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mmu_circAtf1_340

Basic information of circular RNA
PanCircBase ID:

mmu_circAtf1_340

mm39_Chr. Position ID:

chr15|100151974|100152394|+

Gene name:

Atf1

Transcript:

ENSMUST00000023769.11

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

2

Exon/intron indexes:

5,6

Exon/intron offsets:

0,260

Genomic length:

420

Exon/intron sizes in nt:

180,160

Flanking exon/introns:

chr15:100150080-100151974|chr15:100152394-100157695

Splice length:

340

Other database IDs:

CIRCpedia: MMU_CIRCpedia_223880, circAtlas: mmu-Atf1_0001

circBase: hsa_circ_0026285, circAtlas: hsa-ATF1_0001, CIRCpedia: HSA_CIRCpedia_8753

Human Ortholog IDs:
Mature spliced Sequence:

TTGCCATTGCCCCAAACGGAGCCTTACAGTTGGCCAGTCCAAGCACGGATGGAGTGCAGGCACTGCAGACATTAACCATGACAAATTCAAGCAGTACTCAGCAGGGGACGATCCTCCAGTATGCACAGACCTCTGACGGACAGCAGATACTCGTCCCGAGCAACCAGGTGGTTGTACAGACTGCATCAGGAGATATGCAGACCTACCAGATCCGTACCACGCCGTCTGCCACGTCTCTCCCGCAGACCGTGGTGATGACTTCTCCTGTGACTCTTGCATCTCAGACAACAAAGACAGATGACCCTCAACTAAGAAGAGAAATACGACTGATGAAAAACAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GCAGACCGTGGTGATGACTT

60.32

TGGACTGGCCAACTGTAAGG

59.6

140

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GCAGACCGTGGTGATGACTT

60.32

CTCCATCCGTGCTTGGACTG

60.74

153

PCR template sequence:

CGCAGACCGTGGTGATGACTTCTCCTGTGACTCTTGCATCTCAGACAACAAAGACAGATGACCCTCAACTAAGAAGAGAAATACGACTGATGAAAAACAGTTGCCATTGCCCCAAACGGAGCCTTACAGTTGGCCAGTCCAAGCACGGATGGAGTGCAGGCACTGCAGACATTAACCATGACAAATTCAAGCAGTACTCA

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

2

Interacting miRNAs (#binding sites)

mmu-miR-185-5p(1), mmu-miR-193b-3p(1)

siRNAs for circular RNA silencing
Junction sequence

TGATGAAAAACAGTTGCCATTGCCCC

siRNA sets

CAATGGCAACTGTTTTTCA, AATGGCAACTGTTTTTCAT, ATGGCAACTGTTTTTCATC

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCATF1_340_ORF_1

0.8943

0.212003749

0.53746966

399

ORF sequence:

ATGACAAATTCAAGCAGTACTCAGCAGGGGACGATCCTCCAGTATGCACAGACCTCTGACGGACAGCAGATACTCGTCCCGAGCAACCAGGTGGTTGTACAGACTGCATCAGGAGATATGCAGACCTACCAGATCCGTACCACGCCGTCTGCCACGTCTCTCCCGCAGACCGTGGTGATGACTTCTCCTGTGACTCTTGCATCTCAGACAACAAAGACAGATGACCCTCAACTAAGAAGAGAAATACGACTGATGAAAAACAGTTGCCATTGCCCCAAACGGAGCCTTACAGTTGGCCAGTCCAAGCACGGATGGAGTGCAGGCACTGCAGACATTAACCATGACAAATTCAAGCAGTACTCAGCAGGGGACGATCCTCCAGTATGCACAGACCTCTGA

Peptide sequence:

MTNSSSTQQGTILQYAQTSDGQQILVPSNQVVVQTASGDMQTYQIRTTPSATSLPQTVVMTSPVTLASQTTKTDDPQLRREIRLMKNSCHCPKRSLTVGQSKHGWSAGTADINHDKFKQYSAGDDPPVCTDL

IRESfinder result

IRESfinder score

0.344796025

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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