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mmu_circCsnk1d_698
Basic information of circular RNA
PanCircBase ID:
mmu_circCsnk1d_698
mm39_Chr. Position ID:
chr11|120862392|120864795|-
Gene name:
Csnk1d
Transcript:
ENSMUST00000239115.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,810,1399,2254
Genomic length:
2403
Exon/intron sizes in nt:
1,49,17,12,29,149
Flanking exon/introns:
chr11:120860020-120862392|chr11:120864795-120874058
Splice length:
698
Other database IDs:
CIRCpedia: MMU_CIRCpedia_5289, circAtlas: mmu-Csnk1d_0006
circAtlas: hsa-CSNK1D_0007
Human Ortholog IDs:
Mature spliced Sequence:
TGGGCATCCCTACCATCAGATGGTGTGGGGCTGAGGGGGACTACAATGTCATGGTGATGGAGCTACTGGGACCCAGCCTGGAAGACCTGTTCAACTTCTGTTCAAGGAAGTTTAGTCTCAAAACTGTTCTGTTGCTTGCTGACCAAATGATAAGTCGTATTGAGTACATTCATTCGAAGAATTTTATCCACCGAGATGTGAAGCCAGATAACTTCCTCATGGGGCTGGGAAAGAAAGGCAACCTGGTCTACATCATTGACTTTGGGCTGGCCAAGAAGTATCGGGATGCACGCACCCACCAGCATATCCCCTATCGAGAGAACAAGAACCTCACAGGGACAGCACGCTATGCCTCCATCAACACGCACCTTGGCATTGAACAATCTCGAAGGGATGACTTGGAGTCTCTGGGGTACGTGCTGATGTACTTCAACCTGGGCTCTCTCCCCTGGCAGGGGCTGAAGGCCGCCACCAAGAGGCAGAAGTATGAGAGGATCAGTGAGAAGAAGATGTCCACTCCCATTGAAGTGCTGTGCAAGGGCTATCCTTCTGAATTTGCCACATACCTGAATTTCTGCCGTTCCTTACGTTTTGATGACAAACCTGACTACTCCTACCTGAGACAGCTCTTCAGAAATCTGTTCCATCGCCAAGGCTTCTCCTACGACTATGTGTTCGACTGGAACATGCTCAAATTT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCCATCGCCAAGGCTTCTC
60.39
GAACAGGTCTTCCAGGCTGG
60.32
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCCAAGGCTTCTCCTACGAC
60.46
GAACAGGTCTTCCAGGCTGG
60.32
142
PCR template sequence:
CAAACCTGACTACTCCTACCTGAGACAGCTCTTCAGAAATCTGTTCCATCGCCAAGGCTTCTCCTACGACTATGTGTTCGACTGGAACATGCTCAAATTTTGGGCATCCCTACCATCAGATGGTGTGGGGCTGAGGGGGACTACAATGTCATGGTGATGGAGCTACTGGGACCCAGCCTGGAAGACCTGTTCAACTTCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-18a-5p(1), mmu-miR-138-5p(1), mmu-miR-214-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-29b-2-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATGCTCAAATTTTGGGCATCCCTAC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCSNK1D_698_ORF_1
1.1005
0.339147838
0.962490685
705
ORF sequence:
ATGGTGATGGAGCTACTGGGACCCAGCCTGGAAGACCTGTTCAACTTCTGTTCAAGGAAGTTTAGTCTCAAAACTGTTCTGTTGCTTGCTGACCAAATGATAAGTCGTATTGAGTACATTCATTCGAAGAATTTTATCCACCGAGATGTGAAGCCAGATAACTTCCTCATGGGGCTGGGAAAGAAAGGCAACCTGGTCTACATCATTGACTTTGGGCTGGCCAAGAAGTATCGGGATGCACGCACCCACCAGCATATCCCCTATCGAGAGAACAAGAACCTCACAGGGACAGCACGCTATGCCTCCATCAACACGCACCTTGGCATTGAACAATCTCGAAGGGATGACTTGGAGTCTCTGGGGTACGTGCTGATGTACTTCAACCTGGGCTCTCTCCCCTGGCAGGGGCTGAAGGCCGCCACCAAGAGGCAGAAGTATGAGAGGATCAGTGAGAAGAAGATGTCCACTCCCATTGAAGTGCTGTGCAAGGGCTATCCTTCTGAATTTGCCACATACCTGAATTTCTGCCGTTCCTTACGTTTTGATGACAAACCTGACTACTCCTACCTGAGACAGCTCTTCAGAAATCTGTTCCATCGCCAAGGCTTCTCCTACGACTATGTGTTCGACTGGAACATGCTCAAATTTTGGGCATCCCTACCATCAGATGGTGTGGGGCTGAGGGGGACTACAATGTCATGGTGA
Peptide sequence:
MVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLKFWASLPSDGVGLRGTTMSW
IRESfinder result
IRESfinder score
0.515601585
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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