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mmu_circAp4e1_721

Basic information of circular RNA
PanCircBase ID:

mmu_circAp4e1_721

mm39_Chr. Position ID:

chr2|126856089|126879779|+

Gene name:

Ap4e1

Transcript:

ENSMUST00000110394.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

6

Exon/intron indexes:

3,4,5,6,7,8

Exon/intron offsets:

0,5116,14002,19360,20874,23616

Genomic length:

23690

Exon/intron sizes in nt:

124,74,122,160,167,74

Flanking exon/introns:

chr2:126853782-126856089|chr2:126879779-126885340

Splice length:

721

Other database IDs:

circAtlas: mmu-Ap4e1_0007

Human Ortholog IDs:
Mature spliced Sequence:

AAAACGATGAAGGAATGTATGGTGAGACTTATATACTGTGAGATGCTTGGATACGATGCTTCTTTTGGTTATATACATGCAATCAAGTTGGCCCAACAAGGAAACCTCTTAGAAAAAAGAGTGGGTTATTTGGCTGTTTCTTTATTTCTACATGAAAGTCATGAACTTTTGCTTCTCCTTGTGAATACAGTGGTAAAGGACCTGCAGAGCACTAATCTGGTAGAAGTATGTATGGCACTTACTGTTGTCAGCCAGATTTTCCCTCGAGAAATGATTCCAGCCGTTCTTCCACTAATAGAAGATAAACTTCAACATTCTAAGGAGATTATACGAAGAAAAGCAGTTCTGGCATTATACAAATTTTACCTCATTGCCCCCAATCAAGTACAGCACATCCACACTAAATTTCGGAAAGCGCTTTGTGACAGAGATGTTGGGGTCATGGCTGCCTCTTTGCACATATACCTTAGGATGATTAAGGAAAATGCTTCTGGCTATAAAGACTTGACGGAGAGTTTTGTAACAATTTTAAAGCAGGTGGTGGGCGGGAAGCTCCCGGTAGAGTTCAGTTACCACAGCGTGCCAGCACCATGGTTACAGATTCAGCTCCTGAGAATACTGGGACTGCTGGGGAAAGACGATGAAAGGACAAGTGAATTAATGTATGATGTTCTTGATGAATCCTTACGAAGAGCCGAGTTAAATCACAATGTCACTTACG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

ACTGCTGGGGAAAGACGATG

60.04

AGCATCGTATCCAAGCATCTCA

59.63

158

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TGAATCCTTACGAAGAGCCGA

58.9

GTTGGGCCAACTTGATTGCA

59.61

141

PCR template sequence:

GGACTGCTGGGGAAAGACGATGAAAGGACAAGTGAATTAATGTATGATGTTCTTGATGAATCCTTACGAAGAGCCGAGTTAAATCACAATGTCACTTACGAAAACGATGAAGGAATGTATGGTGAGACTTATATACTGTGAGATGCTTGGATACGATGCTTCTTTTGGTTATATACATGCAATCAAGTTGGCCCAACAAG

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

10

Interacting miRNAs (#binding sites)

mmu-let-7a-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-let-7e-5p(1), mmu-let-7c-5p(1), mmu-miR-467b-5p(1), mmu-miR-98-5p(1), mmu-miR-410-3p(1), mmu-miR-344d-3p(1), mmu-miR-350-3p(1)

siRNAs for circular RNA silencing
Junction sequence

AATGTCACTTACGAAAACGATGAAGG

siRNA sets

CATCGTTTTCGTAAGTGAC,TTCATCGTTTTCGTAAGTG,CTTCATCGTTTTCGTAAGT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAP4E1_721_ORF_1

1.0042

0.029515598

0.897234397

756

ORF sequence:

ATGAAGGAATGTATGGTGAGACTTATATACTGTGAGATGCTTGGATACGATGCTTCTTTTGGTTATATACATGCAATCAAGTTGGCCCAACAAGGAAACCTCTTAGAAAAAAGAGTGGGTTATTTGGCTGTTTCTTTATTTCTACATGAAAGTCATGAACTTTTGCTTCTCCTTGTGAATACAGTGGTAAAGGACCTGCAGAGCACTAATCTGGTAGAAGTATGTATGGCACTTACTGTTGTCAGCCAGATTTTCCCTCGAGAAATGATTCCAGCCGTTCTTCCACTAATAGAAGATAAACTTCAACATTCTAAGGAGATTATACGAAGAAAAGCAGTTCTGGCATTATACAAATTTTACCTCATTGCCCCCAATCAAGTACAGCACATCCACACTAAATTTCGGAAAGCGCTTTGTGACAGAGATGTTGGGGTCATGGCTGCCTCTTTGCACATATACCTTAGGATGATTAAGGAAAATGCTTCTGGCTATAAAGACTTGACGGAGAGTTTTGTAACAATTTTAAAGCAGGTGGTGGGCGGGAAGCTCCCGGTAGAGTTCAGTTACCACAGCGTGCCAGCACCATGGTTACAGATTCAGCTCCTGAGAATACTGGGACTGCTGGGGAAAGACGATGAAAGGACAAGTGAATTAATGTATGATGTTCTTGATGAATCCTTACGAAGAGCCGAGTTAAATCACAATGTCACTTACGAAAACGATGAAGGAATGTATGGTGAGACTTATATACTGTGA

Peptide sequence:

MKECMVRLIYCEMLGYDASFGYIHAIKLAQQGNLLEKRVGYLAVSLFLHESHELLLLLVNTVVKDLQSTNLVEVCMALTVVSQIFPREMIPAVLPLIEDKLQHSKEIIRRKAVLALYKFYLIAPNQVQHIHTKFRKALCDRDVGVMAASLHIYLRMIKENASGYKDLTESFVTILKQVVGGKLPVEFSYHSVPAPWLQIQLLRILGLLGKDDERTSELMYDVLDESLRRAELNHNVTYENDEGMYGETYIL

IRESfinder result

IRESfinder score

0.624921481

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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