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mmu_circRapgef1_399
Basic information of circular RNA
PanCircBase ID:
mmu_circRapgef1_399
mm39_Chr. Position ID:
chr2|29579118|29589850|+
Gene name:
Rapgef1
Transcript:
ENSMUST00000095087.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,6,7
Exon/intron offsets:
0,9890,10579
Genomic length:
10732
Exon/intron sizes in nt:
1,57,89,153
Flanking exon/introns:
chr2:29576295-29579118|chr2:29589850-29590197
Splice length:
399
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CTCAGCCCTCTCCTCCTGTTATAGCCGAGTATACCAGAGCCTCGCCAACCTTATCCGATGGTCTGACCAGGTGATGCTAGAGGGCGTGAACTCAGAAGATAAGGAGATGGTGACAACTGTGAAGGGCGTTATCAAAGCTGTCCTGGACGGAGTGAAGGAGCTAGTGAGGCTAACCATTGAGAAGCAGGGGCGGCCATCGCCAACAAGCCCAGTGAAGCCCAGTTCCCCAGCCAGCAAGCCTGATGGCCAGCCTGAGCTCCCTCTGACAGACCGAGAAATGGAGATTCTGAACAAGACGACAAGTGTGTCACCATCTGCTGAACTGCTCCCAGACTCCACCAGTGAAGAGGTCGCACCCCCCAAGCCCCCTTTACCTGGCATCCGGGTGGTTGATAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCATCTGCTGAACTGCTCC
60.04
CCATCGGATAAGGTTGGCGA
59.89
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CATCTGCTGAACTGCTCCCA
60.04
CCATCGGATAAGGTTGGCGA
59.89
149
PCR template sequence:
CAAGTGTGTCACCATCTGCTGAACTGCTCCCAGACTCCACCAGTGAAGAGGTCGCACCCCCCAAGCCCCCTTTACCTGGCATCCGGGTGGTTGATAACAGCTCAGCCCTCTCCTCCTGTTATAGCCGAGTATACCAGAGCCTCGCCAACCTTATCCGATGGTCTGACCAGGTGATGCTAGAGGGCGTGAACTCAGAAGAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-342-5p(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGGTTGATAACAGCTCAGCCCTCTCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAPGEF1_399_ORF_1
1.0951
0.420462272
0.976135594
723
ORF sequence:
ATGCTAGAGGGCGTGAACTCAGAAGATAAGGAGATGGTGACAACTGTGAAGGGCGTTATCAAAGCTGTCCTGGACGGAGTGAAGGAGCTAGTGAGGCTAACCATTGAGAAGCAGGGGCGGCCATCGCCAACAAGCCCAGTGAAGCCCAGTTCCCCAGCCAGCAAGCCTGATGGCCAGCCTGAGCTCCCTCTGACAGACCGAGAAATGGAGATTCTGAACAAGACGACAAGTGTGTCACCATCTGCTGAACTGCTCCCAGACTCCACCAGTGAAGAGGTCGCACCCCCCAAGCCCCCTTTACCTGGCATCCGGGTGGTTGATAACAGCTCAGCCCTCTCCTCCTGTTATAGCCGAGTATACCAGAGCCTCGCCAACCTTATCCGATGGTCTGACCAGGTGATGCTAGAGGGCGTGAACTCAGAAGATAAGGAGATGGTGACAACTGTGAAGGGCGTTATCAAAGCTGTCCTGGACGGAGTGAAGGAGCTAGTGAGGCTAACCATTGAGAAGCAGGGGCGGCCATCGCCAACAAGCCCAGTGAAGCCCAGTTCCCCAGCCAGCAAGCCTGATGGCCAGCCTGAGCTCCCTCTGACAGACCGAGAAATGGAGATTCTGAACAAGACGACAAGTGTGTCACCATCTGCTGAACTGCTCCCAGACTCCACCAGTGAAGAGGTCGCACCCCCCAAGCCCCCTTTACCTGGCATCCGGGTGGTTGATAAC
Peptide sequence:
MLEGVNSEDKEMVTTVKGVIKAVLDGVKELVRLTIEKQGRPSPTSPVKPSSPASKPDGQPELPLTDREMEILNKTTSVSPSAELLPDSTSEEVAPPKPPLPGIRVVDNSSALSSCYSRVYQSLANLIRWSDQVMLEGVNSEDKEMVTTVKGVIKAVLDGVKELVRLTIEKQGRPSPTSPVKPSSPASKPDGQPELPLTDREMEILNKTTSVSPSAELLPDSTSEEVAPPKPPLPGIRVVDN
IRESfinder result
IRESfinder score
0.38698443
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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