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mmu_ciPcdh9_1232
Basic information of circular RNA
PanCircBase ID:
mmu_ciPcdh9_1232
mm39_Chr. Position ID:
chr14|94126324|94127556|-
Gene name:
Pcdh9
Transcript:
ENSMUST00000192221.6
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
1
Exon/intron offsets:
0
Genomic length:
1232
Exon/intron sizes in nt:
1232
Flanking exon/introns:
chr14:94125797-94127556
Splice length:
1232
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTGTAAAGTTTCGCATTAACAATTCGAAATACCGTCTTTAGTTGTGTCCTCGGCGTAGATGAGAGGTGTTTGTAATTGGGTAGCTGGCTAGGGTAGAGCTCGCCTACTGGGTTGTATCTGCATCCCCACCTGCACCACTCAGCTGGAACTAATCGCGGGCATCAGCTACTGTGTAGCCTAATGCAGATAAGATTAGAGCCTGGGAGCTGACCAGTCTTACTCCGGGTGGGTAGCTGCCTGGAGCCTTGCACCCATTTAAACTGCAGTTAGAGGGGCATCTGAGCGGAAGTTCTTCTACGTGTGTTACCGGGTTGCGGTATTTATGTGTAGCAAATGTTACTAATATTCTAATGAGACACCGGATTAAGAAACTGCATTTTTGTTCTTTTATGCTCAATAGAAAAAAAAATACCGTGATGTTACATAGGAATGTTGTCTGTGTTTCACTTCCATCCCGGCATGCTGGTCCACCTCTGTGATAAGCAATTGTCTATTAGGATACGTTTTTTAAAAAGTTTTAATGTGTTTATTTATCTCAACGGGGGCAATGTGGAAATATGGAGAAAGGAGAGCACCCTCCGAGGAAGAAATGCCAAGTCTTGGTTTTGTGCTTTGAGGCAATGAGAACCCTTAGTGGCCAGTGACTACTGCTGTTGCTGCGGCTGCAGCAGCATGTCCGAATGCTCATTTTCCAGGAGGGTTGGATTATGAGACAGTTGAAGAACTGGGAGGAAGGAAAAGCAGTCTTTTGAGAGGAGGAGATGACTCAGTGTGGCAGAGAAGAAAACACATCATATCTAACATGTGACAAAGCAGTTGGCAGCAATCATAGCTAAATACTTGAGCTCTTTCCATCGCAAACAACTAGGGGAGGTGGGCTAGAGACCAGGAGGAGGGTTAAATGGGGGTGGGGGGTGTGTGGGAAAGCAAAATAAGAATGCACACTTTGAATTAAACAGTGTTATAATAAAACCAAAACAGTGTGGGGGTGGGGGGATTCCAGGTAAAAATAGCTGCTGCTGTCCTTAATTCAAAAGTAGATGAATTTCATTTTCTCTGGGCAAATGCAACAAGCAGGGGATATTCAGTGGCCACAGAGTTAACTTACAAACTGTGGCAGAGCAAACTGCCATGTTTACTAATGTGCAGGGAGAGTGTGCTTCGATGTTTTGGTGACTGTGTTTTCATTTACTGAAGAATAATATTGTCTGTACAATTGTGTTGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGGAGAGTGTGCTTCGATGT
59.75
CTCATCTACGCCGAGGACAC
59.97
147
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGGAGAGTGTGCTTCGATGT
59.75
CTACCCTAGCCAGCTACCCA
60.11
180
PCR template sequence:
GCCATGTTTACTAATGTGCAGGGAGAGTGTGCTTCGATGTTTTGGTGACTGTGTTTTCATTTACTGAAGAATAATATTGTCTGTACAATTGTGTTGACAGGTAAGTGTAAAGTTTCGCATTAACAATTCGAAATACCGTCTTTAGTTGTGTCCTCGGCGTAGATGAGAGGTGTTTGTAATTGGGTAGCTGGCTAGGGTAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
10
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-322-5p(1), mmu-miR-30d-5p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-382-5p(1), mmu-miR-207(1), mmu-miR-193b-3p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTGTGTTGACAGGTAAGTGTAAAGT
siRNA sets
TACACTTACCTGTCAACAC, ACTTTACACTTACCTGTCA, TTACACTTACCTGTCAACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.683938382
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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