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mmu_circTimm9_247
Basic information of circular RNA
PanCircBase ID:
mmu_circTimm9_247
mm39_Chr. Position ID:
chr12|71172235|71178860|-
Gene name:
Timm9
Transcript:
ENSMUST00000166120.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,4,3
Exon/intron offsets:
0,871,6539
Genomic length:
6625
Exon/intron sizes in nt:
96,65,86
Flanking exon/introns:
chr12:71170460-71172235|chr12:71178860-71179280
Splice length:
247
Other database IDs:
CIRCpedia: MMU_CIRCpedia_27719, circAtlas: mmu-Timm9_0002
circBase: hsa_circ_0009160, circAtlas: hsa-TIMM9_0002, CIRCpedia: HSA_CIRCpedia_84715
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGAAATCCAGTCTCACTGAAGACAAGCAGAAGGCGGGGCACTTGCTTTTCCAGAGCAGAAAAGAAACTGATGCATCAGAAAAGGTGACTAATAAACATACTGAAAGAATATGGCTGCACAGATACCGGAATCTGACCAGATAAAACAGTTTAAGGAGTTCCTGGGAACCTACAATAAACTTACAGAAACCTGCTTTTTGGACTGTGTTAAAGACTTCACAACAAGAGAGGTGAAACCTGAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTGCTTTTTGGACTGTGT
57.86
AGTCACCTTTTCTGATGCATCA
57.97
149
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTGCTTTTTGGACTGTGTT
58.54
AGTCACCTTTTCTGATGCATCA
57.97
149
PCR template sequence:
ACAGTTTAAGGAGTTCCTGGGAACCTACAATAAACTTACAGAAACCTGCTTTTTGGACTGTGTTAAAGACTTCACAACAAGAGAGGTGAAACCTGAAGAGGTAAGAAATCCAGTCTCACTGAAGACAAGCAGAAGGCGGGGCACTTGCTTTTCCAGAGCAGAAAAGAAACTGATGCATCAGAAAAGGTGACTAATAAACA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-1904(2)
siRNAs for circular RNA silencing
Junction sequence
GAAACCTGAAGAGGTAAGAAATCCAG
siRNA sets
GATTTCTTACCTCTTCAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTIMM9_247_ORF_1
0.6157
0.013065647
0.080719017
225
ORF sequence:
ATGGCTGCACAGATACCGGAATCTGACCAGATAAAACAGTTTAAGGAGTTCCTGGGAACCTACAATAAACTTACAGAAACCTGCTTTTTGGACTGTGTTAAAGACTTCACAACAAGAGAGGTGAAACCTGAAGAGGTAAGAAATCCAGTCTCACTGAAGACAAGCAGAAGGCGGGGCACTTGCTTTTCCAGAGCAGAAAAGAAACTGATGCATCAGAAAAGGTGA
Peptide sequence:
MAAQIPESDQIKQFKEFLGTYNKLTETCFLDCVKDFTTREVKPEEVRNPVSLKTSRRRGTCFSRAEKKLMHQKR
IRESfinder result
IRESfinder score
0.661110563
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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