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mmu_circCdk5rap1_422
Basic information of circular RNA
PanCircBase ID:
mmu_circCdk5rap1_422
mm39_Chr. Position ID:
chr2|154184220|154190701|-
Gene name:
Cdk5rap1
Transcript:
ENSMUST00000109731.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
14,13,12
Exon/intron offsets:
0,3565,6350
Genomic length:
6481
Exon/intron sizes in nt:
14,11,50,131
Flanking exon/introns:
chr2:154177537-154184220|chr2:154190701-154192737
Splice length:
422
Other database IDs:
circAtlas: mmu-Cdk5rap1_0005
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_33708
Human Ortholog IDs:
Mature spliced Sequence:
GTGTGAGCCTTAGCAGCGACTTCATCACTGGCTTTTGTGGAGAGACAGAGGATGATCACCGGCAGACAGTGTCTTTACTTAGAGAAGTGCAGTATAATACCGGTTTTCTCTTTGCATACAGCATGAGGCAAAAGACACGAGCATATCACAGGCTGAAGGATGATGTTCCAGAAGAAGTAAAATTAAGGCGTTTGGAGGAACTCATTACTGTCTTCAGAGAAGAAGCTTCAAAAGCCAATAAGACCTCAGTGGGTTGTAGCCAGCTGGTACTGGTTGAAGGGTTCAGCAAACGTTCTACCACAGACCTTTGTGGCCGGAATGATGCAAACCTTAAGGTGATTTTCCCTGACGCAGAGGTGGAGGATATCACTAACCCTGGGCTCAAGGTCAGAGCTCAACCTGGGGACTATGTGCTGGTGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGACGCAGAGGTGGAGGATA
60.03
ACTGTCTGCCGGTGATCATC
59.82
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGACGCAGAGGTGGAGGATA
60.03
GTCTGCCGGTGATCATCCTC
60.25
143
PCR template sequence:
TGCAAACCTTAAGGTGATTTTCCCTGACGCAGAGGTGGAGGATATCACTAACCCTGGGCTCAAGGTCAGAGCTCAACCTGGGGACTATGTGCTGGTGAAGGTGTGAGCCTTAGCAGCGACTTCATCACTGGCTTTTGTGGAGAGACAGAGGATGATCACCGGCAGACAGTGTCTTTACTTAGAGAAGTGCAGTATAATAC
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-32-5p(1), mmu-miR-25-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGTGCTGGTGAAGGTGTGAGCCTTAG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDK5RAP1_422_ORF_1
1.0045
0.227013842
0.435737668
306
ORF sequence:
ATGAGGCAAAAGACACGAGCATATCACAGGCTGAAGGATGATGTTCCAGAAGAAGTAAAATTAAGGCGTTTGGAGGAACTCATTACTGTCTTCAGAGAAGAAGCTTCAAAAGCCAATAAGACCTCAGTGGGTTGTAGCCAGCTGGTACTGGTTGAAGGGTTCAGCAAACGTTCTACCACAGACCTTTGTGGCCGGAATGATGCAAACCTTAAGGTGATTTTCCCTGACGCAGAGGTGGAGGATATCACTAACCCTGGGCTCAAGGTCAGAGCTCAACCTGGGGACTATGTGCTGGTGAAGGTGTGA
Peptide sequence:
MRQKTRAYHRLKDDVPEEVKLRRLEELITVFREEASKANKTSVGCSQLVLVEGFSKRSTTDLCGRNDANLKVIFPDAEVEDITNPGLKVRAQPGDYVLVKV
IRESfinder result
IRESfinder score
0.596104162
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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