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mmu_circRapgef4_396
Basic information of circular RNA
PanCircBase ID:
mmu_circRapgef4_396
mm39_Chr. Position ID:
chr2|72064420|72069498|+
Gene name:
Rapgef4
Transcript:
ENSMUST00000090826.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
24,25,26
Exon/intron offsets:
0,531,4987
Genomic length:
5078
Exon/intron sizes in nt:
126,179,91
Flanking exon/introns:
chr2:72059447-72064420|chr2:72069498-72071770
Splice length:
396
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_135070
Human Ortholog IDs:
Mature spliced Sequence:
ACTCCCTTGCCGGAACAGGAAGGCCCGACCACTGGGACAGTGGGAACATTTGAGCTGATGAGCTCGAAAGACCTGGCGTACCAGATGACAACCTACGATTGGGAACTCTTCAACTGTGTGCATGAGCTGGAGCTAATCTACCACACATTTGGAAGGCATAATTTTAAAAAGACCACGGCAAACTTGGATTTGTTCCTGAGGAGGTTTAATGAAATTCAGTTTTGGGTTGTCACTGAGGTCTGCCTTTGTTCCCAGCTCAGCAAACGTGTTCAGCTTTTGAAAAAATTTATCAAGATAGCGGCTCACTGCAAGGAGTACAAAAATCTAAATTCCTTTTTCGCCATCGTCATGGGACTCAGCAACGTGGCCGTGAGCCGCTTGGCACTAACGTGGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCGTCATGGGACTCAGCAAC
60.04
GGTTGTCATCTGGTACGCCA
60.04
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATCGTCATGGGACTCAGCA
59.82
GGTTGTCATCTGGTACGCCA
60.04
148
PCR template sequence:
AGCGGCTCACTGCAAGGAGTACAAAAATCTAAATTCCTTTTTCGCCATCGTCATGGGACTCAGCAACGTGGCCGTGAGCCGCTTGGCACTAACGTGGGAGACTCCCTTGCCGGAACAGGAAGGCCCGACCACTGGGACAGTGGGAACATTTGAGCTGATGAGCTCGAAAGACCTGGCGTACCAGATGACAACCTACGATT
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-miR-466a-5p(1), mmu-miR-466p-5p(1), mmu-miR-1199-5p(1), mmu-miR-7a-1-3p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACTAACGTGGGAGACTCCCTTGCCGG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAPGEF4_396_ORF_1
1.1922
0.175442001
0.951513199
735
ORF sequence:
ATGAGCTCGAAAGACCTGGCGTACCAGATGACAACCTACGATTGGGAACTCTTCAACTGTGTGCATGAGCTGGAGCTAATCTACCACACATTTGGAAGGCATAATTTTAAAAAGACCACGGCAAACTTGGATTTGTTCCTGAGGAGGTTTAATGAAATTCAGTTTTGGGTTGTCACTGAGGTCTGCCTTTGTTCCCAGCTCAGCAAACGTGTTCAGCTTTTGAAAAAATTTATCAAGATAGCGGCTCACTGCAAGGAGTACAAAAATCTAAATTCCTTTTTCGCCATCGTCATGGGACTCAGCAACGTGGCCGTGAGCCGCTTGGCACTAACGTGGGAGACTCCCTTGCCGGAACAGGAAGGCCCGACCACTGGGACAGTGGGAACATTTGAGCTGATGAGCTCGAAAGACCTGGCGTACCAGATGACAACCTACGATTGGGAACTCTTCAACTGTGTGCATGAGCTGGAGCTAATCTACCACACATTTGGAAGGCATAATTTTAAAAAGACCACGGCAAACTTGGATTTGTTCCTGAGGAGGTTTAATGAAATTCAGTTTTGGGTTGTCACTGAGGTCTGCCTTTGTTCCCAGCTCAGCAAACGTGTTCAGCTTTTGAAAAAATTTATCAAGATAGCGGCTCACTGCAAGGAGTACAAAAATCTAAATTCCTTTTTCGCCATCGTCATGGGACTCAGCAACGTGGCCGTGAGCCGCTTGGCACTAACGTGGGAG
Peptide sequence:
MSSKDLAYQMTTYDWELFNCVHELELIYHTFGRHNFKKTTANLDLFLRRFNEIQFWVVTEVCLCSQLSKRVQLLKKFIKIAAHCKEYKNLNSFFAIVMGLSNVAVSRLALTWETPLPEQEGPTTGTVGTFELMSSKDLAYQMTTYDWELFNCVHELELIYHTFGRHNFKKTTANLDLFLRRFNEIQFWVVTEVCLCSQLSKRVQLLKKFIKIAAHCKEYKNLNSFFAIVMGLSNVAVSRLALTWE
IRESfinder result
IRESfinder score
0.648767289
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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