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mmu_circArhgef2_252
Basic information of circular RNA
PanCircBase ID:
mmu_circArhgef2_252
mm39_Chr. Position ID:
chr3|88521813|88523961|+
Gene name:
Arhgef2
Transcript:
ENSMUST00000175903.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
3,4,5
Exon/intron offsets:
0,975,2054
Genomic length:
2148
Exon/intron sizes in nt:
118,40,94
Flanking exon/introns:
chr3:88515246-88521813|chr3:88523961-88537093
Splice length:
252
Other database IDs:
CIRCpedia: MMU_CIRCpedia_33142, circAtlas: mmu-Arhgef2_0008
Human Ortholog IDs:
Mature spliced Sequence:
GGTCAGAGTTTCTGCTATCCATCTGCTGCCTCTTCGGTTCCCTCGGTCACTGGCATGCTGTCCAAGGCTGTGTCCATGAGTGATATCAATCTCCTTTCGGACTGCTCAGATCCAAATGGTAACTCACCTCAGTCCTATGTCACAGACCTCAGCAAATGTGGTAAACAGCTGGAAGAGGACTCGGGGACCTGGGCAGGCTCCTCCCTGCGACGGACCTTCAGCTTCCTCTTGGGCATGACCGGCAGGGACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACAGCTGGAAGAGGACTCG
59.39
TCATGGACACAGCCTTGGAC
59.96
168
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AACAGCTGGAAGAGGACTCG
59.39
ATGGACACAGCCTTGGACAG
59.96
166
PCR template sequence:
CAAATGTGGTAAACAGCTGGAAGAGGACTCGGGGACCTGGGCAGGCTCCTCCCTGCGACGGACCTTCAGCTTCCTCTTGGGCATGACCGGCAGGGACAAGGGTCAGAGTTTCTGCTATCCATCTGCTGCCTCTTCGGTTCCCTCGGTCACTGGCATGCTGTCCAAGGCTGTGTCCATGAGTGATATCAATCTCCTTTCGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-let-7a-5p(1), mmu-let-7e-5p(1), mmu-let-7c-5p(1), mmu-miR-709(1), mmu-let-7d-5p(1), mmu-miR-125a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CGGCAGGGACAAGGGTCAGAGTTTCT
siRNA sets
TCTGACCCTTGTCCCTGCC, GAAACTCTGACCCTTGTCC, AGAAACTCTGACCCTTGTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARHGEF2_252_ORF_1
0.8192
0.321026833
0.69601253
450
ORF sequence:
ATGCTGTCCAAGGCTGTGTCCATGAGTGATATCAATCTCCTTTCGGACTGCTCAGATCCAAATGGTAACTCACCTCAGTCCTATGTCACAGACCTCAGCAAATGTGGTAAACAGCTGGAAGAGGACTCGGGGACCTGGGCAGGCTCCTCCCTGCGACGGACCTTCAGCTTCCTCTTGGGCATGACCGGCAGGGACAAGGGTCAGAGTTTCTGCTATCCATCTGCTGCCTCTTCGGTTCCCTCGGTCACTGGCATGCTGTCCAAGGCTGTGTCCATGAGTGATATCAATCTCCTTTCGGACTGCTCAGATCCAAATGGTAACTCACCTCAGTCCTATGTCACAGACCTCAGCAAATGTGGTAAACAGCTGGAAGAGGACTCGGGGACCTGGGCAGGCTCCTCCCTGCGACGGACCTTCAGCTTCCTCTTGGGCATGACCGGCAGGGACAAG
Peptide sequence:
MLSKAVSMSDINLLSDCSDPNGNSPQSYVTDLSKCGKQLEEDSGTWAGSSLRRTFSFLLGMTGRDKGQSFCYPSAASSVPSVTGMLSKAVSMSDINLLSDCSDPNGNSPQSYVTDLSKCGKQLEEDSGTWAGSSLRRTFSFLLGMTGRDK
IRESfinder result
IRESfinder score
0.321205195
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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