigned`	range
`tEnd`	44155802	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	99,	`longblob`
`qStarts`	0,	`longblob`
`tStarts`	44155703,	`longblob`

bin	matches	repMatches	tNumInsert	tBaseInsert	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
921	99	0	0	0	+	FR057497	99	99	chr3	198022430	44155703	44155802	1	99,	0,	44155703,
1515	72	0	0	0	-	FR245535	72	72	chr11	135006516	122017229	122017301	1	72,	0,	122017229,
1015	64	0	0	0	-	FR252415	64	64	chr17	81195210	56408603	56408667	1	64,	0,	56408603,
1557	89	0	0	0	+	FR332462	89	89	chr9	141213431	127455988	127456077	1	89,	0,	127455988,
1768	53	28	1	2	+	FR218864	81	81	chr1	249250621	155164977	155165060	2	73,8,	0,73,	155164977,155165052,
621	110	0	0	0	+	FR150020	110	110	chr19	59128983	4770681	4770791	1	110,	0,	4770681,
998	95	0	0	0	+	FR357095	95	95	chr19	59128983	54244566	54244661	1	95,	0,	54244566,
1359	73	0	0	0	+	FR062023	73	73	chr14	107349540	101521755	101521828	1	73,	0,	101521755,
1009	95	0	0	0	-	FR241346	95	95	chr15	102531392	55665137	55665232	1	95,	0,	55665137,
835	97	0	0	0	+	FR319194	97	97	chr7	159138663	32772592	32772689	1	97,	0,	32772592,

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

Description

This track shows precursor micro RNAs (miRNAs) 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.