Schema for fRNAdb::Misc - fRNAdb::Misc track

Database: hg19 Primary Table: F_misc Row Count: 5,206

field	example	SQL type	info
`bin`	1411	`smallint(5) unsigned`	range
`matches`	201	`int(10) unsigned`	range
`misMatches`	1	`int(10) unsigned`	range
`repMatches`	2	`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`	FR189585	`varchar(255)`	values
`qSize`	204	`int(10) unsigned`	range
`qStart`	0	`int(10) unsigned`	range
`qEnd`	204	`int(10) unsigned`	range
`tName`	chr5	`varchar(255)`	values
`tSize`	180915260	`int(10) unsigned`	range
`tStart`	108388158	`int(10) unsigned`	range
`tEnd`	108388362	`int(10) unsigned`	range
`blockCount`	1	`int(10) unsigned`	range
`blockSizes`	204,	`longblob`
`qStarts`	0,	`longblob`
`tStarts`	108388158,	`longblob`

bin	matches	misMatches	repMatches	qNumInsert	qBaseInsert	tNumInsert	tBaseInsert	strand	qName	qSize	qEnd	tName	tSize	tStart	tEnd	blockCount	blockSizes	qStarts	tStarts
1411	201	1	2	0	0	0	0	-	FR189585	204	204	chr5	180915260	108388158	108388362	1	204,	0,	108388158,
1567	302	0	0	0	0	0	0	+	FR262504	302	302	chr8	146364022	128748489	128748791	1	302,	0,	128748489,
707	320	0	0	0	0	1	1204	+	FR125988	320	320	chr2	243199373	16080689	16082213	2	176,144,	0,176,	16080689,16082069,
1411	200	2	2	0	0	0	0	-	FR378571	204	204	chr5	180915260	108388158	108388362	1	204,	0,	108388158,
1567	301	1	0	0	0	0	0	+	FR155520	302	302	chr8	146364022	128748489	128748791	1	302,	0,	128748489,
918	265	0	37	0	0	6	7	+	FR130232	302	302	chr6	171115067	43738689	43738998	7	149,15,11,9,68,12,38,	0,149,164,175,184,252,264,	43738689,43738839,43738855,43738867,43738877,43738946,43738960,
838	370	0	0	0	0	0	0	-	FR255862	370	370	chr9	141213431	33264324	33264694	1	370,	0,	33264324,
1567	298	2	0	0	0	2	2	+	FR314635	300	300	chr8	146364022	128748489	128748791	3	138,140,22,	0,138,278,	128748489,128748628,128748769,
887	498	2	121	1	1	1	7	-	FR256229	622	622	chr22	51304566	39640145	39640773	3	90,503,28,	0,91,594,	39640145,39640235,39640745,
1250	352	1	0	0	0	0	0	+	FR180438	353	353	chr9	141213431	87285310	87285663	1	353,	0,	87285310,

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

Description

This track shows varieties of non-coding RNAs in the functional RNA database [1], that cannot be classified into any major categories.

Subcategory Population

Histone 3' untraslated region (UTR) stem-loop 75

Selenocysteine insertion sequence 17

Apolipoprotein B (apoB) 5' untraslated region (UTR) cis-regulatory element 4

rbcL 5' untraslated region (UTR) RNA stabilising element 3

Interferon gamma 5' untraslated region (UTR) regulatory element 3

Renin stability regulatory element (REN-SRE) 2

Vimentin 3' untraslated region (UTR) protein-binding region 2

p27 cis-regulatory element 1

spleen focus forming virus proviral integration oncogene spi1 (Spi-1/PU.1) 5' untraslated region (UTR) regulatory element 1

Group I intron 1

Subcategory	Population
Histone 3' untraslated region (UTR) stem-loop	75
Selenocysteine insertion sequence	17
Apolipoprotein B (apoB) 5' untraslated region (UTR) cis-regulatory element	4
rbcL 5' untraslated region (UTR) RNA stabilising element	3
Interferon gamma 5' untraslated region (UTR) regulatory element	3
Renin stability regulatory element (REN-SRE)	2
Vimentin 3' untraslated region (UTR) protein-binding region	2
p27 cis-regulatory element	1
spleen focus forming virus proviral integration oncogene spi1 (Spi-1/PU.1) 5' untraslated region (UTR) regulatory element	1
Group I intron	1

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.