top of page

mmu_circAp4e1_401

Basic information of circular RNA
PanCircBase ID:

mmu_circAp4e1_401

mm39_Chr. Position ID:

chr2|126875449|126879779|+

Gene name:

Ap4e1

Transcript:

ENSMUST00000110394.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

3

Exon/intron indexes:

6,7,8

Exon/intron offsets:

0,1514,4256

Genomic length:

4330

Exon/intron sizes in nt:

160,167,74

Flanking exon/introns:

chr2:126870213-126875449|chr2:126879779-126885340

Splice length:

401

Other database IDs:

circAtlas: mmu-Ap4e1_0001

circAtlas: hsa-AP4E1_0011, CIRCpedia: HSA_CIRCpedia_83202

Human Ortholog IDs:
Mature spliced Sequence:

GGAGATTATACGAAGAAAAGCAGTTCTGGCATTATACAAATTTTACCTCATTGCCCCCAATCAAGTACAGCACATCCACACTAAATTTCGGAAAGCGCTTTGTGACAGAGATGTTGGGGTCATGGCTGCCTCTTTGCACATATACCTTAGGATGATTAAGGAAAATGCTTCTGGCTATAAAGACTTGACGGAGAGTTTTGTAACAATTTTAAAGCAGGTGGTGGGCGGGAAGCTCCCGGTAGAGTTCAGTTACCACAGCGTGCCAGCACCATGGTTACAGATTCAGCTCCTGAGAATACTGGGACTGCTGGGGAAAGACGATGAAAGGACAAGTGAATTAATGTATGATGTTCTTGATGAATCCTTACGAAGAGCCGAGTTAAATCACAATGTCACTTACG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

ACTGCTGGGGAAAGACGATG

60.04

GCTGTACTTGATTGGGGGCA

60.32

169

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

ACTGCTGGGGAAAGACGATG

60.04

TGCTGTACTTGATTGGGGGC

60.32

170

PCR template sequence:

GGACTGCTGGGGAAAGACGATGAAAGGACAAGTGAATTAATGTATGATGTTCTTGATGAATCCTTACGAAGAGCCGAGTTAAATCACAATGTCACTTACGGGAGATTATACGAAGAAAAGCAGTTCTGGCATTATACAAATTTTACCTCATTGCCCCCAATCAAGTACAGCACATCCACACTAAATTTCGGAAAGCGCTT

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-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7c-5p(1), mmu-miR-98-5p(1), mmu-miR-350-3p(1)

siRNAs for circular RNA silencing
Junction sequence

AATGTCACTTACGGGAGATTATACGA

siRNA sets

TATAATCTCCCGTAAGTGA,ATAATCTCCCGTAAGTGAC,TAATCTCCCGTAAGTGACA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCAP4E1_401_ORF_1

0.7288

0.048469091

0.361398055

435

ORF sequence:

ATGGCTGCCTCTTTGCACATATACCTTAGGATGATTAAGGAAAATGCTTCTGGCTATAAAGACTTGACGGAGAGTTTTGTAACAATTTTAAAGCAGGTGGTGGGCGGGAAGCTCCCGGTAGAGTTCAGTTACCACAGCGTGCCAGCACCATGGTTACAGATTCAGCTCCTGAGAATACTGGGACTGCTGGGGAAAGACGATGAAAGGACAAGTGAATTAATGTATGATGTTCTTGATGAATCCTTACGAAGAGCCGAGTTAAATCACAATGTCACTTACGGGAGATTATACGAAGAAAAGCAGTTCTGGCATTATACAAATTTTACCTCATTGCCCCCAATCAAGTACAGCACATCCACACTAAATTTCGGAAAGCGCTTTGTGACAGAGATGTTGGGGTCATGGCTGCCTCTTTGCACATATACCTTAGGATGA

Peptide sequence:

MAASLHIYLRMIKENASGYKDLTESFVTILKQVVGGKLPVEFSYHSVPAPWLQIQLLRILGLLGKDDERTSELMYDVLDESLRRAELNHNVTYGRLYEEKQFWHYTNFTSLPPIKYSTSTLNFGKRFVTEMLGSWLPLCTYTLG

IRESfinder result

IRESfinder score

0.553268413

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

bottom of page