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mmu_circRapgef5_358
Basic information of circular RNA
PanCircBase ID:
mmu_circRapgef5_358
mm39_Chr. Position ID:
chr12|117681936|117689783|+
Gene name:
Rapgef5
Transcript:
ENSMUST00000109691.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
17,18,19,20
Exon/intron offsets:
0,917,3040,7749
Genomic length:
7847
Exon/intron sizes in nt:
31,79,150,98
Flanking exon/introns:
chr12:117679139-117681936|chr12:117689783-117692391
Splice length:
358
Other database IDs:
circAtlas: mmu-Rapgef5_0015
circAtlas: hsa-RAPGEF5_0047
Human Ortholog IDs:
Mature spliced Sequence:
CACTGTTGATGAATACTCACCACAGAAGAAGAATAAAGCCCTTTTCCACCAATTCAGTCTTAAGGAGAACTGGCTCCAGCACAGAGGAACTGTGGCAGAAACAGAGGAAATTTTTTGCCACGTGTATATAACGGAGCACTCCTATATCAGTGTGAAGGCAAAAGTGTCGAGTACAGCCCAGGAGATCCTGAAGGTCGTGGCCGAGAAGCTGCAGCGTGCCGAAGAGGATCTGGCTCTGGTAGCCATTACATTCTCTGGAGAAAAGCATGAATTTCAGCCAAATGACTTGGCCATTTCCAAATCCCTGGAGGCATCTGGTCGGATATATGTCTACCGAAAAGATCTGGCTGACACTTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGAGGCATCTGGTCGGATA
60.11
CAGTTCCTCTGTGCTGGAGC
60.67
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCAAATCCCTGGAGGCATC
59.45
CTGTGCTGGAGCCAGTTCTC
60.67
147
PCR template sequence:
AGAAAAGCATGAATTTCAGCCAAATGACTTGGCCATTTCCAAATCCCTGGAGGCATCTGGTCGGATATATGTCTACCGAAAAGATCTGGCTGACACTTTGCACTGTTGATGAATACTCACCACAGAAGAAGAATAAAGCCCTTTTCCACCAATTCAGTCTTAAGGAGAACTGGCTCCAGCACAGAGGAACTGTGGCAGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-541-5p(1), mmu-miR-499-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGCTGACACTTTGCACTGTTGATGAA
siRNA sets
ATCAACAGTGCAAAGTGTC, AACAGTGCAAAGTGTCAGC, CATCAACAGTGCAAAGTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAPGEF5_358_ORF_1
1.0219
0.215379225
0.683186484
450
ORF sequence:
ATGAATTTCAGCCAAATGACTTGGCCATTTCCAAATCCCTGGAGGCATCTGGTCGGATATATGTCTACCGAAAAGATCTGGCTGACACTTTGCACTGTTGATGAATACTCACCACAGAAGAAGAATAAAGCCCTTTTCCACCAATTCAGTCTTAAGGAGAACTGGCTCCAGCACAGAGGAACTGTGGCAGAAACAGAGGAAATTTTTTGCCACGTGTATATAACGGAGCACTCCTATATCAGTGTGAAGGCAAAAGTGTCGAGTACAGCCCAGGAGATCCTGAAGGTCGTGGCCGAGAAGCTGCAGCGTGCCGAAGAGGATCTGGCTCTGGTAGCCATTACATTCTCTGGAGAAAAGCATGAATTTCAGCCAAATGACTTGGCCATTTCCAAATCCCTGGAGGCATCTGGTCGGATATATGTCTACCGAAAAGATCTGGCTGACACTTTG
Peptide sequence:
MNFSQMTWPFPNPWRHLVGYMSTEKIWLTLCTVDEYSPQKKNKALFHQFSLKENWLQHRGTVAETEEIFCHVYITEHSYISVKAKVSSTAQEILKVVAEKLQRAEEDLALVAITFSGEKHEFQPNDLAISKSLEASGRIYVYRKDLADTL
IRESfinder result
IRESfinder score
0.537051311
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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