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mmu_circAp3b1_324

Basic information of circular RNA
PanCircBase ID:

mmu_circAp3b1_324

mm39_Chr. Position ID:

chr13|94539845|94545351|+

Gene name:

Ap3b1

Transcript:

ENSMUST00000022196.5

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

3

Exon/intron indexes:

4,5,6

Exon/intron offsets:

0,609,5439

Genomic length:

5506

Exon/intron sizes in nt:

96,161,67

Flanking exon/introns:

chr13:94531301-94539845|chr13:94545351-94554468

Splice length:

324

Other database IDs:

CIRCpedia: MMU_CIRCpedia_38088, circAtlas: mmu-Ap3b1_0053

circBase: hsa_circ_0129695, circAtlas: hsa-AP3B1_0015, CIRCpedia: HSA_CIRCpedia_101318

Human Ortholog IDs:
Mature spliced Sequence:

ATCAAGAAGTTGGTGTACGTTTACCTTGTCCGATATGCTGAAGAACAGCAGGACCTGGCTCTTCTGTCCATAAGCACTTTCCAGCGAGCTTTGAAGGACCCGAATCAACTAATCCGTGCAAGTGCCTTGAGAGTTTTGTCAAGTATTAGAGTGCCAATTATCGTGCCTGTCATGATGCTGGCTATTAAGGAGGCTTCAGCTGACCTGTCGCCATATGTTAGGAAGAATGCAGCCCATGCTATTCAGAAGCTGTACAGTCTTGACCCCGAGCAGAAGGAGATGTTAATTGAAGTCATTGAGAAGCTTCTGAAAGACAAGAGCACG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GTACAGTCTTGACCCCGAGC

60.11

GACAGAAGAGCCAGGTCCTG

59.75

141

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

GTACAGTCTTGACCCCGAGC

60.11

GTCCTTCAAAGCTCGCTGGA

60.32

172

PCR template sequence:

GAATGCAGCCCATGCTATTCAGAAGCTGTACAGTCTTGACCCCGAGCAGAAGGAGATGTTAATTGAAGTCATTGAGAAGCTTCTGAAAGACAAGAGCACGATCAAGAAGTTGGTGTACGTTTACCTTGTCCGATATGCTGAAGAACAGCAGGACCTGGCTCTTCTGTCCATAAGCACTTTCCAGCGAGCTTTGAAGGACC

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

8

Interacting miRNAs (#binding sites)

mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-106b-5p(1), mmu-miR-96-5p(1), mmu-miR-338-3p(1)

siRNAs for circular RNA silencing
Junction sequence

AGACAAGAGCACGATCAAGAAGTTGG

siRNA sets

TCTTGATCGTGCTCTTGTC, TTCTTGATCGTGCTCTTGT, AACTTCTTGATCGTGCTCT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAP3B1_324_ORF_1

1.1892

0.350845206

0.861746434

477

ORF sequence:

ATGATGCTGGCTATTAAGGAGGCTTCAGCTGACCTGTCGCCATATGTTAGGAAGAATGCAGCCCATGCTATTCAGAAGCTGTACAGTCTTGACCCCGAGCAGAAGGAGATGTTAATTGAAGTCATTGAGAAGCTTCTGAAAGACAAGAGCACGATCAAGAAGTTGGTGTACGTTTACCTTGTCCGATATGCTGAAGAACAGCAGGACCTGGCTCTTCTGTCCATAAGCACTTTCCAGCGAGCTTTGAAGGACCCGAATCAACTAATCCGTGCAAGTGCCTTGAGAGTTTTGTCAAGTATTAGAGTGCCAATTATCGTGCCTGTCATGATGCTGGCTATTAAGGAGGCTTCAGCTGACCTGTCGCCATATGTTAGGAAGAATGCAGCCCATGCTATTCAGAAGCTGTACAGTCTTGACCCCGAGCAGAAGGAGATGTTAATTGAAGTCATTGAGAAGCTTCTGAAAGACAAGAGCACG

Peptide sequence:

MMLAIKEASADLSPYVRKNAAHAIQKLYSLDPEQKEMLIEVIEKLLKDKSTIKKLVYVYLVRYAEEQQDLALLSISTFQRALKDPNQLIRASALRVLSSIRVPIIVPVMMLAIKEASADLSPYVRKNAAHAIQKLYSLDPEQKEMLIEVIEKLLKDKST

IRESfinder result

IRESfinder score

0.61220027

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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