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mmu_circArid1b_508

Basic information of circular RNA
PanCircBase ID:

mmu_circArid1b_508

mm39_Chr. Position ID:

chr17|5329477|5341558|+

Gene name:

Arid1b

Transcript:

ENSMUST00000092723.11

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

2

Exon/intron indexes:

7,8

Exon/intron offsets:

0,11753

Genomic length:

12081

Exon/intron sizes in nt:

180,328

Flanking exon/introns:

chr17:5314396-5329477|chr17:5341558-5356023

Splice length:

508

Other database IDs:

circBase: mmu_circ_0006834, CIRCpedia: MMU_CIRCpedia_22437, circAtlas: mmu-Arid1b_0010

circAtlas: hsa-ARID1B_0017

Human Ortholog IDs:
Mature spliced Sequence:

GTTTTATGACAGGCACTCAGAGAAACCCTCAGATGTCTCAGTACGGACCTCAGCAGACAGGACCATCCATGTCGCCTCACCCATCTCCTGGGGGCCAGATGCATCCTGGGATCAGTAACTTTCAGCAGAGTAACTCAAGTGGCACGTACGGCCCACAGATGAGCCAGTATGGACCCCAAGGCAACTACTCCAGAACCCCAACATATAGCGGGGTACCCAGTGCAAGCTACAGCGGCCCAGGGCCCGGTATGGGCATCAATGCCAACAACCAGATGCATGGACAAGGGCCAGCCCAGCCATGTGGTGCTATGCCCCTGGGACGAATGCCTTCAGCTGGGATGCAGAACAGACCATTTCCTGGAACCATGAGCAGCGTCACCCCCAGTTCTCCTGGCATGTCTCAACAGGGAGGGCCAGGAATGGGCCCACCAATGCCCACTGTGAACCGGAAGGCCCAGGAAGCTGCCGCAGCTGTGATGCAGGCTGCTGCAAACTCAGCACAAAGCAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CACCAATGCCCACTGTGAAC

59.69

GTCTGCTGAGGTCCGTACTG

59.83

140

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CACCAATGCCCACTGTGAAC

59.69

CTGTCTGCTGAGGTCCGTAC

59.83

142

PCR template sequence:

GAGGGCCAGGAATGGGCCCACCAATGCCCACTGTGAACCGGAAGGCCCAGGAAGCTGCCGCAGCTGTGATGCAGGCTGCTGCAAACTCAGCACAAAGCAGGTTTTATGACAGGCACTCAGAGAAACCCTCAGATGTCTCAGTACGGACCTCAGCAGACAGGACCATCCATGTCGCCTCACCCATCTCCTGGGGGCCAGAT

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

5

Interacting miRNAs (#binding sites)

mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-328-3p(1), mmu-miR-324-5p(1), mmu-miR-673-5p(1)

siRNAs for circular RNA silencing
Junction sequence

CAGCACAAAGCAGGTTTTATGACAGG

siRNA sets

TAAAACCTGCTTTGTGCTG, ATAAAACCTGCTTTGTGCT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCARID1B_508_ORF_1

0.6268

0.220642107

0.782819678

621

ORF sequence:

ATGACAGGCACTCAGAGAAACCCTCAGATGTCTCAGTACGGACCTCAGCAGACAGGACCATCCATGTCGCCTCACCCATCTCCTGGGGGCCAGATGCATCCTGGGATCAGTAACTTTCAGCAGAGTAACTCAAGTGGCACGTACGGCCCACAGATGAGCCAGTATGGACCCCAAGGCAACTACTCCAGAACCCCAACATATAGCGGGGTACCCAGTGCAAGCTACAGCGGCCCAGGGCCCGGTATGGGCATCAATGCCAACAACCAGATGCATGGACAAGGGCCAGCCCAGCCATGTGGTGCTATGCCCCTGGGACGAATGCCTTCAGCTGGGATGCAGAACAGACCATTTCCTGGAACCATGAGCAGCGTCACCCCCAGTTCTCCTGGCATGTCTCAACAGGGAGGGCCAGGAATGGGCCCACCAATGCCCACTGTGAACCGGAAGGCCCAGGAAGCTGCCGCAGCTGTGATGCAGGCTGCTGCAAACTCAGCACAAAGCAGGTTTTATGACAGGCACTCAGAGAAACCCTCAGATGTCTCAGTACGGACCTCAGCAGACAGGACCATCCATGTCGCCTCACCCATCTCCTGGGGGCCAGATGCATCCTGGGATCAGTAA

Peptide sequence:

MTGTQRNPQMSQYGPQQTGPSMSPHPSPGGQMHPGISNFQQSNSSGTYGPQMSQYGPQGNYSRTPTYSGVPSASYSGPGPGMGINANNQMHGQGPAQPCGAMPLGRMPSAGMQNRPFPGTMSSVTPSSPGMSQQGGPGMGPPMPTVNRKAQEAAAAVMQAAANSAQSRFYDRHSEKPSDVSVRTSADRTIHVASPISWGPDASWDQ

IRESfinder result

IRESfinder score

0.163509485

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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