Schema for fRNAdb::snoRNA - fRNAdb::snoRNA track

Database: hg19 Primary Table: F_snoRNA Row Count: 1,070

field	example	SQL type	info
`bin`	779	`smallint(5) unsigned`	range
`matches`	76	`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`	FR247750	`varchar(255)`	values
`qSize`	76	`int(10) unsigned`	range
`qStart`	0	`int(10) unsigned`	range
`qEnd`	76	`int(10) unsigned`	range
`tName`	chr15	`varchar(255)`	values
`tSize`	102531392	`int(10) unsigned`	range
`tStart`	25436568	`int(10) unsigned`	range
`tEnd`	25436644	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	76,	`longblob`
`qStarts`	0,	`longblob`
`tStarts`	25436568,	`longblob`

bin	matches	repMatches	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
779	76	0	+	FR247750	76	76	chr15	102531392	25436568	25436644	1	76,	0,	25436568,
778	91	0	+	FR083178	91	91	chr15	102531392	25332809	25332900	1	91,	0,	25332809,
817	133	0	+	FR098542	133	133	chr2	243199373	30410299	30410432	1	133,	0,	30410299,
2129	118	12	-	FR040725	130	130	chr1	249250621	202496437	202496567	1	130,	0,	202496437,
778	95	0	+	FR277902	95	95	chr15	102531392	25307479	25307574	1	95,	0,	25307479,
824	91	0	-	FR108157	91	91	chr1	249250621	31408532	31408623	1	91,	0,	31408532,
763	124	0	+	FR373065	124	124	chr16	90354753	23453118	23453242	1	124,	0,	23453118,
615	137	0	+	FR157133	137	137	chr11	135006516	3943796	3943933	1	137,	0,	3943796,
1358	71	0	+	FR059319	71	71	chr14	107349540	101442161	101442232	1	71,	0,	101442161,
779	82	0	+	FR089862	82	82	chr15	102531392	25479393	25479475	1	82,	0,	25479393,

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

Description

This track shows small nucleolar RNA (snoRNA) in the functional RNA database [1].

Description provided by Sequence Ontology (SO):

A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA.

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.