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mmu_ciRabl6_1016

Basic information of circular RNA
PanCircBase ID:

mmu_ciRabl6_1016

mm39_Chr. Position ID:

chr2|25491416|25492432|-

Gene name:

Rabl6

Transcript:

ENSMUST00000058137.9

CircRNA type:

Circular intronic (ci)RNA

Exon/Intron count:

1

Exon/intron indexes:

2

Exon/intron offsets:

0

Genomic length:

1016

Exon/intron sizes in nt:

1016

Flanking exon/introns:

chr2:25491410-25492432

Splice length:

1016

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

GTGAGTTCAAGGCCAATAATAGTTCAATGCCACTTTTCCCCTGTACAGTATAGTAGTATCCTGCCTTCCTGGCTCCTAGAAGGTACTTTCTGAAACTGAGAAAATACTACCCATGTGAGAGGCCCCATTAATTAAGGTTGCATGTGAATCAGCCCTTCTGGGTTTTGAATCTGACATTTCTCCTCTGTGGTGCCTCAGGCCCAGGATACTCATGGTTACAAGTAAGGAAGCAAGGACATACCTTCAAAGACTAGAATTCCCTGGCCACCTCTAGGAGCAGATCCACCCATACACATCAGCAACATACATGGCTGCTTTGTCTGATAGGAATGCATTCTGTGATCCATGGCAAGTGCTCACCCCTGGGGAACAGAGTGACAATTTTAACTCTTGTCTTCCCCTTCTGTGTTCTGGGGTCTCCACCATCCTTACAGCCCCATTAGCCCTTAGGACATCCTAAAAATGGAGAATTGCTACTGAGGAGGGGTTGAAGAGTTAACAAGAACTTGGAAAATGGTTTCTGTTCTCATGCAACTTAAGTCTAGTATCAGAGAAAGCCTTAGGAGTCTATGGGCCAGGTAGGCTGAGGACGGTGATGTAGGTGTCGGGGCTACAACTGACCTGGGCCTGCTCAGGTGACCCATCACAGCTCTGGCCTTTGCAACTGACCTGCGTTCTCACTGAGTACTGGCCAGTCAGGTAAAGGAGTAGTAGGCTTGGGGGAGATGTGACTTGGACAGCTGTGCTGTTTCCTCATCTGCCCAGAGAGTGAGCATCCGCTAGGGCACCTGAAGTGGCCCAGGGACCCACAGGCTTCTGAGTGTGAGTTGTTATGTGATGGCTTTGTCTGTGGGCTAATATATGCATTGCTCATGCCAGGGCCTGGAGGAATAGCCCTGAAAACCCTACAGCATGTATTGCAGAGGCCCCAGGGAGCTAGTAATACCAAATGCCCCTGGCCCCATTTGGGATCCTAGAAGGAATGATACAATGCACTAATTTGAGAGTTTTTCTTG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GGCCCCAGGGAGCTAGTAAT

60.77

CCTTCTAGGAGCCAGGAAGG

58.87

175

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GGCCCCAGGGAGCTAGTAAT

60.77

CTGTACAGGGGAAAAGTGGCA

60.2

140

PCR template sequence:

ATTGCAGAGGCCCCAGGGAGCTAGTAATACCAAATGCCCCTGGCCCCATTTGGGATCCTAGAAGGAATGATACAATGCACTAATTTGAGAGTTTTTCTTGGTGAGTTCAAGGCCAATAATAGTTCAATGCCACTTTTCCCCTGTACAGTATAGTAGTATCCTGCCTTCCTGGCTCCTAGAAGGTACTTTCTGAAACTGAG

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

10

Interacting miRNAs (#binding sites)

mmu-miR-7b-5p(1), mmu-miR-223-3p(1), mmu-miR-33-5p(1), mmu-miR-7a-5p(1), mmu-miR-136-5p(1), mmu-miR-297a-5p(1), mmu-miR-342-3p(1), mmu-miR-1187(1), mmu-miR-3087-3p(1), mmu-miR-3470b(1)

siRNAs for circular RNA silencing
Junction sequence

AGAGTTTTTCTTGGTGAGTTCAAGGC

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRABL6_1016_ORF_3

0.7033

-0.244090911

0.016067769

120

ORF sequence:

ATGCCCCTGGCCCCATTTGGGATCCTAGAAGGAATGATACAATGCACTAATTTGAGAGTTTTTCTTGGTGAGTTCAAGGCCAATAATAGTTCAATGCCACTTTTCCCCTGTACAGTATAG

Peptide sequence:

MPLAPFGILEGMIQCTNLRVFLGEFKANNSSMPLFPCTV

IRESfinder result

IRESfinder score

0.62018352

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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