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mmu_circNcaph_570
Basic information of circular RNA
PanCircBase ID:
mmu_circNcaph_570
mm39_Chr. Position ID:
chr2|126947765|126955590|-
Gene name:
Ncaph
Transcript:
ENSMUST00000110387.4
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
17,16,15,14,13
Exon/intron offsets:
0,258,1508,2639,7714
Genomic length:
7825
Exon/intron sizes in nt:
76,92,11,71,74,111
Flanking exon/introns:
chr2:126946200-126947765|chr2:126955590-126958451
Splice length:
570
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
TCACTTAAGATGGACCAGGACCAGAAGGCTAAGACTGAGCACTATGAGGAAATTGAAGACTATGATTACAACAACCCTAACGACACCTCCAACTATTGTCCTGGACTTCAGGCTGCTGACAGTGATTATGAAGAGGCAGACGATTTATTTGCGGATCCAGTCGGGACCCTTGACCTTGAGTCTGATCCAAAGACAACACAAGAGAATGGTCACATTTCTCCTGAAAACCAAGGAGTAGATATCACAACTTACCAAGAGTTGAACTTGGTGGCTGAGCCTCAAAAGGTGAATAAAATAGAAATTCATTACGCCAAGACTGCCAAAAAGATGGACATGAAGAAGCTGAAGCAGAGTATGTGGAGTCTGCTGACGAAGTTTTCTAGGAAGGAGGCTGACACAGAGGCAAACCACACTGAAAGTGGACAGGAAGGTGCCCCCGAGGAAGTGGCTGATGAGAAGAAACTCAGTGGGCTCACAAAGGACCTGCAGACAAGGCTGCCCCCGCTCATGGCTCAGAACCTCTCCATACCCCTGGCTTTTGCCTGTCTTCTGCACTTAGCAAATGAAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCCATACCCCTGGCTTTTGC
60.32
GTTGGAGGTGTCGTTAGGGT
59.32
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCATGGCTCAGAACCTCT
59.46
TGGAGGTGTCGTTAGGGTTG
59.32
158
PCR template sequence:
GCTCACAAAGGACCTGCAGACAAGGCTGCCCCCGCTCATGGCTCAGAACCTCTCCATACCCCTGGCTTTTGCCTGTCTTCTGCACTTAGCAAATGAAAAGTCACTTAAGATGGACCAGGACCAGAAGGCTAAGACTGAGCACTATGAGGAAATTGAAGACTATGATTACAACAACCCTAACGACACCTCCAACTATTGTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-24-3p(1), mmu-miR-384-3p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCAAATGAAAAGTCACTTAAGATGG
siRNA sets
CATCTTAAGTGACTTTTCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNCAPH_570_ORF_1
1.1965
0.34711882
0.998552107
1131
ORF sequence:
ATGGACCAGGACCAGAAGGCTAAGACTGAGCACTATGAGGAAATTGAAGACTATGATTACAACAACCCTAACGACACCTCCAACTATTGTCCTGGACTTCAGGCTGCTGACAGTGATTATGAAGAGGCAGACGATTTATTTGCGGATCCAGTCGGGACCCTTGACCTTGAGTCTGATCCAAAGACAACACAAGAGAATGGTCACATTTCTCCTGAAAACCAAGGAGTAGATATCACAACTTACCAAGAGTTGAACTTGGTGGCTGAGCCTCAAAAGGTGAATAAAATAGAAATTCATTACGCCAAGACTGCCAAAAAGATGGACATGAAGAAGCTGAAGCAGAGTATGTGGAGTCTGCTGACGAAGTTTTCTAGGAAGGAGGCTGACACAGAGGCAAACCACACTGAAAGTGGACAGGAAGGTGCCCCCGAGGAAGTGGCTGATGAGAAGAAACTCAGTGGGCTCACAAAGGACCTGCAGACAAGGCTGCCCCCGCTCATGGCTCAGAACCTCTCCATACCCCTGGCTTTTGCCTGTCTTCTGCACTTAGCAAATGAAAAGTCACTTAAGATGGACCAGGACCAGAAGGCTAAGACTGAGCACTATGAGGAAATTGAAGACTATGATTACAACAACCCTAACGACACCTCCAACTATTGTCCTGGACTTCAGGCTGCTGACAGTGATTATGAAGAGGCAGACGATTTATTTGCGGATCCAGTCGGGACCCTTGACCTTGAGTCTGATCCAAAGACAACACAAGAGAATGGTCACATTTCTCCTGAAAACCAAGGAGTAGATATCACAACTTACCAAGAGTTGAACTTGGTGGCTGAGCCTCAAAAGGTGAATAAAATAGAAATTCATTACGCCAAGACTGCCAAAAAGATGGACATGAAGAAGCTGAAGCAGAGTATGTGGAGTCTGCTGACGAAGTTTTCTAGGAAGGAGGCTGACACAGAGGCAAACCACACTGAAAGTGGACAGGAAGGTGCCCCCGAGGAAGTGGCTGATGAGAAGAAACTCAGTGGGCTCACAAAGGACCTGCAGACAAGGCTGCCCCCGCTCATGGCTCAGAACCTCTCCATACCCCTGGCTTTTGCCTGTCTTCTGCACTTAGCAAATGAAAAG
Peptide sequence:
MDQDQKAKTEHYEEIEDYDYNNPNDTSNYCPGLQAADSDYEEADDLFADPVGTLDLESDPKTTQENGHISPENQGVDITTYQELNLVAEPQKVNKIEIHYAKTAKKMDMKKLKQSMWSLLTKFSRKEADTEANHTESGQEGAPEEVADEKKLSGLTKDLQTRLPPLMAQNLSIPLAFACLLHLANEKSLKMDQDQKAKTEHYEEIEDYDYNNPNDTSNYCPGLQAADSDYEEADDLFADPVGTLDLESDPKTTQENGHISPENQGVDITTYQELNLVAEPQKVNKIEIHYAKTAKKMDMKKLKQSMWSLLTKFSRKEADTEANHTESGQEGAPEEVADEKKLSGLTKDLQTRLPPLMAQNLSIPLAFACLLHLANEK
IRESfinder result
IRESfinder score
0.50481551
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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