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mmu_circArhgef28_486

Basic information of circular RNA
PanCircBase ID:

mmu_circArhgef28_486

mm39_Chr. Position ID:

chr13|98211506|98282103|-

Gene name:

Arhgef28

Transcript:

ENSMUST00000109426.3

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

3

Exon/intron indexes:

4,3,2

Exon/intron offsets:

0,2174,70553

Genomic length:

70597

Exon/intron sizes in nt:

294,148,44

Flanking exon/introns:

chr13:98190482-98211506|chr13:98282103-98342580

Splice length:

486

Other database IDs:

circAtlas: mmu-Arhgef28_0020

circAtlas: hsa-ARHGEF28_0040, CIRCpedia: HSA_CIRCpedia_101245

Human Ortholog IDs:
Mature spliced Sequence:

ATGCAGGAGCCATGGAGTTGAGCTGCAGTGAAGTGCCTCTTTATGGACAGAAGACGGTCTATGCAAAGTTTGGCAAAAACGTGTATCTACCCGAAGATGCGGAGTTTTACTTTGTTTATGGCGGGTCGCATCAGAGGCACGTGGTGATTGCTGACCGTGTCCAGGACAATGTCCTCCAATCTAGCATTCCAGGCCACTGGCTTCAGGAGACGGTGACGGTATCTGTGTGCCTCTGCTCGGAAGGGTACTCCCCAGTGACCATGGGCTCTGGCTCAGTGACCTACGTGGACAACATGGCCTGCAGGCTGGCTCGTCTGCTGGTCACTCAGGCTGACCGACTCACGGCCTGCAGTCACCAGACGCTGCTGACCCCGTTTGCCCTGACAGTGGAAGCGCTGCCTGCCTTGGATGAGGAGCTCGTGCTGGCTCTGACCCAACTGGAGCTGCCTTTGGGTTGGACAGTCCTGGGAAATTCCTCACTTGAAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CTGCCTTGGATGAGGAGCTC

60.18

GCATAGACCGTCTTCTGTCCA

59.52

151

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CTGCCTTGGATGAGGAGCTC

60.18

TGCATAGACCGTCTTCTGTCC

59.52

152

PCR template sequence:

GTGGAAGCGCTGCCTGCCTTGGATGAGGAGCTCGTGCTGGCTCTGACCCAACTGGAGCTGCCTTTGGGTTGGACAGTCCTGGGAAATTCCTCACTTGAAGATGCAGGAGCCATGGAGTTGAGCTGCAGTGAAGTGCCTCTTTATGGACAGAAGACGGTCTATGCAAAGTTTGGCAAAAACGTGTATCTACCCGAAGATGC

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

NA

Interacting miRNAs (#binding sites)

NA

siRNAs for circular RNA silencing
Junction sequence

TCCTCACTTGAAGATGCAGGAGCCAT

siRNA sets

NA

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCARHGEF28_486_ORF_1

1.107

0.337552128

0.993943632

960

ORF sequence:

ATGGAGTTGAGCTGCAGTGAAGTGCCTCTTTATGGACAGAAGACGGTCTATGCAAAGTTTGGCAAAAACGTGTATCTACCCGAAGATGCGGAGTTTTACTTTGTTTATGGCGGGTCGCATCAGAGGCACGTGGTGATTGCTGACCGTGTCCAGGACAATGTCCTCCAATCTAGCATTCCAGGCCACTGGCTTCAGGAGACGGTGACGGTATCTGTGTGCCTCTGCTCGGAAGGGTACTCCCCAGTGACCATGGGCTCTGGCTCAGTGACCTACGTGGACAACATGGCCTGCAGGCTGGCTCGTCTGCTGGTCACTCAGGCTGACCGACTCACGGCCTGCAGTCACCAGACGCTGCTGACCCCGTTTGCCCTGACAGTGGAAGCGCTGCCTGCCTTGGATGAGGAGCTCGTGCTGGCTCTGACCCAACTGGAGCTGCCTTTGGGTTGGACAGTCCTGGGAAATTCCTCACTTGAAGATGCAGGAGCCATGGAGTTGAGCTGCAGTGAAGTGCCTCTTTATGGACAGAAGACGGTCTATGCAAAGTTTGGCAAAAACGTGTATCTACCCGAAGATGCGGAGTTTTACTTTGTTTATGGCGGGTCGCATCAGAGGCACGTGGTGATTGCTGACCGTGTCCAGGACAATGTCCTCCAATCTAGCATTCCAGGCCACTGGCTTCAGGAGACGGTGACGGTATCTGTGTGCCTCTGCTCGGAAGGGTACTCCCCAGTGACCATGGGCTCTGGCTCAGTGACCTACGTGGACAACATGGCCTGCAGGCTGGCTCGTCTGCTGGTCACTCAGGCTGACCGACTCACGGCCTGCAGTCACCAGACGCTGCTGACCCCGTTTGCCCTGACAGTGGAAGCGCTGCCTGCCTTGGATGAGGAGCTCGTGCTGGCTCTGACCCAACTGGAGCTGCCTTTGGGTTGGACAGTCCTGGGAAATTCCTCACTTGAA

Peptide sequence:

MELSCSEVPLYGQKTVYAKFGKNVYLPEDAEFYFVYGGSHQRHVVIADRVQDNVLQSSIPGHWLQETVTVSVCLCSEGYSPVTMGSGSVTYVDNMACRLARLLVTQADRLTACSHQTLLTPFALTVEALPALDEELVLALTQLELPLGWTVLGNSSLEDAGAMELSCSEVPLYGQKTVYAKFGKNVYLPEDAEFYFVYGGSHQRHVVIADRVQDNVLQSSIPGHWLQETVTVSVCLCSEGYSPVTMGSGSVTYVDNMACRLARLLVTQADRLTACSHQTLLTPFALTVEALPALDEELVLALTQLELPLGWTVLGNSSLE

IRESfinder result

IRESfinder score

0.398462806

IRES/non IRES

non-IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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