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mmu_circTrpc4ap_489
Basic information of circular RNA
PanCircBase ID:
mmu_circTrpc4ap_489
mm39_Chr. Position ID:
chr2|155505576|155515038|-
Gene name:
Trpc4ap
Transcript:
ENSMUST00000041059.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
6,5,4,3,2
Exon/intron offsets:
0,2545,4755,7383,9333
Genomic length:
9462
Exon/intron sizes in nt:
12,95,65,81,17,129
Flanking exon/introns:
chr2:155499863-155505576|chr2:155515038-155534058
Splice length:
489
Other database IDs:
circAtlas: mmu-Trpc4ap_0007
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_366158
Human Ortholog IDs:
Mature spliced Sequence:
TTCACTGAGACCTTTTTGACCGAGAGGGACAAATTGTCCAAATGGAGTGGAATTCCTCAGTTGCTCCTTAAGCTGTATGCCACCAGCCATCTGCACAGTGACTTCGTTGAGTGCCAAAGCATTCTCAAGGAGATTTCTCCTCTTCTCTCTATGGAGGCTATGGCGTTTGTAACTGAAGACAGGAAATTTACTCAAGAAGCTACATACCCAAATACATATATTTTTGACTTATTTGGAGGTGTTGATCTTCTTGTAGAAATTCTTATGAGGCCTACCATCTCTATCCGGGGACAGAAACTAAAAATAAGTGACGAGATGTCGAAGGACTGCTTGAGCATCCTGTACAATACCTGTGTCTGCACGGAAGGAGTAACGAAGCGTTTGGCAGAAAAGAATGATTTTGTGATTTTTCTGTTCACACTGATGACAAGTAAGAAGACATTCTTACAAACAGCGACTCTCATTGAAGACATTTTGGGTGTTAAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAAACAGCGACTCTCATTGA
57.89
ACTGTGCAGATGGCTGGTG
60.3
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACAAACAGCGACTCTCATTGA
57.89
CACTGTGCAGATGGCTGGT
60.3
143
PCR template sequence:
AAAGAATGATTTTGTGATTTTTCTGTTCACACTGATGACAAGTAAGAAGACATTCTTACAAACAGCGACTCTCATTGAAGACATTTTGGGTGTTAAGAAGTTCACTGAGACCTTTTTGACCGAGAGGGACAAATTGTCCAAATGGAGTGGAATTCCTCAGTTGCTCCTTAAGCTGTATGCCACCAGCCATCTGCACAGTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-136-5p(1), mmu-miR-96-5p(1), mmu-miR-224-5p(1), mmu-miR-539-5p(1), mmu-miR-350-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GGGTGTTAAGAAGTTCACTGAGACCT
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTRPC4AP_489_ORF_1
1.1114
0.094462053
0.959386017
828
ORF sequence:
ATGGAGGCTATGGCGTTTGTAACTGAAGACAGGAAATTTACTCAAGAAGCTACATACCCAAATACATATATTTTTGACTTATTTGGAGGTGTTGATCTTCTTGTAGAAATTCTTATGAGGCCTACCATCTCTATCCGGGGACAGAAACTAAAAATAAGTGACGAGATGTCGAAGGACTGCTTGAGCATCCTGTACAATACCTGTGTCTGCACGGAAGGAGTAACGAAGCGTTTGGCAGAAAAGAATGATTTTGTGATTTTTCTGTTCACACTGATGACAAGTAAGAAGACATTCTTACAAACAGCGACTCTCATTGAAGACATTTTGGGTGTTAAGAAGTTCACTGAGACCTTTTTGACCGAGAGGGACAAATTGTCCAAATGGAGTGGAATTCCTCAGTTGCTCCTTAAGCTGTATGCCACCAGCCATCTGCACAGTGACTTCGTTGAGTGCCAAAGCATTCTCAAGGAGATTTCTCCTCTTCTCTCTATGGAGGCTATGGCGTTTGTAACTGAAGACAGGAAATTTACTCAAGAAGCTACATACCCAAATACATATATTTTTGACTTATTTGGAGGTGTTGATCTTCTTGTAGAAATTCTTATGAGGCCTACCATCTCTATCCGGGGACAGAAACTAAAAATAAGTGACGAGATGTCGAAGGACTGCTTGAGCATCCTGTACAATACCTGTGTCTGCACGGAAGGAGTAACGAAGCGTTTGGCAGAAAAGAATGATTTTGTGATTTTTCTGTTCACACTGATGACAAGTAAGAAGACATTCTTACAAACAGCGACTCTCATTGAAGACATTTTGGGTGTTAAGAAG
Peptide sequence:
MEAMAFVTEDRKFTQEATYPNTYIFDLFGGVDLLVEILMRPTISIRGQKLKISDEMSKDCLSILYNTCVCTEGVTKRLAEKNDFVIFLFTLMTSKKTFLQTATLIEDILGVKKFTETFLTERDKLSKWSGIPQLLLKLYATSHLHSDFVECQSILKEISPLLSMEAMAFVTEDRKFTQEATYPNTYIFDLFGGVDLLVEILMRPTISIRGQKLKISDEMSKDCLSILYNTCVCTEGVTKRLAEKNDFVIFLFTLMTSKKTFLQTATLIEDILGVKK
IRESfinder result
IRESfinder score
0.709440747
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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