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mmu_circTomm34_571

Basic information of circular RNA
PanCircBase ID:

mmu_circTomm34_571

mm39_Chr. Position ID:

chr2|163900585|163908589|-

Gene name:

Tomm34

Transcript:

ENSMUST00000018466.4

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

5,4,3,2

Exon/intron offsets:

0,2173,6226,7904

Genomic length:

8004

Exon/intron sizes in nt:

1,48,17,01,53,100

Flanking exon/introns:

chr2:163896747-163900585|chr2:163908589-163912386

Splice length:

571

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

GTTCTGCAGACCCCGAAGAAGAAAGTGTTCTGTACTCCAACCGTGCAGCGTGCTACTTGAAGGATGGGAACTGCACAGATTGCATCAAAGATTGCACTTCCGCGCTGGCCTTGGTTCCCTTCAGCATCAAGCCCTTGCTGCGCAGAGCATCTGCATATGAAGCCCTGGAGAAGTACGCCCTGGCCTACGTTGACTATAAGACTGTGCTGCAGATCGATAACAGTGTGGCATCCGCCCTGGAAGGCATCAACAGAATAACCAGAGCTCTCATGGACTCCCTGGGACCTGAGTGGCGCCTGAAGCTGCCCCCTATCCCTGTGGTGCCTGTTTCAGCCCAGAAGAGATGGAATTCCTTGCCTTCAGATAACCACAAAGAGACAGCTAAAACCAAATCCAAAGAAGCCACAGCTACGAAGAGCAGAGTGCCTTCTGCTGGGGATGTGGAGAGAGCCAAAGCTCTGAAGGAAGAAGGCAATGACCTTGTAAAGAAGGGCAACCATAAGAAAGCTATTGAGAAGTACAGTGAGAGCCTCTTGTGTAGTAGCCTGGAGTCTGCCACATACAGCAACAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TGAGAAGTACAGTGAGAGCCTC

58.91

ATCTGTGCAGTTCCCATCCT

58.71

140

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TGAGAAGTACAGTGAGAGCCT

57.84

ATCTGTGCAGTTCCCATCCT

58.71

140

PCR template sequence:

GCAATGACCTTGTAAAGAAGGGCAACCATAAGAAAGCTATTGAGAAGTACAGTGAGAGCCTCTTGTGTAGTAGCCTGGAGTCTGCCACATACAGCAACAGGTTCTGCAGACCCCGAAGAAGAAAGTGTTCTGTACTCCAACCGTGCAGCGTGCTACTTGAAGGATGGGAACTGCACAGATTGCATCAAAGATTGCACTTC

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

4

Interacting miRNAs (#binding sites)

mmu-miR-130a-3p(1), mmu-miR-130b-3p(1), mmu-miR-297a-5p(1), mmu-miR-207(1)

siRNAs for circular RNA silencing
Junction sequence

CATACAGCAACAGGTTCTGCAGACCC

siRNA sets

GGTCTGCAGAACCTGTTGC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCTOMM34_571_ORF_1

0.5857

0.155235761

0.447193739

462

ORF sequence:

ATGGACTCCCTGGGACCTGAGTGGCGCCTGAAGCTGCCCCCTATCCCTGTGGTGCCTGTTTCAGCCCAGAAGAGATGGAATTCCTTGCCTTCAGATAACCACAAAGAGACAGCTAAAACCAAATCCAAAGAAGCCACAGCTACGAAGAGCAGAGTGCCTTCTGCTGGGGATGTGGAGAGAGCCAAAGCTCTGAAGGAAGAAGGCAATGACCTTGTAAAGAAGGGCAACCATAAGAAAGCTATTGAGAAGTACAGTGAGAGCCTCTTGTGTAGTAGCCTGGAGTCTGCCACATACAGCAACAGGTTCTGCAGACCCCGAAGAAGAAAGTGTTCTGTACTCCAACCGTGCAGCGTGCTACTTGAAGGATGGGAACTGCACAGATTGCATCAAAGATTGCACTTCCGCGCTGGCCTTGGTTCCCTTCAGCATCAAGCCCTTGCTGCGCAGAGCATCTGCATATGA

Peptide sequence:

MDSLGPEWRLKLPPIPVVPVSAQKRWNSLPSDNHKETAKTKSKEATATKSRVPSAGDVERAKALKEEGNDLVKKGNHKKAIEKYSESLLCSSLESATYSNRFCRPRRRKCSVLQPCSVLLEGWELHRLHQRLHFRAGLGSLQHQALAAQSICI

IRESfinder result

IRESfinder score

0.558142696

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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