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mmu_circClock_828
Basic information of circular RNA
PanCircBase ID:
mmu_circClock_828
mm39_Chr. Position ID:
chr5|76390925|76414263|-
Gene name:
Clock
Transcript:
ENSMUST00000202651.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
8
Exon/intron indexes:
12,11,10,9,8,7,6,5
Exon/intron offsets:
0,2117,2343,5263,11295,19596,22712,23278
Genomic length:
23338
Exon/intron sizes in nt:
83,119,114,121,90,92,149,60
Flanking exon/introns:
chr5:76390735-76390925|chr5:76414263-76414646
Splice length:
828
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGATGACAGTAGTATTTTTGATGGATTGGTGGAAGAAGATGACAAGGACAAAGCAAAAAGAGTATCTAGAAACAAATCAGAAAAGAAACGTAGAGATCAGTTCAATGTCCTCATTAAGGAGCTGGGGTCTATGCTTCCTGGTAACGCGAGAAAGATGGACAAGTCTACTGTTCTACAGAAGAGCATTGATTTTTTGCGCAAACATAAAGAGACCACTGCACAGTCAGATGCTAGTGAGATTCGACAGGACTGGAAACCCACATTCCTTAGTAATGAAGAGTTTACACAGTTAATGTTAGAGGCTCTTGATGGTTTTTTTTTAGCGATCATGACAGATGGAAGTATAATATATGTATCTGAGAGTGTAACTTCGTTACTTGAACATTTACCATCTGATCTTGTGGATCAAAGTATATTTAATTTTATCCCAGAGGGAGAACATTCAGAGGTTTATAAGATACTCTCTACTCATCTGCTGGAAAGTGACTCATTAACCCCTGAGTACTTAAAATCAAAAAATCAGTTAGAATTCTGTTGTCACATGCTTCGAGGAACAATAGACCCAAAGGAGCCATCCACCTATGAATATGTGAGATTTATAGGAAATTTTAAATCTTTAACCAGTGTATCAACTTCAACACACAATGGTTTTGAAGGAACTATACAACGCACACATAGGCCTTCTTATGAAGATAGAGTTTGTTTTGTAGCTACTGTCAGATTAGCTACACCTCAGTTCATCAAGGAAATGTGTACTGTTGAAGAACCAAATGAAGAGTTTACATCTAGACACAGTTTAGAATGGAAGTTTCTATTTTTAGATCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCTCAGTTCATCAAGGAAATGTGT
59.24
TCCTTGTCATCTTCTTCCACCA
59.02
146
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTCAGTTCATCAAGGAAATGTG
59.24
TCCTTGTCATCTTCTTCCACCA
59.02
147
PCR template sequence:
CACCTCAGTTCATCAAGGAAATGTGTACTGTTGAAGAACCAAATGAAGAGTTTACATCTAGACACAGTTTAGAATGGAAGTTTCTATTTTTAGATCACAGAGATGACAGTAGTATTTTTGATGGATTGGTGGAAGAAGATGACAAGGACAAAGCAAAAAGAGTATCTAGAAACAAATCAGAAAAGAAACGTAGAGATCAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-26a-5p(1), mmu-miR-335-5p(1), mmu-miR-216a-5p(1), mmu-miR-26b-5p(1), mmu-miR-362-5p(1), mmu-miR-383-5p(1), mmu-miR-466a-5p(1), mmu-miR-1187(1), mmu-miR-466p-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTAGATCACAGAGATGACAGTAGT
siRNA sets
TACTGTCATCTCTGTGATC, ACTACTGTCATCTCTGTGA, ACTGTCATCTCTGTGATCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCLOCK_828_ORF_1
0.8774
-0.072576792
0.999134025
1524
ORF sequence:
ATGCTTCCTGGTAACGCGAGAAAGATGGACAAGTCTACTGTTCTACAGAAGAGCATTGATTTTTTGCGCAAACATAAAGAGACCACTGCACAGTCAGATGCTAGTGAGATTCGACAGGACTGGAAACCCACATTCCTTAGTAATGAAGAGTTTACACAGTTAATGTTAGAGGCTCTTGATGGTTTTTTTTTAGCGATCATGACAGATGGAAGTATAATATATGTATCTGAGAGTGTAACTTCGTTACTTGAACATTTACCATCTGATCTTGTGGATCAAAGTATATTTAATTTTATCCCAGAGGGAGAACATTCAGAGGTTTATAAGATACTCTCTACTCATCTGCTGGAAAGTGACTCATTAACCCCTGAGTACTTAAAATCAAAAAATCAGTTAGAATTCTGTTGTCACATGCTTCGAGGAACAATAGACCCAAAGGAGCCATCCACCTATGAATATGTGAGATTTATAGGAAATTTTAAATCTTTAACCAGTGTATCAACTTCAACACACAATGGTTTTGAAGGAACTATACAACGCACACATAGGCCTTCTTATGAAGATAGAGTTTGTTTTGTAGCTACTGTCAGATTAGCTACACCTCAGTTCATCAAGGAAATGTGTACTGTTGAAGAACCAAATGAAGAGTTTACATCTAGACACAGTTTAGAATGGAAGTTTCTATTTTTAGATCACAGAGATGACAGTAGTATTTTTGATGGATTGGTGGAAGAAGATGACAAGGACAAAGCAAAAAGAGTATCTAGAAACAAATCAGAAAAGAAACGTAGAGATCAGTTCAATGTCCTCATTAAGGAGCTGGGGTCTATGCTTCCTGGTAACGCGAGAAAGATGGACAAGTCTACTGTTCTACAGAAGAGCATTGATTTTTTGCGCAAACATAAAGAGACCACTGCACAGTCAGATGCTAGTGAGATTCGACAGGACTGGAAACCCACATTCCTTAGTAATGAAGAGTTTACACAGTTAATGTTAGAGGCTCTTGATGGTTTTTTTTTAGCGATCATGACAGATGGAAGTATAATATATGTATCTGAGAGTGTAACTTCGTTACTTGAACATTTACCATCTGATCTTGTGGATCAAAGTATATTTAATTTTATCCCAGAGGGAGAACATTCAGAGGTTTATAAGATACTCTCTACTCATCTGCTGGAAAGTGACTCATTAACCCCTGAGTACTTAAAATCAAAAAATCAGTTAGAATTCTGTTGTCACATGCTTCGAGGAACAATAGACCCAAAGGAGCCATCCACCTATGAATATGTGAGATTTATAGGAAATTTTAAATCTTTAACCAGTGTATCAACTTCAACACACAATGGTTTTGAAGGAACTATACAACGCACACATAGGCCTTCTTATGAAGATAGAGTTTGTTTTGTAGCTACTGTCAGATTAGCTACACCTCAGTTCATCAAGGAAATGTGTACTGTTGAAGAACCAAATGAAGAGTTTACATCTAGACACAGTTTAGAATGGAAGTTTCTATTTTTAGATCAC
Peptide sequence:
MLPGNARKMDKSTVLQKSIDFLRKHKETTAQSDASEIRQDWKPTFLSNEEFTQLMLEALDGFFLAIMTDGSIIYVSESVTSLLEHLPSDLVDQSIFNFIPEGEHSEVYKILSTHLLESDSLTPEYLKSKNQLEFCCHMLRGTIDPKEPSTYEYVRFIGNFKSLTSVSTSTHNGFEGTIQRTHRPSYEDRVCFVATVRLATPQFIKEMCTVEEPNEEFTSRHSLEWKFLFLDHRDDSSIFDGLVEEDDKDKAKRVSRNKSEKKRRDQFNVLIKELGSMLPGNARKMDKSTVLQKSIDFLRKHKETTAQSDASEIRQDWKPTFLSNEEFTQLMLEALDGFFLAIMTDGSIIYVSESVTSLLEHLPSDLVDQSIFNFIPEGEHSEVYKILSTHLLESDSLTPEYLKSKNQLEFCCHMLRGTIDPKEPSTYEYVRFIGNFKSLTSVSTSTHNGFEGTIQRTHRPSYEDRVCFVATVRLATPQFIKEMCTVEEPNEEFTSRHSLEWKFLFLDH
IRESfinder result
IRESfinder score
0.766400335
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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