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mmu_ciHdac2_462
Basic information of circular RNA
PanCircBase ID:
mmu_ciHdac2_462
mm39_Chr. Position ID:
chr10|36873498|36873960|+
Gene name:
Hdac2
Transcript:
ENSMUST00000019911.14
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
10
Exon/intron offsets:
0
Genomic length:
462
Exon/intron sizes in nt:
462
Flanking exon/introns:
chr10:36873498-36873962
Splice length:
462
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGAAATCACTTCGGCTTAATGAAACTTCAGGAGGCTATAGAAGGTCAAATAAAGGAAGTTGGTTTAGCATATACATCAGATACTTCCTAACCTTAGGCTATTCCTGTTTTTTAATCTCTTATATTAATACAAATATGTAACCTTTGTAAATAGAAACATTCTTATTAGATCAAATGCTTTATGTCTACAGAATGTAGAAACATTGATCAGAACGGGCTGTGTCCTCTCTCCCATAGACCAGTTGTATGACATTTATAAGTACACCTCATTGTCAAATAGAGGTGAAAAGGTACATGTTTGTGTGCTGTGGGTTCAGTCAGCTAATATATGCAGTGATCTGATGCTTAGATAGTGTCCCATTCAGTGGTTAGTAAATGAAAGCTCGTTCTTGTTTAGTTCCTCCTGTGTATAACAGAAACTTTACATACAGTGGATTTTGTCTAATAAATTGTGTCATTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGTGGTTAGTAAATGAAAGCTCGT
59.59
TGACCTTCTATAGCCTCCTGA
57.03
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGGTTAGTAAATGAAAGCTCGT
58.45
TGACCTTCTATAGCCTCCTGA
57.03
147
PCR template sequence:
TTCAGTGGTTAGTAAATGAAAGCTCGTTCTTGTTTAGTTCCTCCTGTGTATAACAGAAACTTTACATACAGTGGATTTTGTCTAATAAATTGTGTCATTTGTAAGAAATCACTTCGGCTTAATGAAACTTCAGGAGGCTATAGAAGGTCAAATAAAGGAAGTTGGTTTAGCATATACATCAGATACTTCCTAACCTTAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-217-5p(1), mmu-miR-185-5p(1), mmu-miR-425-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AATTGTGTCATTTGTAAGAAATCACT
siRNA sets
ATTTCTTACAAATGACACA,AGTGATTTCTTACAAATGA,GATTTCTTACAAATGACAC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIHDAC2_462_ORF_1
0.9422
-0.414239742
0.027629449
228
ORF sequence:
ATGAAAGCTCGTTCTTGTTTAGTTCCTCCTGTGTATAACAGAAACTTTACATACAGTGGATTTTGTCTAATAAATTGTGTCATTTGTAAGAAATCACTTCGGCTTAATGAAACTTCAGGAGGCTATAGAAGGTCAAATAAAGGAAGTTGGTTTAGCATATACATCAGATACTTCCTAACCTTAGGCTATTCCTGTTTTTTAATCTCTTATATTAATACAAATATGTAA
Peptide sequence:
MKARSCLVPPVYNRNFTYSGFCLINCVICKKSLRLNETSGGYRRSNKGSWFSIYIRYFLTLGYSCFLISYINTNM
IRESfinder result
IRESfinder score
0.817766321
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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