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mmu_circClk1_646
Basic information of circular RNA
PanCircBase ID:
mmu_circClk1_646
mm39_Chr. Position ID:
chr1|58451805|58456338|-
Gene name:
Clk1
Transcript:
ENSMUST00000156931.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
10,9,8,7,6,5
Exon/intron offsets:
0,300,743,1725,1943,4366
Genomic length:
4533
Exon/intron sizes in nt:
9,18,08,31,30,95,167
Flanking exon/introns:
chr1:58451499-58451805|chr1:58456338-58456425
Splice length:
646
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CCGTTGTGTCCAGATGTTGGAGTGGTTTGAGCATCGAGGTCACATTTGCATTGTGTTTGAACTTCTGGGGCTTAGTACTTATGATTTCATTAAGGAAAACAGTTTTCTGCCGTTTCGAATGGATCATATCAGGAAGATGGCATATCAAATATGCAAATCTGTAAACTTTTTGCATAGTAATAAATTGACTCATACAGACTTGAAGCCTGAAAACATCTTATTTGTGAAGTCTGACTACACAGAGGCTTATAATCCCAAAATGAAACGTGATGAACGTACTATAGTAAATCCAGATATTAAAGTGGTGGACTTTGGAAGTGCAACATATGATGATGAACACCACAGCACATTGGTATCTACAAGACATTATAGAGCACCGGAAGTTATTTTAGCCCTCGGGTGGTCACAGCCATGTGATGTCTGGAGCATAGGATGTATTCTTATCGAGTATTATCTTGGATTTACAGTTTTTCCGACTCATGATAGCAGGGAACATTTAGCAATGATGGAAAGGATTCTTGGACCACTACCAAAGCACATGATACAGAAAACCAGGAAACGCAGATATTTCCATCATGATCGATTAGATTGGGATGAACACAGTTCTGCTGGCAGATATGTTTCTCGGCGCTGTAAACCTCTGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GAAAACCAGGAAACGCAGAT
56.63
TGACCTCGATGCTCAAACCA
59.32
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GAAAACCAGGAAACGCAGAT
56.63
ACCTCGATGCTCAAACCACT
59.31
140
PCR template sequence:
GAAAACCAGGAAACGCAGATATTTCCATCATGATCGATTAGATTGGGATGAACACAGTTCTGCTGGCAGATATGTTTCTCGGCGCTGTAAACCTCTGAAGCCGTTGTGTCCAGATGTTGGAGTGGTTTGAGCATCGAGGTCACATTTGCATTGTGTTTGAACTTCTGGGGCTTAGTACTTATGATTTCATTAAGGAAAAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-433-3p(1), mmu-miR-335-3p(1), mmu-miR-697(1), mmu-miR-146b-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TAAACCTCTGAAGCCGTTGTGTCCAG
siRNA sets
ACACAACGGCTTCAGAGGT, GACACAACGGCTTCAGAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCLK1_646_ORF_1
0.7744
-0.051138657
0.677461446
663
ORF sequence:
ATGTTGGAGTGGTTTGAGCATCGAGGTCACATTTGCATTGTGTTTGAACTTCTGGGGCTTAGTACTTATGATTTCATTAAGGAAAACAGTTTTCTGCCGTTTCGAATGGATCATATCAGGAAGATGGCATATCAAATATGCAAATCTGTAAACTTTTTGCATAGTAATAAATTGACTCATACAGACTTGAAGCCTGAAAACATCTTATTTGTGAAGTCTGACTACACAGAGGCTTATAATCCCAAAATGAAACGTGATGAACGTACTATAGTAAATCCAGATATTAAAGTGGTGGACTTTGGAAGTGCAACATATGATGATGAACACCACAGCACATTGGTATCTACAAGACATTATAGAGCACCGGAAGTTATTTTAGCCCTCGGGTGGTCACAGCCATGTGATGTCTGGAGCATAGGATGTATTCTTATCGAGTATTATCTTGGATTTACAGTTTTTCCGACTCATGATAGCAGGGAACATTTAGCAATGATGGAAAGGATTCTTGGACCACTACCAAAGCACATGATACAGAAAACCAGGAAACGCAGATATTTCCATCATGATCGATTAGATTGGGATGAACACAGTTCTGCTGGCAGATATGTTTCTCGGCGCTGTAAACCTCTGAAGCCGTTGTGTCCAGATGTTGGAGTGGTTTGA
Peptide sequence:
MLEWFEHRGHICIVFELLGLSTYDFIKENSFLPFRMDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVKSDYTEAYNPKMKRDERTIVNPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSREHLAMMERILGPLPKHMIQKTRKRRYFHHDRLDWDEHSSAGRYVSRRCKPLKPLCPDVGVV
IRESfinder result
IRESfinder score
0.62222647
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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