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mmu_circTtc3_1171
Basic information of circular RNA
PanCircBase ID:
mmu_circTtc3_1171
mm39_Chr. Position ID:
chr16|94204172|94225046|+
Gene name:
Ttc3
Transcript:
ENSMUST00000117648.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
12
Exon/intron indexes:
11,12,13,14,15,16,17,18,19,20,21,22
Exon/intron offsets:
0,5240,6370,7519,8746,12635,12968,15293,16084,16934,18913,20751
Genomic length:
20874
Exon/intron sizes in nt:
5,51,63,46,12,46,46,18,00,00,00,00,00,00,000
Flanking exon/introns:
chr16:94194033-94204172|chr16:94225046-94225945
Splice length:
1171
Other database IDs:
CIRCpedia: MMU_CIRCpedia_34810, circAtlas: mmu-Ttc3_0005
circBase: hsa_circ_0061668, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_35448
Human Ortholog IDs:
Mature spliced Sequence:
AAATGCACTTAGCGATGGAAAGAGGGCCATTGTTTTGAAGAACACCTGGCCAAAGGGTCATTATCGTTATTGTGATGCTCTTTGTATGCTGGGGGAATATGACTGGGCCCTGCAAGCAAACATAAAAGCTCAAAAACTCTGTAAAAATGACCCTGAGGGAATCAAGGATCTAATTCAGCAGCATGTAAAGTTACAAAAACAAATAGAAGACCTACAAGGTCGGACATCAAATAAGAATCCAATTAAAGCTTTTTATGAAAGCAGGGCTTACATACCTAGAAACTCATCAGCACCTGCTTTTAGGACATCACTTAACTTTGTGGAAACAGAAAGAGGTTTCAGAAAAACTAAGTACAAAATGGCAAATGGTGGCGATCAGAATCAAAAGGTGGCAGATGAGGCTTTGAAGGGGGACGATTGTGACTGTCATCCTGAATTTCTGCCACCTCCAAGTCAGCCTCCAAGACACAAAGGAAAACAAAAATCACGAAACAATGAATCAGAAAAGCCCAGTTCTAATTCAGAAGTGAGTTTACAAGTAGATTTGAAAAGCATTTTGGAGAAACAGTTTTCAAAATCTTCCAGAGCTGCACACCAGGATTTTGCTAACATCATGAAAATGCTAAGGAGCTTGATTCAGGATGGGTACACGGCCCTGTTAGAGCAGCGCTGCCGCAGCGCTGCCCAGGCCTTTACAGAGCTGCTCAATGGTTTAGACCCTCAGAAAATAAAGCAATTGAACCTGGCCATGATTAATTATGTATTAGTAGTCTATGGACTTGCCGTTTCTCTCCTTGGAATAGGACGACCAGAGGAGCTGTCTGAAGCCGAAAACCAGTTTAAGAGGATTATCGAACACTATCCCAATGAGGGGCTGGACTGCTTGGCCTACTGCGGAATAGGAAAAGTGTATTTGAAAAAGAACAGATTTCTCGAAGCTCTTAATCACTTTGAAAAGGCAAAGACTTTAATTAGTCGTCTCCCTGGAATTCTAACTTGGCCCACAAGTAATGTGATTATTGAAGAATCTAAGCCAGAAAAAGTCAAGGTGATGTTAGAGAAGTTTGTTGAAGAATGCAAGTTTCCCCCAGTGCCAGATGCTGTTTGTTGCTATCAGAAGTGCCGTGGATATTCTAAAATTCAGATTTACTTAACTGATCCAGACTTTAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCCAGATGCTGTTTGTTGC
59.97
CCCCCAGCATACAAAGAGCA
60.03
175
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTATCAGAAGTGCCGTGG
60.11
CCCCCAGCATACAAAGAGCA
60.03
158
PCR template sequence:
AGAATGCAAGTTTCCCCCAGTGCCAGATGCTGTTTGTTGCTATCAGAAGTGCCGTGGATATTCTAAAATTCAGATTTACTTAACTGATCCAGACTTTAAGAAATGCACTTAGCGATGGAAAGAGGGCCATTGTTTTGAAGAACACCTGGCCAAAGGGTCATTATCGTTATTGTGATGCTCTTTGTATGCTGGGGGAATAT
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-3065-5p(2), mmu-miR-23b-3p(1), mmu-miR-328-3p(1), mmu-miR-185-5p(1), mmu-miR-495-3p(1), mmu-miR-541-5p(1), mmu-miR-362-5p(1), mmu-miR-369-3p(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCCAGACTTTAAGAAATGCACTTAGC
siRNA sets
AAGTGCATTTCTTAAAGTC, AGTGCATTTCTTAAAGTCT, GTGCATTTCTTAAAGTCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTTC3_1171_ORF_1
0.7725
0.054253173
0.986400949
1098
ORF sequence:
ATGCTGGGGGAATATGACTGGGCCCTGCAAGCAAACATAAAAGCTCAAAAACTCTGTAAAAATGACCCTGAGGGAATCAAGGATCTAATTCAGCAGCATGTAAAGTTACAAAAACAAATAGAAGACCTACAAGGTCGGACATCAAATAAGAATCCAATTAAAGCTTTTTATGAAAGCAGGGCTTACATACCTAGAAACTCATCAGCACCTGCTTTTAGGACATCACTTAACTTTGTGGAAACAGAAAGAGGTTTCAGAAAAACTAAGTACAAAATGGCAAATGGTGGCGATCAGAATCAAAAGGTGGCAGATGAGGCTTTGAAGGGGGACGATTGTGACTGTCATCCTGAATTTCTGCCACCTCCAAGTCAGCCTCCAAGACACAAAGGAAAACAAAAATCACGAAACAATGAATCAGAAAAGCCCAGTTCTAATTCAGAAGTGAGTTTACAAGTAGATTTGAAAAGCATTTTGGAGAAACAGTTTTCAAAATCTTCCAGAGCTGCACACCAGGATTTTGCTAACATCATGAAAATGCTAAGGAGCTTGATTCAGGATGGGTACACGGCCCTGTTAGAGCAGCGCTGCCGCAGCGCTGCCCAGGCCTTTACAGAGCTGCTCAATGGTTTAGACCCTCAGAAAATAAAGCAATTGAACCTGGCCATGATTAATTATGTATTAGTAGTCTATGGACTTGCCGTTTCTCTCCTTGGAATAGGACGACCAGAGGAGCTGTCTGAAGCCGAAAACCAGTTTAAGAGGATTATCGAACACTATCCCAATGAGGGGCTGGACTGCTTGGCCTACTGCGGAATAGGAAAAGTGTATTTGAAAAAGAACAGATTTCTCGAAGCTCTTAATCACTTTGAAAAGGCAAAGACTTTAATTAGTCGTCTCCCTGGAATTCTAACTTGGCCCACAAGTAATGTGATTATTGAAGAATCTAAGCCAGAAAAAGTCAAGGTGATGTTAGAGAAGTTTGTTGAAGAATGCAAGTTTCCCCCAGTGCCAGATGCTGTTTGTTGCTATCAGAAGTGCCGTGGATATTCTAAAATTCAGATTTACTTAACTGATCCAGACTTTAAGAAATGCACTTAG
Peptide sequence:
MLGEYDWALQANIKAQKLCKNDPEGIKDLIQQHVKLQKQIEDLQGRTSNKNPIKAFYESRAYIPRNSSAPAFRTSLNFVETERGFRKTKYKMANGGDQNQKVADEALKGDDCDCHPEFLPPPSQPPRHKGKQKSRNNESEKPSSNSEVSLQVDLKSILEKQFSKSSRAAHQDFANIMKMLRSLIQDGYTALLEQRCRSAAQAFTELLNGLDPQKIKQLNLAMINYVLVVYGLAVSLLGIGRPEELSEAENQFKRIIEHYPNEGLDCLAYCGIGKVYLKKNRFLEALNHFEKAKTLISRLPGILTWPTSNVIIEESKPEKVKVMLEKFVEECKFPPVPDAVCCYQKCRGYSKIQIYLTDPDFKKCT
IRESfinder result
IRESfinder score
0.655233569
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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