Skip to main content

Advertisement

Table 2 Rfam non-coding RNAs in CORG A + sign indicates that a sequence fragment from the corresponding species (hsa Homo sapiens, mmu Mus musculus, rno Rattus norvegicus, dre Danio rerio, tru Takifugu rubripes) is contained in the CORG CNB; indicates that a blast search for an orhologous sequence in the Ensemble database was unsuccessful; n.d. mean no descriptive Ensemble gene annotation. The CNBs containing mir-196a-2 are shifted compared to the known microRNA sequences, preventing the detection of the correct stem-loop structure. The B columns marks whether a candidate was identified by a blast search against the Rfam or microRNA Registry, the A column shows whether a hairpin structure was identified by RNAalifold.pRNAz is the p-value for being an evolutionary conserved RNA secondary structure element returned by RNAz.

From: Comparative promoter region analysis powered by CORG

CNB B A p RNAz ncRNA hsa mmu rno dre tru gene
119596 + + 0.995 mir-34c + + + + n.d. (BCT-4)
119607 + + 0.938        mir-34b in hsa
119658 + + 0.985        
159914 + + 0.998 mir-138-2 + + + + SLC12A3, n.d. in teleosts
159932 + + 0.999        
159939 + + 0.998        
194777 + + 0.998 mir-196b + - + + + HOXA9, dre: HOXA9a and HOXA9b
194820 + + 0.999        
194839 + + 0.999        
194941 + + 0.999        
226470 + + 0.999 mir-10a + + + + + HOXB4, dre: HOXB4a and HOXB4b
226514 + + 0.999        
226555 + + 0.999        
226677 + - 0.004        
238163 + + 0.992 mir-10b + + + + + HOXD4, dre: HOXD4a, n.d in tru
238188 + + 0.984        
238265 + + 0.994        
391314 + - 0.125 mir-196a-2 + + - + + HOXC9, dre: HOXC9a
391315 + - 0.999        
391318 + - 0.511        
470004 + - 0.218 U93 + + + 0 + n.d.
110374 - + 0.995 IRES ? + + + + + DGCR8
146100 - + 0.891   + + + + 0 Ptf1a
393794 - + 0.999 IRE + + + + + SLCA1