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mmu_circArfip1_743
Basic information of circular RNA
PanCircBase ID:
mmu_circArfip1_743
mm39_Chr. Position ID:
chr3|84417114|84436572|-
Gene name:
Arfip1
Transcript:
ENSMUST00000107687.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
8,7,6,5,4
Exon/intron offsets:
0,5825,9674,17878,19383
Genomic length:
19458
Exon/intron sizes in nt:
175,158,222,113,75
Flanking exon/introns:
chr3:84405198-84417114|chr3:84436572-84441893
Splice length:
743
Other database IDs:
circAtlas: hsa-ARFIP1_0009, CIRCpedia: HSA_CIRCpedia_153840
Human Ortholog IDs:
Mature spliced Sequence:
GTTCCTCAGCACCACCTTTGCCATGTGTTCTGTCTCCCAGCAGGGTGGCAGCTAGTAAGCTGACCCAGCAAGCAGGTGGCCAAAGAACACACACAAAAGGAGGACCAGTTATTCTAGCAGATGAAATAAAAAATCCTGCAATGGAGAAGTTAGAACTTGTTAGAAAATGGAGTCTCAACACATATAAGTGTACCCGGCAAATTATATCTGAGAAACTAGGCCGTGGCTCAAGAACTGTGGACCTTGAACTTGAAGCTCAGATTGATATATTAAGAGATAATAAGAAAAAATATGAAAACATTCTGAAACTGGCTCAGACCTTGTCGACGCAGCTTTTCCAGATGGTGCACACCCAAAAGCAACTCGGAGATGCCTTTGCTGACCTGAGTTTGAAGTCTCTAGAGCTCCATGAAGAATTTGGCTATAATGCAGATACACAGAAGCTGCTGGCTAAAAATGGAGAGACTCTTCTTGGGGCCATTAATTTTTTCATTGCTAGTGTGAACACCTTGGTGAATAAAACAATTGAAGATACATTAATGACTGTAAAACAGTATGAAAATGCCAGAGTTGAATATGATGCGTACCGCACTGATTTGGAAGAACTGAACCTTGGGCCACGTGATGCAAACACTCTGCCAAAAATTGAGCAGTCGCAGCATCTGTTCCAAATACATAAGGAAAAATATGATAAAATGCGCAGTGATGTTTCTGTCAAATTGAAATTTCTCGAGGAAAATAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCGCAGCATCTGTTCCAA
59.96
GTTCTTTGGCCACCTGCTTG
59.97
180
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTCGCAGCATCTGTTCCAA
59.96
CTTACTAGCTGCCACCCTGC
60.46
151
PCR template sequence:
AATTGAGCAGTCGCAGCATCTGTTCCAAATACATAAGGAAAAATATGATAAAATGCGCAGTGATGTTTCTGTCAAATTGAAATTTCTCGAGGAAAATAAGGTTCCTCAGCACCACCTTTGCCATGTGTTCTGTCTCCCAGCAGGGTGGCAGCTAGTAAGCTGACCCAGCAAGCAGGTGGCCAAAGAACACACACAAAAGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-33-5p(1), mmu-miR-320-3p(1), mmu-miR-136-5p(1), mmu-miR-370-3p(1), mmu-miR-680(1), mmu-miR-335-3p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CGAGGAAAATAAGGTTCCTCAGCACC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARFIP1_743_ORF_1
1.0908
0.09532897
0.875064517
666
ORF sequence:
ATGGAGAAGTTAGAACTTGTTAGAAAATGGAGTCTCAACACATATAAGTGTACCCGGCAAATTATATCTGAGAAACTAGGCCGTGGCTCAAGAACTGTGGACCTTGAACTTGAAGCTCAGATTGATATATTAAGAGATAATAAGAAAAAATATGAAAACATTCTGAAACTGGCTCAGACCTTGTCGACGCAGCTTTTCCAGATGGTGCACACCCAAAAGCAACTCGGAGATGCCTTTGCTGACCTGAGTTTGAAGTCTCTAGAGCTCCATGAAGAATTTGGCTATAATGCAGATACACAGAAGCTGCTGGCTAAAAATGGAGAGACTCTTCTTGGGGCCATTAATTTTTTCATTGCTAGTGTGAACACCTTGGTGAATAAAACAATTGAAGATACATTAATGACTGTAAAACAGTATGAAAATGCCAGAGTTGAATATGATGCGTACCGCACTGATTTGGAAGAACTGAACCTTGGGCCACGTGATGCAAACACTCTGCCAAAAATTGAGCAGTCGCAGCATCTGTTCCAAATACATAAGGAAAAATATGATAAAATGCGCAGTGATGTTTCTGTCAAATTGAAATTTCTCGAGGAAAATAAGGTTCCTCAGCACCACCTTTGCCATGTGTTCTGTCTCCCAGCAGGGTGGCAGCTAGTAAGCTGA
Peptide sequence:
MEKLELVRKWSLNTYKCTRQIISEKLGRGSRTVDLELEAQIDILRDNKKKYENILKLAQTLSTQLFQMVHTQKQLGDAFADLSLKSLELHEEFGYNADTQKLLAKNGETLLGAINFFIASVNTLVNKTIEDTLMTVKQYENARVEYDAYRTDLEELNLGPRDANTLPKIEQSQHLFQIHKEKYDKMRSDVSVKLKFLEENKVPQHHLCHVFCLPAGWQLVS
IRESfinder result
IRESfinder score
0.556004956
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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