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mmu_circArfip1_324
Basic information of circular RNA
PanCircBase ID:
mmu_circArfip1_324
mm39_Chr. Position ID:
chr3|84434992|84455342|-
Gene name:
Arfip1
Transcript:
ENSMUST00000098990.10
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
4,3,2
Exon/intron offsets:
0,6901,20248
Genomic length:
20350
Exon/intron sizes in nt:
113,109,102
Flanking exon/introns:
chr3:84427010-84434992|chr3:84455342-84489720
Splice length:
324
Other database IDs:
circBase: mmu_circ_0010818, CIRCpedia: MMU_CIRCpedia_31703, circAtlas: mmu-Arfip1_0004
circBase: hsa_circ_0071278, circAtlas: hsa-ARFIP1_0004, CIRCpedia: HSA_CIRCpedia_47770
Human Ortholog IDs:
Mature spliced Sequence:
GTGTCTGCCATGGCTCAAGAATCTCCCAAAAACTCTGCAGCAGAAATCCCAGTAACTAGTAATGGAGAAGTTGACGATGCTCATGAGCATGGCTACAATAGGGATTTGAAGCATTCATTACCATCTGGACTTGGACTCTCAGAAACTCAGATCACATCTCATGGCTTTGACAGTACCAAAGAGGGGGTTACTGAAGCAGGAGCACCCCAAGGTGGCCAAAGAACACACACAAAAGGAGGACCAGTTATTCTAGCAGATGAAATAAAAAATCCTGCAATGGAGAAGTTAGAACTTGTTAGAAAATGGAGTCTCAACACATATAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACACACAAAAGGAGGACCAGT
59.44
TGGGATTTCTGCTGCAGAGT
59.31
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACACACAAAAGGAGGACCAGT
59.44
ACTGGGATTTCTGCTGCAGA
59.31
153
PCR template sequence:
ACACACAAAAGGAGGACCAGTTATTCTAGCAGATGAAATAAAAAATCCTGCAATGGAGAAGTTAGAACTTGTTAGAAAATGGAGTCTCAACACATATAAGGTGTCTGCCATGGCTCAAGAATCTCCCAAAAACTCTGCAGCAGAAATCCCAGTAACTAGTAATGGAGAAGTTGACGATGCTCATGAGCATGGCTACAATA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-136-5p(1), mmu-miR-342-5p(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAACACATATAAGGTGTCTGCCATGG
siRNA sets
ATGGCAGACACCTTATATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARFIP1_324_ORF_1
1.037
0.031441214
0.803762707
639
ORF sequence:
ATGGCTCAAGAATCTCCCAAAAACTCTGCAGCAGAAATCCCAGTAACTAGTAATGGAGAAGTTGACGATGCTCATGAGCATGGCTACAATAGGGATTTGAAGCATTCATTACCATCTGGACTTGGACTCTCAGAAACTCAGATCACATCTCATGGCTTTGACAGTACCAAAGAGGGGGTTACTGAAGCAGGAGCACCCCAAGGTGGCCAAAGAACACACACAAAAGGAGGACCAGTTATTCTAGCAGATGAAATAAAAAATCCTGCAATGGAGAAGTTAGAACTTGTTAGAAAATGGAGTCTCAACACATATAAGGTGTCTGCCATGGCTCAAGAATCTCCCAAAAACTCTGCAGCAGAAATCCCAGTAACTAGTAATGGAGAAGTTGACGATGCTCATGAGCATGGCTACAATAGGGATTTGAAGCATTCATTACCATCTGGACTTGGACTCTCAGAAACTCAGATCACATCTCATGGCTTTGACAGTACCAAAGAGGGGGTTACTGAAGCAGGAGCACCCCAAGGTGGCCAAAGAACACACACAAAAGGAGGACCAGTTATTCTAGCAGATGAAATAAAAAATCCTGCAATGGAGAAGTTAGAACTTGTTAGAAAATGGAGTCTCAACACATATAAG
Peptide sequence:
MAQESPKNSAAEIPVTSNGEVDDAHEHGYNRDLKHSLPSGLGLSETQITSHGFDSTKEGVTEAGAPQGGQRTHTKGGPVILADEIKNPAMEKLELVRKWSLNTYKVSAMAQESPKNSAAEIPVTSNGEVDDAHEHGYNRDLKHSLPSGLGLSETQITSHGFDSTKEGVTEAGAPQGGQRTHTKGGPVILADEIKNPAMEKLELVRKWSLNTYK
IRESfinder result
IRESfinder score
0.53831275
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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