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mmu_circAp3d1_452

Basic information of circular RNA
PanCircBase ID:

mmu_circAp3d1_452

mm39_Chr. Position ID:

chr10|80559366|80563823|-

Gene name:

Ap3d1

Transcript:

ENSMUST00000020420.9

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

4

Exon/intron indexes:

8,7,6,5

Exon/intron offsets:

0,158,3521,4349

Genomic length:

4457

Exon/intron sizes in nt:

74,14,01,30,108

Flanking exon/introns:

chr10:80558796-80559366|chr10:80563823-80565811

Splice length:

452

Other database IDs:

​

circAtlas: hsa-SCAF8_0001

Human Ortholog IDs:
Mature spliced Sequence:

GACCTGAGCAGCCCCAGCCAGTACGACACTGGAGTGGCACTGACTGGTCTGTCCTGTTTTGTCACCCCAGATCTTGCCAGAGACCTGGCAAATGACATCATGACCCTGATGTCTCACACGAAGCCGTACATCAGGAAGAAGGCAGTGCTGATCATGTACAAAGTATTCCTCAAGTACCCAGAGTCGCTGCGTCCTGCCTTTCCCCGGCTTAAGGAGAAGCTGGAGGACCCAGACCCAGGGGTACAGTCTGCGGCTGTTAATGTCATCTGCGAGCTGGCACGCCGCAACCCTAAAAACTACCTGTCTCTGGCGCCACTGTTTTTCAAGCTCATGACATCCTCCACCAACAACTGGGTCCTCATCAAGATCATCAAGCTGTTCGGTGCCCTGACTCCTCTGGAGCCCAGGCTGGGCAAGAAGCTGATCGAGCCTCTCACCAACCTCATTCACAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TCATCAAGCTGTTCGGTGCC

60.96

GGCAAGATCTGGGGTGACAA

59.96

163

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TCATCAAGCTGTTCGGTGCC

60.96

CTCTGGCAAGATCTGGGGTG

60.11

167

PCR template sequence:

GGGTCCTCATCAAGATCATCAAGCTGTTCGGTGCCCTGACTCCTCTGGAGCCCAGGCTGGGCAAGAAGCTGATCGAGCCTCTCACCAACCTCATTCACAGGACCTGAGCAGCCCCAGCCAGTACGACACTGGAGTGGCACTGACTGGTCTGTCCTGTTTTGTCACCCCAGATCTTGCCAGAGACCTGGCAAATGACATCA

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

6

Interacting miRNAs (#binding sites)

mmu-miR-199a-5p(1), mmu-miR-31-5p(1), mmu-miR-196a-5p(1), mmu-miR-382-5p(1), mmu-miR-129-5p(1), mmu-miR-296-3p(1)

siRNAs for circular RNA silencing
Junction sequence

ACCTCATTCACAGGACCTGAGCAGCC

siRNA sets

CAGGTCCTGTGAATGAGGT, TCAGGTCCTGTGAATGAGG

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAP3D1_452_ORF_1

1.2539

0.448841298

0.817658325

360

ORF sequence:

ATGACCCTGATGTCTCACACGAAGCCGTACATCAGGAAGAAGGCAGTGCTGATCATGTACAAAGTATTCCTCAAGTACCCAGAGTCGCTGCGTCCTGCCTTTCCCCGGCTTAAGGAGAAGCTGGAGGACCCAGACCCAGGGGTACAGTCTGCGGCTGTTAATGTCATCTGCGAGCTGGCACGCCGCAACCCTAAAAACTACCTGTCTCTGGCGCCACTGTTTTTCAAGCTCATGACATCCTCCACCAACAACTGGGTCCTCATCAAGATCATCAAGCTGTTCGGTGCCCTGACTCCTCTGGAGCCCAGGCTGGGCAAGAAGCTGATCGAGCCTCTCACCAACCTCATTCACAGGACCTGA

Peptide sequence:

MTLMSHTKPYIRKKAVLIMYKVFLKYPESLRPAFPRLKEKLEDPDPGVQSAAVNVICELARRNPKNYLSLAPLFFKLMTSSTNNWVLIKIIKLFGALTPLEPRLGKKLIEPLTNLIHRT

IRESfinder result

IRESfinder score

0.365924901

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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