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mmu_ciDnajc13_1349
Basic information of circular RNA
PanCircBase ID:
mmu_ciDnajc13_1349
mm39_Chr. Position ID:
chr9|104077737|104079086|-
Gene name:
Dnajc13
Transcript:
ENSMUST00000035170.13
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
25
Exon/intron offsets:
0
Genomic length:
1349
Exon/intron sizes in nt:
1349
Flanking exon/introns:
chr9:104077737-104079086
Splice length:
1349
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTACAGTATCCCTGTGAGTTACTGTCACTTAATAAGGTACAGTATCCCTGTGAGTCACTGTCACTTAATAAGGTACAGTGTTCCCTATGAGTCACTGTCACTTAATAAGGTACAGTATCCCTGTGAGTCACTGTCACTTAATAAGGTACAGTATTCCCTATGAGTCACTGTCACTTAATAAGGTACAGTGTTACCTATGAGTCACTGTCACTTAATAAGGTACAGTATTCCCTGTGAGTCACTGTCACTTAATAAGGTACAGTGTTACCTATGAGTCACTGTCACTTAATAAGGTACAGTATTCCCTATGAGTCACTGTCACTTAATAAGGTACAGTATTCCCTATGAGTCACTGTCACTTAATAAGGTACAGTGTTACCTATGAGTCACTGTCACTTAATAAGGTACAGTATTCCCTATGAGTCACTGTCACTTAATAAGGTACAGTATCCCTGTGAGTCACTGTCACTTAATAAGGTACAGTATTCCCTATGAGTCACTGTCACTTAATAAGGTACAGTATCCCTGTGAGTCACTGTCACTTAATAAGGTACAGTATCCCTGTGAGTCACTGTCACTTAATAAGGTACAGTATCCCTGTGAGTCACTGTCACTTAATAAGGTACAGTGTTACCTATGAGTTACTGTCACTTAATAAGGTACAGTATTCCCTATGAGTCACTGTAATACGGTACAGTAGTCCCTATGAGTCACGGTCACTTAATAAGGTACAGTGTTCCCTATGAGTCACTGTCACTCCCCAGGCCTGCGCCCGGGCACTGCTGACCTGCCAGACAGGTCACCCACGGGGGCTGCTTTTCTCTAAGATGAGAAAACTGGGTTTATAGAGGGAAAGGTTTGCTGGTTTTCCTGAGTGGTCTGTCCTGGTGTTCCAGGCGCTAGATGGAGCCTAGTCCTTTATGTTTACAGAAACAGACAGGAGGTGCTGGAGGTATGTATGGCTCAGAGGTAGAGTACTTCCCCAGTGTGTGTGCAGCACTGCATAATTTAGAACATGGAAGAGTTCTTTAATGTACCATTTTATTTCTGGTTACTGGATAACCTGTTTACTGGTGGGCAGGATAATTGTAGGGCTAGGGTTTATCATGCCGCTTTGTCTTTATTGGGGGAGGAAAGTGCTTACTCAGACTGTATTAAGTGGACATTCTTACATGATCTCTTTATGGGATAATTTTGTCTTTTGAATCCTACAAATGCCAAGTAAGTATGGTTGCATGCCAGCATGTCTAAAGAAATTCCACATGTGCTCATCCTAGAGAGTGTTCTAGGTTACAGTGCCGATTGAAGAGAAAGGCTTTCAATTATGCAAAAATGCTTTCCTCTTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCACATGTGCTCATCCTAGAGA
59.3
GTGACAGTGACTCACAGGGA
58.96
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCCACATGTGCTCATCCTAGAG
59.3
GTGACAGTGACTCACAGGGA
58.96
156
PCR template sequence:
AAAGAAATTCCACATGTGCTCATCCTAGAGAGTGTTCTAGGTTACAGTGCCGATTGAAGAGAAAGGCTTTCAATTATGCAAAAATGCTTTCCTCTTTCAGGTACAGTATCCCTGTGAGTTACTGTCACTTAATAAGGTACAGTATCCCTGTGAGTCACTGTCACTTAATAAGGTACAGTGTTCCCTATGAGTCACTGTCA
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-429-3p(7), mmu-miR-200b-3p(7), mmu-miR-141-3p(6), mmu-miR-30e-5p(1), mmu-miR-30a-5p(1), mmu-miR-30d-5p(1), mmu-miR-466d-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTCCTCTTTCAGGTACAGTATCCCT
siRNA sets
ATACTGTACCTGAAAGAGG, GATACTGTACCTGAAAGAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIDNAJC13_1349_ORF_5
0.656
-0.209767438
0.025457536
180
ORF sequence:
ATGCTTTCCTCTTTCAGGTACAGTATCCCTGTGAGTTACTGTCACTTAATAAGGTACAGTATCCCTGTGAGTCACTGTCACTTAATAAGGTACAGTGTTCCCTATGAGTCACTGTCACTTAATAAGGTACAGTATCCCTGTGAGTCACTGTCACTTAATAAGGTACAGTATTCCCTATGA
Peptide sequence:
MLSSFRYSIPVSYCHLIRYSIPVSHCHLIRYSVPYESLSLNKVQYPCESLSLNKVQYSL
IRESfinder result
IRESfinder score
0.850499702
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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