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mmu_ciDdx18_1007

Basic information of circular RNA
PanCircBase ID:

mmu_ciDdx18_1007

mm39_Chr. Position ID:

chr1|121488002|121489009|-

Gene name:

Ddx18

Transcript:

ENSMUST00000001724.12

CircRNA type:

Circular intronic (ci)RNA

Exon/Intron count:

1

Exon/intron indexes:

6

Exon/intron offsets:

0

Genomic length:

1007

Exon/intron sizes in nt:

1007

Flanking exon/introns:

chr1:121488000-121489009

Splice length:

1007

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

GTAAGTAGACGGCATCTGCATGGGGCTCACAGGGTAGTTAGAGGTCCGTGGTTGGTGATCTTGTAGGAAAAATAGTATCTTAATACCAGAATTTTACTATGGCCACATGAGGAATGTGGGCCTGTTGACTTCAGAAGTAGTTCTTTTCTGCTGGCTTCATACAGCACATTACCATAGCTCATAAACTAAAATTTAAATGCAGGGTCAGTAGTCTGGCCATGACCCTGTGCTTAGTGCAGTGTTGTGCTGAAATGATTGACATGAAGAAAAGCAAGTGTGGAAGCAAGAGTCAAGGGCATCCCTGAGACCTTGACCCCAGAGCTGCTGAGACTCGGCCTCAAAAAATAAACTAGGGCCCAGAGAGATGGCCCAGCAACTAAGAACACATACTGCTTTTGCAGAGACCCAGGTTTGGTTCCCATCACCCCACACCACACGGTCATCCATCACCTGTATGTAACTCTTAACCCTAGGGGAATCTACCCCTCTGGCCCCCTGAGGCAGCTTACTTAGTGTACAGACACACAAACACTTATTTAAAAATAAGTATACCTATTGCCTTTAAATATCTAATCTCTGATACTCTTGTGGACCGCAAACAAAGTGATGGCACGTCACCTGCGCTGTTTGTTTGTTCAGCCAGCTGTTGACAGGTGTGTGTGTATTGTTTGCGGCATGAGACTGCTAAAATTTCCCCGTGAACATTGACTACAAGTTGTAGGGTTATATAGCTCCTTTTCTTTTGAATAGTTTGAAGGAGGCATTGCTGGTGCCTGGAGAAGCCATAACTCCCATCACTCGGGTTTAATGTGCTTAAATTTTGTCCGTTTCACCTAAGCTATCATGTCTATAGACCTGAAATTCACATTATAACCTTACTCTTGGTGTATGTATCTCAGGGTATGTATACCAACAGCATATCCCCTCTTCCAGGACTCTCTTCCTAAAGTGTAATTGTGAAGCAGTTATGGGATTCTTTGGTAGGTTGGCAACCTTTGTGTCTTTTT

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CAGCATATCCCCTCTTCCAGG

59.65

AAGATCACCAACCACGGACC

59.96

156

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CAGCATATCCCCTCTTCCAGG

59.65

TCACCAACCACGGACCTCTA

60.18

152

PCR template sequence:

TACCAACAGCATATCCCCTCTTCCAGGACTCTCTTCCTAAAGTGTAATTGTGAAGCAGTTATGGGATTCTTTGGTAGGTTGGCAACCTTTGTGTCTTTTTGTAAGTAGACGGCATCTGCATGGGGCTCACAGGGTAGTTAGAGGTCCGTGGTTGGTGATCTTGTAGGAAAAATAGTATCTTAATACCAGAATTTTACTAT

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

12

Interacting miRNAs (#binding sites)

mmu-miR-141-3p(1), mmu-miR-326-3p(1), mmu-miR-10b-5p(1), mmu-miR-10a-5p(1), mmu-miR-495-3p(1), mmu-miR-125a-5p(1), mmu-miR-466d-3p(1), mmu-miR-1198-5p(1), mmu-miR-344d-3p(1), mmu-miR-207(1), mmu-miR-452-3p(1), mmu-miR-466b-3p(1)

siRNAs for circular RNA silencing
Junction sequence

TTTGTGTCTTTTTGTAAGTAGACGGC

siRNA sets

TACTTACAAAAAGACACAA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

NA

NA

NA

NA

NA

ORF sequence:

NA

Peptide sequence:

NA

IRESfinder result

IRESfinder score

0.752231834

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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Institute of Life sciences, Bhubaneswar, India

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