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mmu_circTrappc8_979
Basic information of circular RNA
PanCircBase ID:
mmu_circTrappc8_979
mm39_Chr. Position ID:
chr18|20993489|21003809|-
Gene name:
Trappc8
Transcript:
ENSMUST00000225661.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
11,10,9,8,7,6,5
Exon/intron offsets:
0,2462,3035,4594,5517,7327,10166
Genomic length:
10320
Exon/intron sizes in nt:
1,06,10,11,51,11,62,57,00,000
Flanking exon/introns:
chr18:20988133-20993489|chr18:21003809-21006939
Splice length:
979
Other database IDs:
CIRCpedia: MMU_CIRCpedia_13070, circAtlas: mmu-Trappc8_0002
circBase: hsa_circ_0108231, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_23667
Human Ortholog IDs:
Mature spliced Sequence:
GGCTGAATCAATTTATGAAGAAATGAAACAGAAATATGGAACTCAGGGTTGCTATTTACTTAAAATCAATTCTCGAGCACCAAATCGAGCATCAGATGAACAGATACCAGATCCGTGGAGTCAGTATCTCCAGAAAAATAGTATTCAAAACCAGGAATCATATGAAGATGGCCCTTGTACTATGACCTCCAGTAAGAATTCTGATAGTAACTTGCTTTCATTGGATGGACTAGATAACGAAGTCAAAGTAGATGGCCTACCAAATAACTTCAGAATTCATCCACTTCAAATAGACCAATGCGGTGACCCTCCTAACAATACTGACGGCTCAGAGTCAAAGTCTGCTTCTTCAGTTCACGAGACAAAGAAAGCAAGTACTGCAGTGATTCGTGGTGCTTGCTTAACACTCACTGACCATGATAGAATCCGACAGTTTATACAAGAGTTTACATTCCGTGGCCTTTTGCCACACATAGAGAAAACAATTCGTCAGTTAAATGATCAGCTAATATCAAGGAAAGGTTTGAGTCGATCTCTGTTTTCTGCCACTAAGAAATGGTTTAGTGGTAGTAAAGTTCCAGAAAAGAGCATTAATGAGCTGAAGAATACATCTGGGTTGTTGTATCCGCCAGAAGCGCCCGAGCTTCAGATCAGGAAGATGGCTGACTTGTGCTTCTTGGTGCAACATTATGATTTGGCTTACAGTTGTTATCACACTGCAAAGAAGGATTTTCTTAACGATCAAGCAATGCTTTATGCAGCAGGTGCCTTGGAAATGGCAGCAGTGTCAGCCTTTCTTCAGCCAGGAGCTCCTAGGCCATACCCTGCTCATTACATGGACACAGCAATTCAGACATACAGGGATATCTGCAAGAATATGGTGTTGGCTGAAAGATGTGTGTTGCTTAGTGCTGAAATTTTAAAAAGTCAAAGCAAGTACTCAGAGGCTGCAGCTCTTCTGATACGATTGACAAGTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAAGTACTCAGAGGCTGCA
60.04
GATGCTCGATTTGGTGCTCG
59.7
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCAAGTACTCAGAGGCTGC
59.75
ATGCTCGATTTGGTGCTCGA
60.11
140
PCR template sequence:
GGTGTTGGCTGAAAGATGTGTGTTGCTTAGTGCTGAAATTTTAAAAAGTCAAAGCAAGTACTCAGAGGCTGCAGCTCTTCTGATACGATTGACAAGTGAGGGCTGAATCAATTTATGAAGAAATGAAACAGAAATATGGAACTCAGGGTTGCTATTTACTTAAAATCAATTCTCGAGCACCAAATCGAGCATCAGATGAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
13
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-1a-3p(1), mmu-miR-206-3p(1), mmu-miR-15b-5p(1), mmu-miR-29b-3p(1), mmu-miR-125b-5p(1), mmu-miR-10a-5p(1), mmu-miR-125a-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-127-5p(1), mmu-miR-297a-5p(1), mmu-miR-680(1), mmu-miR-466a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
ATTGACAAGTGAGGGCTGAATCAATT
siRNA sets
AATTGATTCAGCCCTCACT, TTCAGCCCTCACTTGTCAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTRAPPC8_979_ORF_1
0.8411
0.020919649
0.964774481
963
ORF sequence:
ATGAAACAGAAATATGGAACTCAGGGTTGCTATTTACTTAAAATCAATTCTCGAGCACCAAATCGAGCATCAGATGAACAGATACCAGATCCGTGGAGTCAGTATCTCCAGAAAAATAGTATTCAAAACCAGGAATCATATGAAGATGGCCCTTGTACTATGACCTCCAGTAAGAATTCTGATAGTAACTTGCTTTCATTGGATGGACTAGATAACGAAGTCAAAGTAGATGGCCTACCAAATAACTTCAGAATTCATCCACTTCAAATAGACCAATGCGGTGACCCTCCTAACAATACTGACGGCTCAGAGTCAAAGTCTGCTTCTTCAGTTCACGAGACAAAGAAAGCAAGTACTGCAGTGATTCGTGGTGCTTGCTTAACACTCACTGACCATGATAGAATCCGACAGTTTATACAAGAGTTTACATTCCGTGGCCTTTTGCCACACATAGAGAAAACAATTCGTCAGTTAAATGATCAGCTAATATCAAGGAAAGGTTTGAGTCGATCTCTGTTTTCTGCCACTAAGAAATGGTTTAGTGGTAGTAAAGTTCCAGAAAAGAGCATTAATGAGCTGAAGAATACATCTGGGTTGTTGTATCCGCCAGAAGCGCCCGAGCTTCAGATCAGGAAGATGGCTGACTTGTGCTTCTTGGTGCAACATTATGATTTGGCTTACAGTTGTTATCACACTGCAAAGAAGGATTTTCTTAACGATCAAGCAATGCTTTATGCAGCAGGTGCCTTGGAAATGGCAGCAGTGTCAGCCTTTCTTCAGCCAGGAGCTCCTAGGCCATACCCTGCTCATTACATGGACACAGCAATTCAGACATACAGGGATATCTGCAAGAATATGGTGTTGGCTGAAAGATGTGTGTTGCTTAGTGCTGAAATTTTAAAAAGTCAAAGCAAGTACTCAGAGGCTGCAGCTCTTCTGATACGATTGACAAGTGAGGGCTGA
Peptide sequence:
MKQKYGTQGCYLLKINSRAPNRASDEQIPDPWSQYLQKNSIQNQESYEDGPCTMTSSKNSDSNLLSLDGLDNEVKVDGLPNNFRIHPLQIDQCGDPPNNTDGSESKSASSVHETKKASTAVIRGACLTLTDHDRIRQFIQEFTFRGLLPHIEKTIRQLNDQLISRKGLSRSLFSATKKWFSGSKVPEKSINELKNTSGLLYPPEAPELQIRKMADLCFLVQHYDLAYSCYHTAKKDFLNDQAMLYAAGALEMAAVSAFLQPGAPRPYPAHYMDTAIQTYRDICKNMVLAERCVLLSAEILKSQSKYSEAAALLIRLTSEG
IRESfinder result
IRESfinder score
0.638836079
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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