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 |
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.
[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.