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mmu_circClint1_513
Basic information of circular RNA
PanCircBase ID:
mmu_circClint1_513
mm39_Chr. Position ID:
chr11|45793037|45798871|+
Gene name:
Clint1
Transcript:
ENSMUST00000109260.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
9,10,11
Exon/intron offsets:
0,3970,5683
Genomic length:
5834
Exon/intron sizes in nt:
7,52,87,151
Flanking exon/introns:
chr11:45785956-45793037|chr11:45798871-45799767
Splice length:
513
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_50957
Human Ortholog IDs:
Mature spliced Sequence:
GTGGATCAGCTGATTTATTTGGGGGATTTGCTGACTTTGGCTCAGCTGCTGCATCAGGCAATTTCCCTTCCCAAGCAACAAGTGGGAATGGTGACTTTGGTGACTGGAGTGCCTTCAACCAAGCCCCATCAGGCCCTGTGGCTTCTGGTGGTGAGCTCTTCGGCAGTGCCCCACAGTCGGCTGTGGAGCTTATCAGTGCTTCACAGCCAGCTTTAGGCCCACCGCCTGCTGCCTCAAACTCGGCAGACCTGTTTGATCTTATGGGCTCATCCCAGGCAACCATGACGTCTTCCCAGAGCATGAATTTCTCTCTCATGAGCACTAACACCGTGGGACTTGGTTTGCCCATGTCCAGATCACAGAATACAGATATGGTCCAGAAGTCGGCCAGCAAAACCCTGCCCTCTACTTGGTCTGACCCCAGTGTCAACATCAGCCTAGACAACTTACTACCTGGTATGCAGCCTTCCAAGCCCCAGCAGCCATCGCTTAATACAATGATTCAACAACAGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCCAGTGTCAACATCAGCCT
59.96
GCTTGGGAAGGGAAATTGCC
59.75
170
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCCCAGTGTCAACATCAGC
60.25
GCTTGGGAAGGGAAATTGCC
59.75
172
PCR template sequence:
TCTGACCCCAGTGTCAACATCAGCCTAGACAACTTACTACCTGGTATGCAGCCTTCCAAGCCCCAGCAGCCATCGCTTAATACAATGATTCAACAACAGAGTGGATCAGCTGATTTATTTGGGGGATTTGCTGACTTTGGCTCAGCTGCTGCATCAGGCAATTTCCCTTCCCAAGCAACAAGTGGGAATGGTGACTTTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
16
Interacting miRNAs (#binding sites)
mmu-let-7b-5p(2), mmu-let-7a-5p(1), mmu-miR-7b-5p(1), mmu-let-7e-5p(1), mmu-let-7c-5p(1), mmu-miR-7a-5p(1), mmu-miR-196a-5p(1), mmu-miR-709(1), mmu-miR-320-3p(1), mmu-let-7d-5p(1), mmu-miR-382-5p(1), mmu-miR-370-3p(1), mmu-miR-324-3p(1), mmu-miR-98-5p(1), mmu-miR-27a-5p(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTCAACAACAGAGTGGATCAGCTGA
siRNA sets
TGATCCACTCTGTTGTTGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCLINT1_513_ORF_1
0.7491
0.181899876
0.916072314
765
ORF sequence:
ATGGGCTCATCCCAGGCAACCATGACGTCTTCCCAGAGCATGAATTTCTCTCTCATGAGCACTAACACCGTGGGACTTGGTTTGCCCATGTCCAGATCACAGAATACAGATATGGTCCAGAAGTCGGCCAGCAAAACCCTGCCCTCTACTTGGTCTGACCCCAGTGTCAACATCAGCCTAGACAACTTACTACCTGGTATGCAGCCTTCCAAGCCCCAGCAGCCATCGCTTAATACAATGATTCAACAACAGAGTGGATCAGCTGATTTATTTGGGGGATTTGCTGACTTTGGCTCAGCTGCTGCATCAGGCAATTTCCCTTCCCAAGCAACAAGTGGGAATGGTGACTTTGGTGACTGGAGTGCCTTCAACCAAGCCCCATCAGGCCCTGTGGCTTCTGGTGGTGAGCTCTTCGGCAGTGCCCCACAGTCGGCTGTGGAGCTTATCAGTGCTTCACAGCCAGCTTTAGGCCCACCGCCTGCTGCCTCAAACTCGGCAGACCTGTTTGATCTTATGGGCTCATCCCAGGCAACCATGACGTCTTCCCAGAGCATGAATTTCTCTCTCATGAGCACTAACACCGTGGGACTTGGTTTGCCCATGTCCAGATCACAGAATACAGATATGGTCCAGAAGTCGGCCAGCAAAACCCTGCCCTCTACTTGGTCTGACCCCAGTGTCAACATCAGCCTAGACAACTTACTACCTGGTATGCAGCCTTCCAAGCCCCAGCAGCCATCGCTTAATACAATGATTCAACAACAG
Peptide sequence:
MGSSQATMTSSQSMNFSLMSTNTVGLGLPMSRSQNTDMVQKSASKTLPSTWSDPSVNISLDNLLPGMQPSKPQQPSLNTMIQQQSGSADLFGGFADFGSAAASGNFPSQATSGNGDFGDWSAFNQAPSGPVASGGELFGSAPQSAVELISASQPALGPPPAASNSADLFDLMGSSQATMTSSQSMNFSLMSTNTVGLGLPMSRSQNTDMVQKSASKTLPSTWSDPSVNISLDNLLPGMQPSKPQQPSLNTMIQQQ
IRESfinder result
IRESfinder score
0.618414611
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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