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mmu_circTtc3_796
Basic information of circular RNA
PanCircBase ID:
mmu_circTtc3_796
mm39_Chr. Position ID:
chr16|94258179|94263489|+
Gene name:
Ttc3
Transcript:
ENSMUST00000117648.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
40,41,42,43,44
Exon/intron offsets:
0,610,2441,4901,5175
Genomic length:
5310
Exon/intron sizes in nt:
9,11,02,34,11,27,135
Flanking exon/introns:
chr16:94257670-94258179|chr16:94263489-94267761
Splice length:
796
Other database IDs:
CIRCpedia: MMU_CIRCpedia_221596, circAtlas: mmu-Ttc3_0091
Human Ortholog IDs:
Mature spliced Sequence:
TGATTCTGCAACGTATCCCGATGTGGAGTATGATATACTTTCATGGGAGTCATTTCTTTCTACTGTAAGAGAAGAGATCGAGAGCAAAAAGTCTCAGTTTGAAGAGCATATTAAGGCCATTAAGAATGGTTCTCGACTCAGTGACCTTTCCAGTGTGCAGCTTTCTGAGGTTTCATTTCCTGGTTGTTCGACGATCCATCCTCAGTTCCTCTCTGAGTCTTCAGGCCATGAGGATCCCGGACTGGTGGCTTGTGTAGACAGCATGACTGGAGCAGTCCTCAATGATCCTTACATGGACTCTGCTAGTGGCTGCCCAGAGGAGGTTCCAGAACTGTCGCTGGGATCACCCACCCATCAGCCAGAAGTTACTCAACAGCTTGAGCTCAAGGGGGCTAGCCAGGTGTCTCCATCAGAACAGAGCCCTGAGGCCGACGAGAAACTATCTGGACAGGCTACTCGGTCAAGCCAGTCTCCAAAAAAGCCTTCCAACAGTATTATTGAACACCTGTCAGTGATATTCCCATGTTATACCAGCACTGAGCTTGCTGGGTTTATTAAGAAAGTTAGAAACAAAACCAAGAACTCATTCTCGGGATTAACTATTGAGGAGATTGTGGAGAAAGTGACAGAACACATTGTCGATGAGCAAAAGAAGAAAAAGCCAAATCCAGGAAAAGACAAGAAGACATCTGAGGCTCATTCGGCTGCCTCTGTGGCCAAGTCCTCCCAGAGTCCACCCTTGGCAGCTGCTGGACCATCAGCTAGAACCAAAGGCCAGAAAAAAGATGATGTCCCT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCAAGTCCTCCCAGAGTCCA
60.55
ACTGAGACTTTTTGCTCTCGA
57.26
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAGTCCTCCCAGAGTCCACC
60.55
ACTGAGACTTTTTGCTCTCGA
57.26
176
PCR template sequence:
TCATTCGGCTGCCTCTGTGGCCAAGTCCTCCCAGAGTCCACCCTTGGCAGCTGCTGGACCATCAGCTAGAACCAAAGGCCAGAAAAAAGATGATGTCCCTTGATTCTGCAACGTATCCCGATGTGGAGTATGATATACTTTCATGGGAGTCATTTCTTTCTACTGTAAGAGAAGAGATCGAGAGCAAAAAGTCTCAGTTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-429-3p(1), mmu-miR-135a-5p(1), mmu-miR-196a-5p(1), mmu-miR-709(1), mmu-miR-320-3p(1), mmu-miR-22-3p(1), mmu-miR-1198-5p(1), mmu-miR-369-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGATGATGTCCCTTGATTCTGCAACG
siRNA sets
GAATCAAGGGACATCATCT, TTGCAGAATCAAGGGACAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTTC3_796_ORF_1
1.116
0.183595324
0.987972045
951
ORF sequence:
ATGAGCAAAAGAAGAAAAAGCCAAATCCAGGAAAAGACAAGAAGACATCTGAGGCTCATTCGGCTGCCTCTGTGGCCAAGTCCTCCCAGAGTCCACCCTTGGCAGCTGCTGGACCATCAGCTAGAACCAAAGGCCAGAAAAAAGATGATGTCCCTTGATTCTGCAACGTATCCCGATGTGGAGTATGATATACTTTCATGGGAGTCATTTCTTTCTACTGTAAGAGAAGAGATCGAGAGCAAAAAGTCTCAGTTTGAAGAGCATATTAAGGCCATTAAGAATGGTTCTCGACTCAGTGACCTTTCCAGTGTGCAGCTTTCTGAGGTTTCATTTCCTGGTTGTTCGACGATCCATCCTCAGTTCCTCTCTGAGTCTTCAGGCCATGAGGATCCCGGACTGGTGGCTTGTGTAGACAGCATGACTGGAGCAGTCCTCAATGATCCTTACATGGACTCTGCTAGTGGCTGCCCAGAGGAGGTTCCAGAACTGTCGCTGGGATCACCCACCCATCAGCCAGAAGTTACTCAACAGCTTGAGCTCAAGGGGGCTAGCCAGGTGTCTCCATCAGAACAGAGCCCTGAGGCCGACGAGAAACTATCTGGACAGGCTACTCGGTCAAGCCAGTCTCCAAAAAAGCCTTCCAACAGTATTATTGAACACCTGTCAGTGATATTCCCATGTTATACCAGCACTGAGCTTGCTGGGTTTATTAAGAAAGTTAGAAACAAAACCAAGAACTCATTCTCGGGATTAACTATTGAGGAGATTGTGGAGAAAGTGACAGAACACATTGTCGATGAGCAAAAGAAGAAAAAGCCAAATCCAGGAAAAGACAAGAAGACATCTGAGGCTCATTCGGCTGCCTCTGTGGCCAAGTCCTCCCAGAGTCCACCCTTGGCAGCTGCTGGACCATCAGCTAGAACCAAAGGCCAGAAAAAAGATGATGTCCCT
Peptide sequence:
MSKRRKSQIQEKTRRHLRLIRLPLWPSPPRVHPWQLLDHQLEPKARKKMMSLDSATYPDVEYDILSWESFLSTVREEIESKKSQFEEHIKAIKNGSRLSDLSSVQLSEVSFPGCSTIHPQFLSESSGHEDPGLVACVDSMTGAVLNDPYMDSASGCPEEVPELSLGSPTHQPEVTQQLELKGASQVSPSEQSPEADEKLSGQATRSSQSPKKPSNSIIEHLSVIFPCYTSTELAGFIKKVRNKTKNSFSGLTIEEIVEKVTEHIVDEQKKKKPNPGKDKKTSEAHSAASVAKSSQSPPLAAAGPSARTKGQKKDDVP
IRESfinder result
IRESfinder score
0.632365159
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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