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mmu_circCacna1c_1567
Basic information of circular RNA
PanCircBase ID:
mmu_circCacna1c_1567
mm39_Chr. Position ID:
chr6|118644461|118682530|-
Gene name:
Cacna1c
Transcript:
ENSMUST00000186889.7
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
13
Exon/intron indexes:
23,22,21,20,19,18,17,16,15,14,13,12,11
Exon/intron offsets:
0,2849,6845,8319,8805,15494,15831,16649,18616,19505,28920,30132,38042
Genomic length:
38069
Exon/intron sizes in nt:
88,107,60,130,133,70,121,115,121,208,226,161,27
Flanking exon/introns:
chr6:118634383-118644461|chr6:118682530-118690217
Splice length:
1567
Other database IDs:
circAtlas: mmu-Cac1c_0026
Human Ortholog IDs:
Mature spliced Sequence:
CCATCGGATCTCCAAATCCAAATTCAGCCGCTACTGGCGCAGGTGGAATCGATTCTGCAGAAGAAAATGCCGTGCAGCAGTTAAGTCCAACGTCTTCTACTGGCTCGTGATCTTCCTGGTGTTCCTCAACACCCTCACCATTGCCTCCGAACATTACAACCAGCCTCACTGGCTCACAGAAGTGCAAGACACAGCCAATAAAGCCCTCCTGGCCCTTTTCACTGCAGAAATGCTCCTGAAGATGTACAGCCTGGGTCTTCAGGCCTATTTTGTGTCCCTCTTCAACCGCTTTGACTGTTTCATTGTGTGTGGGGGCATCCTGGAGACCATCCTGGTGGAGACGAAGATCATGTCTCCCCTGGGCATCTCTGTGCTGAGATGTGTGCGGTTGCTCAGGATCTTCAAGATCACCAGGTACTGGAATTCCTTGAGCAACCTTGTGGCATCCTTGCTGAACTCAGTGCGCTCCATTGCCTCCCTGCTGCTGCTCCTCTTCCTCTTCATCATCATCTTCTCCCTCCTGGGGATGCAGCTCTTTGGAGGGAAGTTCAATTTCGATGAGATGCAGACCCGTAGGAGCACGTTCGATAACTTCCCGCAGTCTCTCCTCACTGTGTTTCAGATCCTGACCGGGGAGGACTGGAATTCGGTGATGTATGATGGGATCATGGCTTATGGCGGCCCCTCTTTTCCAGGGATGTTAGTCTGTATTTACTTCATCATCCTCTTCATCTGTGGAAATTATATCCTACTGAATGTGTTCTTGGCCATTGCGGTGGACAACCTGGCTGATGCGGAGAGCCTGACCTCAGCCCAAAAGGAGGAGGAAGAAGAGAAGGAGAGGAAGAAGCTGGCCAGGACTGCCAGCCCAGAAAAGAAACAGGAGGTGATGGAGAAGCCAGCCGTGGAGGAGAGCAAAGAGGAGAAAATTGAACTGAAATCCATTACAGCCGATGGAGAATCCCCACCCACTACCAAGATCAACATGGATGACCTCCAGCCCAGTGAAAACGAGGATAAGAGTCCCCACTCCAACCCAGACACTGCAGGGGAAGAGGATGAAGAGGAGCCAGAGATGCCTGTGGGGCCACGCCCCCGGCCCCTGTCTGAGCTGCACCTTAAGGAAAAGGCAGTTCCCATGCCGGAAGCCAGTGCATTTTTCATCTTCAGCCCAAACAACAGGTTCCGCCTGCAGTGCCACCGTATTGTCAATGACACGATCTTCACCAACCTCATCCTCTTCTTCATTCTGCTCAGCAGCATCTCTCTGGCTGCTGAGGACCCCGTCCAGCACACCTCCTTCAGGAACCATATCCTAGGCAATGCAGACTATGTCTTCACTAGTATCTTTACATTAGAAATTATCCTTAAGATGACTGCTTACGGGGCTTTCCTGCACAAGGGCTCTTTCTGCCGAAACTACTTCAATATCCTGGACCTGCTGGTGGTTAGCGTGTCCCTCATCTCCTTTGGCATCCAGTCCAGCGCGATCAACGTTGTGAAGATTTTACGAGTGCTGCGAGTCCTCAGACCCCTGAGGGCCATCAACAGGGCCAAGGGGCTAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTTACGAGTGCTGCGAGTCC
60.39
CTGCTGCACGGCATTTTCTT
60.04
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTTACGAGTGCTGCGAGTCC
60.39
TGCTGCACGGCATTTTCTTC
60.04
140
PCR template sequence:
CTTTGGCATCCAGTCCAGCGCGATCAACGTTGTGAAGATTTTACGAGTGCTGCGAGTCCTCAGACCCCTGAGGGCCATCAACAGGGCCAAGGGGCTAAAGCCATCGGATCTCCAAATCCAAATTCAGCCGCTACTGGCGCAGGTGGAATCGATTCTGCAGAAGAAAATGCCGTGCAGCAGTTAAGTCCAACGTCTTCTAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-207(3), mmu-miR-16-5p(1), mmu-miR-7b-5p(1), mmu-miR-18a-5p(1), mmu-miR-328-3p(1), mmu-miR-324-5p(1), mmu-miR-143-3p(1), mmu-miR-128-3p(1), mmu-miR-149-5p(1), mmu-miR-136-5p(1), mmu-miR-27a-5p(1), mmu-miR-5101(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
CAAGGGGCTAAAGCCATCGGATCTCC
siRNA sets
GAGATCCGATGGCTTTAGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCACNA1C_1567_ORF_1
1.3147
0.415780062
0.999887236
1422
ORF sequence:
ATGCTCCTGAAGATGTACAGCCTGGGTCTTCAGGCCTATTTTGTGTCCCTCTTCAACCGCTTTGACTGTTTCATTGTGTGTGGGGGCATCCTGGAGACCATCCTGGTGGAGACGAAGATCATGTCTCCCCTGGGCATCTCTGTGCTGAGATGTGTGCGGTTGCTCAGGATCTTCAAGATCACCAGGTACTGGAATTCCTTGAGCAACCTTGTGGCATCCTTGCTGAACTCAGTGCGCTCCATTGCCTCCCTGCTGCTGCTCCTCTTCCTCTTCATCATCATCTTCTCCCTCCTGGGGATGCAGCTCTTTGGAGGGAAGTTCAATTTCGATGAGATGCAGACCCGTAGGAGCACGTTCGATAACTTCCCGCAGTCTCTCCTCACTGTGTTTCAGATCCTGACCGGGGAGGACTGGAATTCGGTGATGTATGATGGGATCATGGCTTATGGCGGCCCCTCTTTTCCAGGGATGTTAGTCTGTATTTACTTCATCATCCTCTTCATCTGTGGAAATTATATCCTACTGAATGTGTTCTTGGCCATTGCGGTGGACAACCTGGCTGATGCGGAGAGCCTGACCTCAGCCCAAAAGGAGGAGGAAGAAGAGAAGGAGAGGAAGAAGCTGGCCAGGACTGCCAGCCCAGAAAAGAAACAGGAGGTGATGGAGAAGCCAGCCGTGGAGGAGAGCAAAGAGGAGAAAATTGAACTGAAATCCATTACAGCCGATGGAGAATCCCCACCCACTACCAAGATCAACATGGATGACCTCCAGCCCAGTGAAAACGAGGATAAGAGTCCCCACTCCAACCCAGACACTGCAGGGGAAGAGGATGAAGAGGAGCCAGAGATGCCTGTGGGGCCACGCCCCCGGCCCCTGTCTGAGCTGCACCTTAAGGAAAAGGCAGTTCCCATGCCGGAAGCCAGTGCATTTTTCATCTTCAGCCCAAACAACAGGTTCCGCCTGCAGTGCCACCGTATTGTCAATGACACGATCTTCACCAACCTCATCCTCTTCTTCATTCTGCTCAGCAGCATCTCTCTGGCTGCTGAGGACCCCGTCCAGCACACCTCCTTCAGGAACCATATCCTAGGCAATGCAGACTATGTCTTCACTAGTATCTTTACATTAGAAATTATCCTTAAGATGACTGCTTACGGGGCTTTCCTGCACAAGGGCTCTTTCTGCCGAAACTACTTCAATATCCTGGACCTGCTGGTGGTTAGCGTGTCCCTCATCTCCTTTGGCATCCAGTCCAGCGCGATCAACGTTGTGAAGATTTTACGAGTGCTGCGAGTCCTCAGACCCCTGAGGGCCATCAACAGGGCCAAGGGGCTAAAGCCATCGGATCTCCAAATCCAAATTCAGCCGCTACTGGCGCAGGTGGAATCGATTCTGCAGAAGAAAATGCCGTGCAGCAGTTAA
Peptide sequence:
MLLKMYSLGLQAYFVSLFNRFDCFIVCGGILETILVETKIMSPLGISVLRCVRLLRIFKITRYWNSLSNLVASLLNSVRSIASLLLLLFLFIIIFSLLGMQLFGGKFNFDEMQTRRSTFDNFPQSLLTVFQILTGEDWNSVMYDGIMAYGGPSFPGMLVCIYFIILFICGNYILLNVFLAIAVDNLADAESLTSAQKEEEEEKERKKLARTASPEKKQEVMEKPAVEESKEEKIELKSITADGESPPTTKINMDDLQPSENEDKSPHSNPDTAGEEDEEEPEMPVGPRPRPLSELHLKEKAVPMPEASAFFIFSPNNRFRLQCHRIVNDTIFTNLILFFILLSSISLAAEDPVQHTSFRNHILGNADYVFTSIFTLEIILKMTAYGAFLHKGSFCRNYFNILDLLVVSVSLISFGIQSSAINVVKILRVLRVLRPLRAINRAKGLKPSDLQIQIQPLLAQVESILQKKMPCSS
IRESfinder result
IRESfinder score
0.540586025
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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