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mmu_circCcdc40_830
Basic information of circular RNA
PanCircBase ID:
mmu_circCcdc40_830
mm39_Chr. Position ID:
chr11|119133252|119137176|+
Gene name:
Ccdc40
Transcript:
ENSMUST00000235971.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
7,8,9,10,11
Exon/intron offsets:
0,286,570,3408,3741
Genomic length:
3924
Exon/intron sizes in nt:
15,81,23,12,22,44,183
Flanking exon/introns:
chr11:119129074-119133252|chr11:119137176-119141764
Splice length:
830
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TGGCCGCCCTGCAGACAGAGGTGGAGAGCCTGGCCCTGCACCTCTTCTACATGCAGAACATAGAGCAGGACGTGCGCGATGACATCCAAGTCATGAAGCAGGTGGTGAGGAAGACCGAGACGGAGAAGATGCACGCCGAGGTGGAGAAGAAAAAGCAGGACCTGTTTGTGGACCAGCTCACCGAAAGGTCACACCAGCTAGAAGAAAACATCGCCCTGTTTGAGGCTCAATACTTGTCCCAGGCTGAGGACACCCGGGTCCTCAAGAAAGCAGTGACTGAGGCCATCACAGAGATTGACACCATTGCCGTGGAGAAGAAGCGAATCCTACAGCAGTGGACCACCAGCCTAGTGGGCATGAAGCACCGTAACGAGGCATACAAGACAGTGATGGATGCGCTCAGGGAGTGTCAGCATCAGGTGAAGTCCACCGACAGTGAGATCGAAGTCTGCAAGAAGTCCATCATGCAGGAGGAAGAGAAGAATGAGAAGCTGGCCCGTCTCCTGAACCGCGCAGAGACAGAAGCCACACTGGTGCAGAAAATGACCGCCCAGTGCTTAAGCAAGCAAGAGGCTCTGCAGACGGAGTTTAACACGTACCAGCTCGCCCTGCAGGACACGGAGGAGATGCTGAACAAGGGCTATGTGGAACACTCGGCAGTCTTGAGCGAGCTCCAGGCCACACGCCAGGCTTTCCACCAGGAACAGGAGCTACGGCAAAAGATGGACATGTCCATGGTGGACAAGCTGCAGGAACAGGGGACCTCCAGCAAGATGACCAAGTACTTTCATCAGCTCCTTCGGAAGCTGCAAAAGGAAAACACCAACCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGACCTCCAGCAAGATGACC
60.11
CGCACGTCCTGCTCTATGTT
60.46
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGACCTCCAGCAAGATGAC
60.11
CGCACGTCCTGCTCTATGTT
60.46
148
PCR template sequence:
GTCCATGGTGGACAAGCTGCAGGAACAGGGGACCTCCAGCAAGATGACCAAGTACTTTCATCAGCTCCTTCGGAAGCTGCAAAAGGAAAACACCAACCTGTGGCCGCCCTGCAGACAGAGGTGGAGAGCCTGGCCCTGCACCTCTTCTACATGCAGAACATAGAGCAGGACGTGCGCGATGACATCCAAGTCATGAAGCA
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-433-3p(1), mmu-miR-125a-5p(1), mmu-miR-207(1), mmu-miR-484(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAACACCAACCTGTGGCCGCCCTGCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCCDC40_830_ORF_1
1.2234
0.529568632
0.994736695
843
ORF sequence:
ATGCAGAACATAGAGCAGGACGTGCGCGATGACATCCAAGTCATGAAGCAGGTGGTGAGGAAGACCGAGACGGAGAAGATGCACGCCGAGGTGGAGAAGAAAAAGCAGGACCTGTTTGTGGACCAGCTCACCGAAAGGTCACACCAGCTAGAAGAAAACATCGCCCTGTTTGAGGCTCAATACTTGTCCCAGGCTGAGGACACCCGGGTCCTCAAGAAAGCAGTGACTGAGGCCATCACAGAGATTGACACCATTGCCGTGGAGAAGAAGCGAATCCTACAGCAGTGGACCACCAGCCTAGTGGGCATGAAGCACCGTAACGAGGCATACAAGACAGTGATGGATGCGCTCAGGGAGTGTCAGCATCAGGTGAAGTCCACCGACAGTGAGATCGAAGTCTGCAAGAAGTCCATCATGCAGGAGGAAGAGAAGAATGAGAAGCTGGCCCGTCTCCTGAACCGCGCAGAGACAGAAGCCACACTGGTGCAGAAAATGACCGCCCAGTGCTTAAGCAAGCAAGAGGCTCTGCAGACGGAGTTTAACACGTACCAGCTCGCCCTGCAGGACACGGAGGAGATGCTGAACAAGGGCTATGTGGAACACTCGGCAGTCTTGAGCGAGCTCCAGGCCACACGCCAGGCTTTCCACCAGGAACAGGAGCTACGGCAAAAGATGGACATGTCCATGGTGGACAAGCTGCAGGAACAGGGGACCTCCAGCAAGATGACCAAGTACTTTCATCAGCTCCTTCGGAAGCTGCAAAAGGAAAACACCAACCTGTGGCCGCCCTGCAGACAGAGGTGGAGAGCCTGGCCCTGCACCTCTTCTACATGCAGAACATAG
Peptide sequence:
MQNIEQDVRDDIQVMKQVVRKTETEKMHAEVEKKKQDLFVDQLTERSHQLEENIALFEAQYLSQAEDTRVLKKAVTEAITEIDTIAVEKKRILQQWTTSLVGMKHRNEAYKTVMDALRECQHQVKSTDSEIEVCKKSIMQEEEKNEKLARLLNRAETEATLVQKMTAQCLSKQEALQTEFNTYQLALQDTEEMLNKGYVEHSAVLSELQATRQAFHQEQELRQKMDMSMVDKLQEQGTSSKMTKYFHQLLRKLQKENTNLWPPCRQRWRAWPCTSSTCRT
IRESfinder result
IRESfinder score
0.211777334
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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