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mmu_circCdk5rap1_240
Basic information of circular RNA
PanCircBase ID:
mmu_circCdk5rap1_240
mm39_Chr. Position ID:
chr2|154207881|154210835|-
Gene name:
Cdk5rap1
Transcript:
ENSMUST00000109731.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,5,4
Exon/intron offsets:
0,2252,2850
Genomic length:
2954
Exon/intron sizes in nt:
1,01,35,104
Flanking exon/introns:
chr2:154202687-154207881|chr2:154210835-154212555
Splice length:
240
Other database IDs:
CIRCpedia: MMU_CIRCpedia_228509, circAtlas: mmu-Cdk5rap1_0007
circAtlas: hsa-CDK5RAP1_0007, CIRCpedia: HSA_CIRCpedia_33728
Human Ortholog IDs:
Mature spliced Sequence:
TCTACCTCGAGACCTATGGCTGTCAGATGAACGTGAACGACACAGAGATAGCCTGGTCCATCTTACAGAAGAGTGGCTACCTTCGGACCAGCAACCTCCAAGAGGCTGATGTGATCCTTCTTGTCACGTGTTCTATCAGGGAGAAGGCCGAGCAGACCATCTGGAACCGCTTACATCAGCTCAAAGTCCTGAAGACAAAGCGGCCACGCTCTCGAGTACCTCTGAGGATTGGGATTCTAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGACCATCTGGAACCGCTT
60.04
GACCAGGCTATCTCTGTGTCG
59.93
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAGACCATCTGGAACCGCTT
60.04
CCAGGCTATCTCTGTGTCGT
58.89
144
PCR template sequence:
GAGAAGGCCGAGCAGACCATCTGGAACCGCTTACATCAGCTCAAAGTCCTGAAGACAAAGCGGCCACGCTCTCGAGTACCTCTGAGGATTGGGATTCTAGTCTACCTCGAGACCTATGGCTGTCAGATGAACGTGAACGACACAGAGATAGCCTGGTCCATCTTACAGAAGAGTGGCTACCTTCGGACCAGCAACCTCCA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTGGGATTCTAGTCTACCTCGAGAC
siRNA sets
TCGAGGTAGACTAGAATCC,CGAGGTAGACTAGAATCCC,GAGGTAGACTAGAATCCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDK5RAP1_240_ORF_1
1.2023
0.391791329
0.864405842
453
ORF sequence:
ATGAACGTGAACGACACAGAGATAGCCTGGTCCATCTTACAGAAGAGTGGCTACCTTCGGACCAGCAACCTCCAAGAGGCTGATGTGATCCTTCTTGTCACGTGTTCTATCAGGGAGAAGGCCGAGCAGACCATCTGGAACCGCTTACATCAGCTCAAAGTCCTGAAGACAAAGCGGCCACGCTCTCGAGTACCTCTGAGGATTGGGATTCTAGTCTACCTCGAGACCTATGGCTGTCAGATGAACGTGAACGACACAGAGATAGCCTGGTCCATCTTACAGAAGAGTGGCTACCTTCGGACCAGCAACCTCCAAGAGGCTGATGTGATCCTTCTTGTCACGTGTTCTATCAGGGAGAAGGCCGAGCAGACCATCTGGAACCGCTTACATCAGCTCAAAGTCCTGAAGACAAAGCGGCCACGCTCTCGAGTACCTCTGAGGATTGGGATTCTA
Peptide sequence:
MNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKVLKTKRPRSRVPLRIGILVYLETYGCQMNVNDTEIAWSILQKSGYLRTSNLQEADVILLVTCSIREKAEQTIWNRLHQLKVLKTKRPRSRVPLRIGIL
IRESfinder result
IRESfinder score
0.350183737
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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