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mmu_circHipk3_342
Basic information of circular RNA
PanCircBase ID:
mmu_circHipk3_342
mm39_Chr. Position ID:
chr2|104268195|104269759|-
Gene name:
Hipk3
Transcript:
ENSMUST00000028600.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
7,6
Exon/intron offsets:
0,1379
Genomic length:
1564
Exon/intron sizes in nt:
1,57,185
Flanking exon/introns:
chr2:104267465-104268195|chr2:104269759-104270550
Splice length:
342
Other database IDs:
circAtlas: mmu-Hipk3_0013
Human Ortholog IDs:
Mature spliced Sequence:
GTGAACACAGTGATGGACTTGGAAGGAGGTGATCTCTTGGCTGAGAAAGCTGATAGAAGAGAATTTGTTAATCTGTTGAAGAAAATGTTGCTGATTGATGCAGATTTAAGAATTACTCCAATTGAGACTCTGAACCACCCATTCGTTAATATGAAGCATCTACTAGATTTTCCTCACAGCAACCATGTAAAGTCCTGTTTTCATATCATGGATATTTGTAAGTCTCCGAGTTCATGTGAAACAAATAACCACAGTAAAATGTCACTCTTACGACCAGTCGCATCGAATGGCACTGCTGCTCTAGCAGCAAACTTTACTAAAGTCGGGACACTAAGAAGTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGAATGGCACTGCTGCTCTA
60.46
TCAGCAACATTTTCTTCAACAGA
57.17
153
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGAATGGCACTGCTGCTCTA
60.46
CAGCAACATTTTCTTCAACAGA
55.76
152
PCR template sequence:
AAATAACCACAGTAAAATGTCACTCTTACGACCAGTCGCATCGAATGGCACTGCTGCTCTAGCAGCAAACTTTACTAAAGTCGGGACACTAAGAAGTCAGGTGAACACAGTGATGGACTTGGAAGGAGGTGATCTCTTGGCTGAGAAAGCTGATAGAAGAGAATTTGTTAATCTGTTGAAGAAAATGTTGCTGATTGATG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-322-5p(1), mmu-miR-5101(1)
siRNAs for circular RNA silencing
Junction sequence
ACTAAGAAGTCAGGTGAACACAGTGA
siRNA sets
TCACTGTGTTCACCTGACT, TGTTCACCTGACTTCTTAG, ACTGTGTTCACCTGACTTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCHIPK3_342_ORF_1
0.9973
-0.009127077
0.803384281
672
ORF sequence:
ATGGACTTGGAAGGAGGTGATCTCTTGGCTGAGAAAGCTGATAGAAGAGAATTTGTTAATCTGTTGAAGAAAATGTTGCTGATTGATGCAGATTTAAGAATTACTCCAATTGAGACTCTGAACCACCCATTCGTTAATATGAAGCATCTACTAGATTTTCCTCACAGCAACCATGTAAAGTCCTGTTTTCATATCATGGATATTTGTAAGTCTCCGAGTTCATGTGAAACAAATAACCACAGTAAAATGTCACTCTTACGACCAGTCGCATCGAATGGCACTGCTGCTCTAGCAGCAAACTTTACTAAAGTCGGGACACTAAGAAGTCAGGTGAACACAGTGATGGACTTGGAAGGAGGTGATCTCTTGGCTGAGAAAGCTGATAGAAGAGAATTTGTTAATCTGTTGAAGAAAATGTTGCTGATTGATGCAGATTTAAGAATTACTCCAATTGAGACTCTGAACCACCCATTCGTTAATATGAAGCATCTACTAGATTTTCCTCACAGCAACCATGTAAAGTCCTGTTTTCATATCATGGATATTTGTAAGTCTCCGAGTTCATGTGAAACAAATAACCACAGTAAAATGTCACTCTTACGACCAGTCGCATCGAATGGCACTGCTGCTCTAGCAGCAAACTTTACTAAAGTCGGGACACTAAGAAGTCAG
Peptide sequence:
MDLEGGDLLAEKADRREFVNLLKKMLLIDADLRITPIETLNHPFVNMKHLLDFPHSNHVKSCFHIMDICKSPSSCETNNHSKMSLLRPVASNGTAALAANFTKVGTLRSQVNTVMDLEGGDLLAEKADRREFVNLLKKMLLIDADLRITPIETLNHPFVNMKHLLDFPHSNHVKSCFHIMDICKSPSSCETNNHSKMSLLRPVASNGTAALAANFTKVGTLRSQ
IRESfinder result
IRESfinder score
0.694226346
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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