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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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