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mmu_circAtf6_397

Basic information of circular RNA
PanCircBase ID:

mmu_circAtf6_397

mm39_Chr. Position ID:

chr1|170614914|170622339|-

Gene name:

Atf6

Transcript:

ENSMUST00000027974.7

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

14,13,12,11

Exon/intron offsets:

0,1262,6611,7311

Genomic length:

7425

Exon/intron sizes in nt:

11,56,81,00,114

Flanking exon/introns:

chr1:170574759-170614914|chr1:170622339-170627182

Splice length:

397

Other database IDs:

CIRCpedia: MMU_CIRCpedia_11812, circAtlas: mmu-Atf6_0022

circBase: hsa_circ_0110996, circAtlas: hsa-ATF6_0010, CIRCpedia: HSA_CIRCpedia_140040

Human Ortholog IDs:
Mature spliced Sequence:

CTATGATCACTCTGTGTCCAATGACAAAGCTTTAATGGTGCTAAGTGAAGAGCCATTGCTTTATATGCCTCCACCTCCATGTCAACCCCTGATTAACACAACAGAGTCTCTCAGGTTGAACCATGAACTTCGAGGCTGGGTTCATAGACATGAAGTGGAAAGGACCAAATCTAGAAGAATGACAAATAGCCAACAGAAAGCCCGCATTCTCCAGGGTGCTCTGGAACAGGGCTCTAATTCTCAGCTGATGGCTGTCCAGTACACAGAAACCACTAGCATCAGTAGGAATTCTGGGAGTGAGCTGCAAGTGTATTACGCCTCCCCTGGAAGTTACCAAGGCTTCTTTGACGCCATCCGCAGGAGGGGAGATACGTTTTACGTTGTCTCATTTCGAAGG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TGTATTACGCCTCCCCTGGA

60.03

GGTTGACATGGAGGTGGAGG

60.04

176

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TGTATTACGCCTCCCCTGGA

60.03

GGGTTGACATGGAGGTGGAG

60.04

177

PCR template sequence:

TGAGCTGCAAGTGTATTACGCCTCCCCTGGAAGTTACCAAGGCTTCTTTGACGCCATCCGCAGGAGGGGAGATACGTTTTACGTTGTCTCATTTCGAAGGCTATGATCACTCTGTGTCCAATGACAAAGCTTTAATGGTGCTAAGTGAAGAGCCATTGCTTTATATGCCTCCACCTCCATGTCAACCCCTGATTAACACA

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-140-5p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-340-5p(1)

siRNAs for circular RNA silencing
Junction sequence

CTCATTTCGAAGGCTATGATCACTCT

siRNA sets

AGAGTGATCATAGCCTTCG,GAGTGATCATAGCCTTCGA,GATCATAGCCTTCGAAATG

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCATF6_397_ORF_1

0.7407

0.086894014

0.296053799

369

ORF sequence:

ATGGTGCTAAGTGAAGAGCCATTGCTTTATATGCCTCCACCTCCATGTCAACCCCTGATTAACACAACAGAGTCTCTCAGGTTGAACCATGAACTTCGAGGCTGGGTTCATAGACATGAAGTGGAAAGGACCAAATCTAGAAGAATGACAAATAGCCAACAGAAAGCCCGCATTCTCCAGGGTGCTCTGGAACAGGGCTCTAATTCTCAGCTGATGGCTGTCCAGTACACAGAAACCACTAGCATCAGTAGGAATTCTGGGAGTGAGCTGCAAGTGTATTACGCCTCCCCTGGAAGTTACCAAGGCTTCTTTGACGCCATCCGCAGGAGGGGAGATACGTTTTACGTTGTCTCATTTCGAAGGCTATGA

Peptide sequence:

MVLSEEPLLYMPPPPCQPLINTTESLRLNHELRGWVHRHEVERTKSRRMTNSQQKARILQGALEQGSNSQLMAVQYTETTSISRNSGSELQVYYASPGSYQGFFDAIRRRGDTFYVVSFRRL

IRESfinder result

IRESfinder score

0.499639634

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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