top of page
mmu_circCcdc40_597
Basic information of circular RNA
PanCircBase ID:
mmu_circCcdc40_597
mm39_Chr. Position ID:
chr11|119142628|119145288|+
Gene name:
Ccdc40
Transcript:
ENSMUST00000235971.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
13,14,15,16
Exon/intron offsets:
0,1447,1817,2539
Genomic length:
2660
Exon/intron sizes in nt:
21,41,70,92,121
Flanking exon/introns:
chr11:119142010-119142628|chr11:119145288-119150680
Splice length:
597
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGGGAAGAAGCTGGACCCCTGGAACTGGAGATCAAAAGGCTGTCGAAGCTGACAGAAGAGTACAACACGGGAGTGGCTGAGGCGCAGATGACCTGGTTGCGCCTGCAGCAGGAACTGGTCCAGGTCACGCATGAGCGCGAGGAGCAGCTGGTGTCCGTGGACCAACTGAAGAAGGAGGTGCACATCATGGAACAAAAGAAGCTTCGCATAGAGAGCAAGATTGCACATGAGAAGAAGGAACAAAAGATAGTGAGCCGCCACATGAGGGACCTGGACAACGACCTGAGCAAGCTCAACATGCTGTTGGACAAGAACCGATGCAGTTCGGAAGAGCTGGAGCAGAACAATATAGCAACTGAGACGGAGTTTCTGCGCACGCTGAAGGACTCAGAAAGAGAGACCATTCAAATGCAGGAAAAGCTGATGGAACTCTCTGAGGAAAAGGCCACCCTCCTCAACAGCTTCATGGAGGCAGAGCACCAAATCATGCTGTGGGAGAAGAAAATCCAACTGGCCAAGGAGATGCGCAGCTCGGTGGATTCTGAGACCGGGCAGACAGAGATCCGTGCTATGAAGGCCGAGATCCACAGGATGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCGGTGGATTCTGAGACC
60.18
GCCACTCCCGTGTTGTACTC
60.67
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCAACTGGCCAAGGAGATG
59.67
GCCACTCCCGTGTTGTACTC
60.67
169
PCR template sequence:
GAAGAAAATCCAACTGGCCAAGGAGATGCGCAGCTCGGTGGATTCTGAGACCGGGCAGACAGAGATCCGTGCTATGAAGGCCGAGATCCACAGGATGAAGGGGGAAGAAGCTGGACCCCTGGAACTGGAGATCAAAAGGCTGTCGAAGCTGACAGAAGAGTACAACACGGGAGTGGCTGAGGCGCAGATGACCTGGTTGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-205-5p(1), mmu-miR-217-5p(1), mmu-miR-433-3p(1), mmu-miR-370-3p(1), mmu-miR-188-3p(1), mmu-miR-1199-5p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
CCACAGGATGAAGGGGGAAGAAGCTG
siRNA sets
TTCTTCCCCCTTCATCCTG, CTTCTTCCCCCTTCATCCT, TTCCCCCTTCATCCTGTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCCDC40_597_ORF_1
1.2169
0.594673845
0.99939629
1107
ORF sequence:
ATGACCTGGTTGCGCCTGCAGCAGGAACTGGTCCAGGTCACGCATGAGCGCGAGGAGCAGCTGGTGTCCGTGGACCAACTGAAGAAGGAGGTGCACATCATGGAACAAAAGAAGCTTCGCATAGAGAGCAAGATTGCACATGAGAAGAAGGAACAAAAGATAGTGAGCCGCCACATGAGGGACCTGGACAACGACCTGAGCAAGCTCAACATGCTGTTGGACAAGAACCGATGCAGTTCGGAAGAGCTGGAGCAGAACAATATAGCAACTGAGACGGAGTTTCTGCGCACGCTGAAGGACTCAGAAAGAGAGACCATTCAAATGCAGGAAAAGCTGATGGAACTCTCTGAGGAAAAGGCCACCCTCCTCAACAGCTTCATGGAGGCAGAGCACCAAATCATGCTGTGGGAGAAGAAAATCCAACTGGCCAAGGAGATGCGCAGCTCGGTGGATTCTGAGACCGGGCAGACAGAGATCCGTGCTATGAAGGCCGAGATCCACAGGATGAAGGGGGAAGAAGCTGGACCCCTGGAACTGGAGATCAAAAGGCTGTCGAAGCTGACAGAAGAGTACAACACGGGAGTGGCTGAGGCGCAGATGACCTGGTTGCGCCTGCAGCAGGAACTGGTCCAGGTCACGCATGAGCGCGAGGAGCAGCTGGTGTCCGTGGACCAACTGAAGAAGGAGGTGCACATCATGGAACAAAAGAAGCTTCGCATAGAGAGCAAGATTGCACATGAGAAGAAGGAACAAAAGATAGTGAGCCGCCACATGAGGGACCTGGACAACGACCTGAGCAAGCTCAACATGCTGTTGGACAAGAACCGATGCAGTTCGGAAGAGCTGGAGCAGAACAATATAGCAACTGAGACGGAGTTTCTGCGCACGCTGAAGGACTCAGAAAGAGAGACCATTCAAATGCAGGAAAAGCTGATGGAACTCTCTGAGGAAAAGGCCACCCTCCTCAACAGCTTCATGGAGGCAGAGCACCAAATCATGCTGTGGGAGAAGAAAATCCAACTGGCCAAGGAGATGCGCAGCTCGGTGGATTCTGAGACCGGGCAGACAGAGATCCGTGCTATGAAGGCCGAGATCCACAGGATGAAG
Peptide sequence:
MTWLRLQQELVQVTHEREEQLVSVDQLKKEVHIMEQKKLRIESKIAHEKKEQKIVSRHMRDLDNDLSKLNMLLDKNRCSSEELEQNNIATETEFLRTLKDSERETIQMQEKLMELSEEKATLLNSFMEAEHQIMLWEKKIQLAKEMRSSVDSETGQTEIRAMKAEIHRMKGEEAGPLELEIKRLSKLTEEYNTGVAEAQMTWLRLQQELVQVTHEREEQLVSVDQLKKEVHIMEQKKLRIESKIAHEKKEQKIVSRHMRDLDNDLSKLNMLLDKNRCSSEELEQNNIATETEFLRTLKDSERETIQMQEKLMELSEEKATLLNSFMEAEHQIMLWEKKIQLAKEMRSSVDSETGQTEIRAMKAEIHRMK
IRESfinder result
IRESfinder score
0.235527869
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page