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mmu_ciTm9sf3_738
Basic information of circular RNA
PanCircBase ID:
mmu_ciTm9sf3_738
mm39_Chr. Position ID:
chr19|41205870|41206608|-
Gene name:
Tm9sf3
Transcript:
ENSMUST00000025989.10
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
12
Exon/intron offsets:
0
Genomic length:
738
Exon/intron sizes in nt:
738
Flanking exon/introns:
chr19:41205870-41206608
Splice length:
738
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTGCCAGAGGGTGGGTGGGGCCTCTCAAGATTTTTTTTTTTTTGGTCTTTAAGACAGGATCTCTTTGTTATGTAGCTCTGGCTGTCCTGGAACTTGCTGTATAGACCAGGCTGTCCTCAAACTCAAAGATATCCACCTGCCTCTGCCTCCCAGGTTCTGGGATTAAAGGTGTGTGCTACCATATCCCGCCAGTACGCTAATAGCATAGCATAGCATAGCATAGCATAGCATAGCATAGCATATAATAGCATAGGTTTGCATCTGAAACTTGTCAAGCTGAGGAGAGGACTGTGCAGAATTGCATCGCTGGAGAGAATAGAGGACCTGGGCGTGGCAGTGCACACTTGCAGTCCTAGCCCTGGGGAGGCAAAGAAGATGGTGAATAAAAAAGATATAGTAGAGGGATGTGTTTTCTCTAGTTGTAAATGTGATGTGAAGTTGATGGGAAAATAGTTTGAGTCAAATTGTTTGTCCGGTTTGGGATATTTCTGCAAAGCGCCCTGCATTGAGCTCTGAGGGAGCTGGAGTACTTAAAGTCACTCCGAGAACCTGGCCAGACTCAGGCATTTCTAGTTCCTAGACTCTTCTCTCTTAATACTCAAGCACCAGGTACAAGGATTTGTTTTTAAGCATGCAGGCTTATAAAGGATATTTTTGTAAAATTCTTTGCCTTATAATTTGGAGTGCCGTTCATTCCAGAAGCATAACTGGTTTTAATTTTGGTTTGATTGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGCCGTTCATTCCAGAAGC
59.83
CAAGTTCCAGGACAGCCAGA
59.6
151
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCGTTCATTCCAGAAGCA
60.25
CAAGTTCCAGGACAGCCAGA
59.6
150
PCR template sequence:
CAGGCTTATAAAGGATATTTTTGTAAAATTCTTTGCCTTATAATTTGGAGTGCCGTTCATTCCAGAAGCATAACTGGTTTTAATTTTGGTTTGATTGCAGGTAAGTGCCAGAGGGTGGGTGGGGCCTCTCAAGATTTTTTTTTTTTTGGTCTTTAAGACAGGATCTCTTTGTTATGTAGCTCTGGCTGTCCTGGAACTTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-19a-3p(1), mmu-miR-298-5p(1), mmu-miR-709(1), mmu-miR-362-5p(1), mmu-miR-324-3p(1), mmu-miR-410-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGTTTGATTGCAGGTAAGTGCCAGAG
siRNA sets
ACTTACCTGCAATCAAACC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CITM9SF3_738_ORF_1
0.8501
-0.52681485
0.008984541
159
ORF sequence:
ATGCAGGCTTATAAAGGATATTTTTGTAAAATTCTTTGCCTTATAATTTGGAGTGCCGTTCATTCCAGAAGCATAACTGGTTTTAATTTTGGTTTGATTGCAGGTAAGTGCCAGAGGGTGGGTGGGGCCTCTCAAGATTTTTTTTTTTTTGGTCTTTAA
Peptide sequence:
MQAYKGYFCKILCLIIWSAVHSRSITGFNFGLIAGKCQRVGGASQDFFFFGL
IRESfinder result
IRESfinder score
0.808314887
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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