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mmu_circAtf7ip_428

Basic information of circular RNA
PanCircBase ID:

mmu_circAtf7ip_428

mm39_Chr. Position ID:

chr6|136540757|136548536|+

Gene name:

Atf7ip

Transcript:

ENSMUST00000032335.13

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

3,4,5,6

Exon/intron offsets:

0,1257,2888,7713

Genomic length:

7779

Exon/intron sizes in nt:

78,146,138,66

Flanking exon/introns:

chr6:136538437-136540757|chr6:136548536-136552242

Splice length:

428

Other database IDs:

circBase: mmu_circ_0013136, CIRCpedia: MMU_CIRCpedia_8436, circAtlas: mmu-Atf7ip_0017

circAtlas: hsa-ATF7IP_0030

Human Ortholog IDs:
Mature spliced Sequence:

AGGGAGAAAAGAGTGAGAAGGACGGCAAAGCTGAGGAAGAGGAGCGAGTTCCAGCCGAGGAGCAGCCACCTGTGAGAAATGAGTTTTCTAGACGAAAACGTTCTAAGTCAGAAGACATGGACAGTGTAGAGTCCAAACGCCGGCGATATATGGATGAAGAATACGAGGCTGAGTTTCAAGTAAAGATCACAGCTAAAGGTGACATCAACCAGAAGCTTCAAAAGGTCATACAGTGGTTGCTACAAGAAAAACTGTGTGCCCTACAGTGTGCTGTGTTTGATAAGACGTTGGCAGAATTAAAAACTCGAGTGGAGAAGATAGAGTGCAACAAGAGGCATAAGGCAGTGCTCACCGAGCTGCAGGCCAAGATAGCCAGGTTAACCAAACGTTTTGGAGCAGCCAAAGATGATCTTAAGAAAAGACAAGAA

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CATAAGGCAGTGCTCACCGA

60.11

CTGGAACTCGCTCCTCTTCC

59.83

147

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

ATAAGGCAGTGCTCACCGAG

59.82

CTGGAACTCGCTCCTCTTCC

59.83

146

PCR template sequence:

CAAGAGGCATAAGGCAGTGCTCACCGAGCTGCAGGCCAAGATAGCCAGGTTAACCAAACGTTTTGGAGCAGCCAAAGATGATCTTAAGAAAAGACAAGAAAGGGAGAAAAGAGTGAGAAGGACGGCAAAGCTGAGGAAGAGGAGCGAGTTCCAGCCGAGGAGCAGCCACCTGTGAGAAATGAGTTTTCTAGACGAAAACG

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-9-5p(1), mmu-miR-146a-5p(1), mmu-miR-433-5p(1), mmu-miR-146b-5p(1)

siRNAs for circular RNA silencing
Junction sequence

GAAAAGACAAGAAAGGGAGAAAAGAG

siRNA sets

CTTTTCTCCCTTTCTTGTC, TTTTCTCCCTTTCTTGTCT, TCTTTTCTCCCTTTCTTGT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCATF7IP_428_ORF_1

1.009

0.274825024

0.629391868

387

ORF sequence:

ATGGACAGTGTAGAGTCCAAACGCCGGCGATATATGGATGAAGAATACGAGGCTGAGTTTCAAGTAAAGATCACAGCTAAAGGTGACATCAACCAGAAGCTTCAAAAGGTCATACAGTGGTTGCTACAAGAAAAACTGTGTGCCCTACAGTGTGCTGTGTTTGATAAGACGTTGGCAGAATTAAAAACTCGAGTGGAGAAGATAGAGTGCAACAAGAGGCATAAGGCAGTGCTCACCGAGCTGCAGGCCAAGATAGCCAGGTTAACCAAACGTTTTGGAGCAGCCAAAGATGATCTTAAGAAAAGACAAGAAAGGGAGAAAAGAGTGAGAAGGACGGCAAAGCTGAGGAAGAGGAGCGAGTTCCAGCCGAGGAGCAGCCACCTGTGA

Peptide sequence:

MDSVESKRRRYMDEEYEAEFQVKITAKGDINQKLQKVIQWLLQEKLCALQCAVFDKTLAELKTRVEKIECNKRHKAVLTELQAKIARLTKRFGAAKDDLKKRQEREKRVRRTAKLRKRSEFQPRSSHL

IRESfinder result

IRESfinder score

0.294817948

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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