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mmu_circArhgef38_312

Basic information of circular RNA
PanCircBase ID:

mmu_circArhgef38_312

mm39_Chr. Position ID:

chr3|132882131|132912841|-

Gene name:

Arhgef38

Transcript:

ENSMUST00000147041.10

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

2

Exon/intron indexes:

3,2

Exon/intron offsets:

0,30522

Genomic length:

30710

Exon/intron sizes in nt:

1,24,188

Flanking exon/introns:

chr3:132866627-132882131|chr3:132912841-132940388

Splice length:

312

Other database IDs:

CIRCpedia: MMU_CIRCpedia_7943, circAtlas: mmu-Arhgef38_0001

circAtlas: hsa-ARHGEF38_0002, CIRCpedia: HSA_CIRCpedia_357639

Human Ortholog IDs:
Mature spliced Sequence:

AAAAGATGACTCCACAGGCTGAGTGCTCCTCAGCAGAAACTCCCACCCCTGAGGATGAGCAACAAGTGGGACGGATGATGGCAAAGCGGGCCAAGATCATCAGGGAGCTGATACAGACGGAGAGGGATTACCTCACAGATCTAGAGCTGTGCCTTAGAGAAGTGGTCCAGCCACTGCGAAGCAAACAGATTGACAGGCTGGACGTGGAGGGCTTGTTTAGCAACATTGAATCTGTGCATCAAATATCAGCCAAGCTACTGTCCTTGCTGGAAGAGGCCACAACAGACGTGGAACCGGCCATGCAAGTAATCG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

GCCAAGCTACTGTCCTTGCT

60.32

CCATCATCCGTCCCACTTGT

59.75

145

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

AGCCAAGCTACTGTCCTTGC

60.32

CCATCATCCGTCCCACTTGT

59.75

146

PCR template sequence:

TTGTTTAGCAACATTGAATCTGTGCATCAAATATCAGCCAAGCTACTGTCCTTGCTGGAAGAGGCCACAACAGACGTGGAACCGGCCATGCAAGTAATCGAAAAGATGACTCCACAGGCTGAGTGCTCCTCAGCAGAAACTCCCACCCCTGAGGATGAGCAACAAGTGGGACGGATGATGGCAAAGCGGGCCAAGATCAT

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

1

Interacting miRNAs (#binding sites)

mmu-miR-5101(1)

siRNAs for circular RNA silencing
Junction sequence

ATGCAAGTAATCGAAAAGATGACTCC

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCARHGEF38_312_ORF_1

1.0533

0.381251913

0.938168428

618

ORF sequence:

ATGACTCCACAGGCTGAGTGCTCCTCAGCAGAAACTCCCACCCCTGAGGATGAGCAACAAGTGGGACGGATGATGGCAAAGCGGGCCAAGATCATCAGGGAGCTGATACAGACGGAGAGGGATTACCTCACAGATCTAGAGCTGTGCCTTAGAGAAGTGGTCCAGCCACTGCGAAGCAAACAGATTGACAGGCTGGACGTGGAGGGCTTGTTTAGCAACATTGAATCTGTGCATCAAATATCAGCCAAGCTACTGTCCTTGCTGGAAGAGGCCACAACAGACGTGGAACCGGCCATGCAAGTAATCGAAAAGATGACTCCACAGGCTGAGTGCTCCTCAGCAGAAACTCCCACCCCTGAGGATGAGCAACAAGTGGGACGGATGATGGCAAAGCGGGCCAAGATCATCAGGGAGCTGATACAGACGGAGAGGGATTACCTCACAGATCTAGAGCTGTGCCTTAGAGAAGTGGTCCAGCCACTGCGAAGCAAACAGATTGACAGGCTGGACGTGGAGGGCTTGTTTAGCAACATTGAATCTGTGCATCAAATATCAGCCAAGCTACTGTCCTTGCTGGAAGAGGCCACAACAGACGTGGAACCGGCCATGCAAGTAATC

Peptide sequence:

MTPQAECSSAETPTPEDEQQVGRMMAKRAKIIRELIQTERDYLTDLELCLREVVQPLRSKQIDRLDVEGLFSNIESVHQISAKLLSLLEEATTDVEPAMQVIEKMTPQAECSSAETPTPEDEQQVGRMMAKRAKIIRELIQTERDYLTDLELCLREVVQPLRSKQIDRLDVEGLFSNIESVHQISAKLLSLLEEATTDVEPAMQVI

IRESfinder result

IRESfinder score

0.240096007

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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