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mmu_circCaprin1_460
Basic information of circular RNA
PanCircBase ID:
mmu_circCaprin1_460
mm39_Chr. Position ID:
chr2|103608307|103609916|-
Gene name:
Caprin1
Transcript:
ENSMUST00000028607.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
7,6,5
Exon/intron offsets:
0,1201,1370
Genomic length:
1609
Exon/intron sizes in nt:
1,38,83,239
Flanking exon/introns:
chr2:103606502-103608307|chr2:103609916-103613300
Splice length:
460
Other database IDs:
CIRCpedia: MMU_CIRCpedia_216426, circAtlas: mmu-Caprin1_0002
circAtlas: hsa-CAPRIN1_0002, CIRCpedia: HSA_CIRCpedia_350729
Human Ortholog IDs:
Mature spliced Sequence:
ATTCAGAAAACAATAAAGAAGACAGCACGTCGGGAACAGCTTATGAGAGAAGAAGCAGAACAGAAGCGCTTAAAAACTGTACTTGAGTTACAGTATGTATTGGATAAGCTGGGAGATGATGATGTGAGAACAGATCTGAAACAAGGTTTGAGTGGAGTGCCAATATTGTCTGAGGAGGAGTTGTCATTGCTGGATGAGTTCTACAAGCTCGTAGATCCTGAGCGTGACATGAGTTTAAGGTTAAATGAGCAGTATGAACATGCCTCAATTCACTTGTGGGATTTGCTGGAAGGGAAAGAAAAGCCTGTGTGTGGAACAACCTATAAAGCTCTAAAGGAAATTGTTGAGCGTGTTTTCCAGTCAAACTACTTTGATAGCACTCACAATCATCAAAATGGGTTGTGTGAGGAGGAAGAGGCGGCTTCAGCGCCCACAGTGGAGGACCAGGTAGCTGAAGCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAAAATGGGTTGTGTGAGGAGG
59.7
AGCGCTTCTGTTCTGCTTCT
59.97
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAAATGGGTTGTGTGAGGAGGA
59.82
AAGCGCTTCTGTTCTGCTTC
59.13
140
PCR template sequence:
TCAAACTACTTTGATAGCACTCACAATCATCAAAATGGGTTGTGTGAGGAGGAAGAGGCGGCTTCAGCGCCCACAGTGGAGGACCAGGTAGCTGAAGCTGATTCAGAAAACAATAAAGAAGACAGCACGTCGGGAACAGCTTATGAGAGAAGAAGCAGAACAGAAGCGCTTAAAAACTGTACTTGAGTTACAGTATGTAT
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-96-5p(1), mmu-miR-466d-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTAGCTGAAGCTGATTCAGAAAACAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCAPRIN1_460_ORF_1
1.064
0.154703159
0.727819987
504
ORF sequence:
ATGAGAGAAGAAGCAGAACAGAAGCGCTTAAAAACTGTACTTGAGTTACAGTATGTATTGGATAAGCTGGGAGATGATGATGTGAGAACAGATCTGAAACAAGGTTTGAGTGGAGTGCCAATATTGTCTGAGGAGGAGTTGTCATTGCTGGATGAGTTCTACAAGCTCGTAGATCCTGAGCGTGACATGAGTTTAAGGTTAAATGAGCAGTATGAACATGCCTCAATTCACTTGTGGGATTTGCTGGAAGGGAAAGAAAAGCCTGTGTGTGGAACAACCTATAAAGCTCTAAAGGAAATTGTTGAGCGTGTTTTCCAGTCAAACTACTTTGATAGCACTCACAATCATCAAAATGGGTTGTGTGAGGAGGAAGAGGCGGCTTCAGCGCCCACAGTGGAGGACCAGGTAGCTGAAGCTGATTCAGAAAACAATAAAGAAGACAGCACGTCGGGAACAGCTTATGAGAGAAGAAGCAGAACAGAAGCGCTTAAAAACTGTACTTGA
Peptide sequence:
MREEAEQKRLKTVLELQYVLDKLGDDDVRTDLKQGLSGVPILSEEELSLLDEFYKLVDPERDMSLRLNEQYEHASIHLWDLLEGKEKPVCGTTYKALKEIVERVFQSNYFDSTHNHQNGLCEEEEAASAPTVEDQVAEADSENNKEDSTSGTAYERRSRTEALKNCT
IRESfinder result
IRESfinder score
0.521137556
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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