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mmu_circTtc13_570
Basic information of circular RNA
PanCircBase ID:
mmu_circTtc13_570
mm39_Chr. Position ID:
chr8|125400186|125405825|-
Gene name:
Ttc13
Transcript:
ENSMUST00000117624.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
19,18,17,16,15,14
Exon/intron offsets:
0,209,914,1774,2893,5554
Genomic length:
5639
Exon/intron sizes in nt:
80,79,80,136,110,85
Flanking exon/introns:
chr8:125398936-125400186|chr8:125405825-125406726
Splice length:
570
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGCAAATAATCCAAAGGGCTTATTGGAAGTCAGAGAAGCTCTGGAAAAGGTACACAAAGTGGAAGACCTCCTTCCAATTATGAAGCAGTTTAATACCAAAACAAAGGACGGGTTCACCGTGAACACCAAAGTCCCCAGCCTCAAAGATCAAGGGAAGGAATATGACGGCTTCACCATCACCATCACAGGAGACAAGGTCGGCAATATCCTATTTTCTGTGGAAACTCAAACCACAGAAGAGAGGACACAGCTGTATCACGCTGAAATAGATGCACTTTATAAAGACCTGACAGCGAAGGGCAAAGTACTGACCCTCTCGGCAGAATTCGGGGAGGCTGATGCTGTCTGCAACTTAATCTTATCCTTAGTGTATTACTTTTATAATTTAATGCCCCTGTCTCGAGGATCTAGTGTCATTGCGTATTCAGTCATTGTGGGAGCGCTGATGGCCAGTGGCAAAGAAGTGGCTGGGAAGATCCCCAAAGGGAAGTTAGTCGACTTTGAAGCCATGACAGCCCCTGGCTCAGAGGCCTTCAGCAAAATAGCAAAAAGCTGGATGAACTTGAAGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTTTGAAGCCATGACAGCCC
59.47
GGAGGTCTTCCACTTTGTGT
57.36
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTTGAAGCCATGACAGCCCC
60.9
GGAGGTCTTCCACTTTGTGT
57.36
142
PCR template sequence:
GGAAGATCCCCAAAGGGAAGTTAGTCGACTTTGAAGCCATGACAGCCCCTGGCTCAGAGGCCTTCAGCAAAATAGCAAAAAGCTGGATGAACTTGAAGAGAGCAAATAATCCAAAGGGCTTATTGGAAGTCAGAGAAGCTCTGGAAAAGGTACACAAAGTGGAAGACCTCCTTCCAATTATGAAGCAGTTTAATACCAAA
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-9-5p(1), mmu-miR-20b-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-204-5p(1), mmu-miR-18a-5p(1), mmu-miR-433-5p(1), mmu-miR-425-5p(1), mmu-miR-193b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TGAACTTGAAGAGAGCAAATAATCCA
siRNA sets
TTATTTGCTCTCTTCAAGT, ATTTGCTCTCTTCAAGTTC, TATTTGCTCTCTTCAAGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTTC13_570_ORF_1
1.0292
0.25355285
0.995145306
1059
ORF sequence:
ATGAAGCAGTTTAATACCAAAACAAAGGACGGGTTCACCGTGAACACCAAAGTCCCCAGCCTCAAAGATCAAGGGAAGGAATATGACGGCTTCACCATCACCATCACAGGAGACAAGGTCGGCAATATCCTATTTTCTGTGGAAACTCAAACCACAGAAGAGAGGACACAGCTGTATCACGCTGAAATAGATGCACTTTATAAAGACCTGACAGCGAAGGGCAAAGTACTGACCCTCTCGGCAGAATTCGGGGAGGCTGATGCTGTCTGCAACTTAATCTTATCCTTAGTGTATTACTTTTATAATTTAATGCCCCTGTCTCGAGGATCTAGTGTCATTGCGTATTCAGTCATTGTGGGAGCGCTGATGGCCAGTGGCAAAGAAGTGGCTGGGAAGATCCCCAAAGGGAAGTTAGTCGACTTTGAAGCCATGACAGCCCCTGGCTCAGAGGCCTTCAGCAAAATAGCAAAAAGCTGGATGAACTTGAAGAGAGCAAATAATCCAAAGGGCTTATTGGAAGTCAGAGAAGCTCTGGAAAAGGTACACAAAGTGGAAGACCTCCTTCCAATTATGAAGCAGTTTAATACCAAAACAAAGGACGGGTTCACCGTGAACACCAAAGTCCCCAGCCTCAAAGATCAAGGGAAGGAATATGACGGCTTCACCATCACCATCACAGGAGACAAGGTCGGCAATATCCTATTTTCTGTGGAAACTCAAACCACAGAAGAGAGGACACAGCTGTATCACGCTGAAATAGATGCACTTTATAAAGACCTGACAGCGAAGGGCAAAGTACTGACCCTCTCGGCAGAATTCGGGGAGGCTGATGCTGTCTGCAACTTAATCTTATCCTTAGTGTATTACTTTTATAATTTAATGCCCCTGTCTCGAGGATCTAGTGTCATTGCGTATTCAGTCATTGTGGGAGCGCTGATGGCCAGTGGCAAAGAAGTGGCTGGGAAGATCCCCAAAGGGAAGTTAGTCGACTTTGAAGCCATGACAGCCCCTGGCTCAGAGGCCTTCAGCAAAATAGCAAAAAGCTGGATGAACTTGAAG
Peptide sequence:
MKQFNTKTKDGFTVNTKVPSLKDQGKEYDGFTITITGDKVGNILFSVETQTTEERTQLYHAEIDALYKDLTAKGKVLTLSAEFGEADAVCNLILSLVYYFYNLMPLSRGSSVIAYSVIVGALMASGKEVAGKIPKGKLVDFEAMTAPGSEAFSKIAKSWMNLKRANNPKGLLEVREALEKVHKVEDLLPIMKQFNTKTKDGFTVNTKVPSLKDQGKEYDGFTITITGDKVGNILFSVETQTTEERTQLYHAEIDALYKDLTAKGKVLTLSAEFGEADAVCNLILSLVYYFYNLMPLSRGSSVIAYSVIVGALMASGKEVAGKIPKGKLVDFEAMTAPGSEAFSKIAKSWMNLK
IRESfinder result
IRESfinder score
0.471820891
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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