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mmu_circTarbp1_645
Basic information of circular RNA
PanCircBase ID:
mmu_circTarbp1_645
mm39_Chr. Position ID:
chr8|127163441|127171064|-
Gene name:
Tarbp1
Transcript:
ENSMUST00000170518.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
22,21,20,19,18
Exon/intron offsets:
0,2100,4051,7227,7432
Genomic length:
7623
Exon/intron sizes in nt:
1,50,11,11,21,72,191
Flanking exon/introns:
chr8:127161623-127163441|chr8:127171064-127173778
Splice length:
645
Other database IDs:
circAtlas: mmu-Gm17296_0002
circBase: hsa_circ_0112454, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_30655
Human Ortholog IDs:
Mature spliced Sequence:
ATTATGTGCAAGATGATTGAAATGTCCTCCATAAAATCAGGTGTCTTCAATATTCTGATACGTCACTGCTGCCAGTCATGGCTAGTGGCTGCTTCCGGCGTGTCCCAGGGGTCATTCTCCAGTGCTAAGGATTACAGTGAACTTGTCCTGGAGGCTTGCGTGTTTGGAACAGTGTTTAGGCGCGATCAGAGACTTATTCAGGATGTCCAAACCTTCATAGAAAACCTTGGACAAGGCTGTGCAGCAAACGTCATCATTGAGAATGCTAAGAGAGAAGATTATTACGTGAGAATCTGTGCCATCAAATTCTTGTGTCTGCTAGATGGCTCCGATGTGTCCCACAAGTTGTTCTTAGAAGCTCTTGCCATCAAGCTCTTGGATAAGGATGAGTCAGCATCCAGGTCCAGAACTCGATACCATGAGAACTCCCTCCAGCACCGGGTGAAGAACCGTGTGTGGCAGACTCTGCTTGTCCTCTTCCCTGCATTTGATCAGAACTTCTTACATGGAATTATTGATAAGGTCTTTCACGCTGGCTTCACCAACAATCAAGCGTCCATAAAATATTTTATTGAGTGGCTTATTATATTGATTCTTCATAAATTCCCTGAGTTTCTTCCAAAGTTCTGGGCGTGTTTTTCTTAC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAATTCCCTGAGTTTCTTCCAAAGT
59.1
GAAGCAGCCACTAGCCATGA
60.11
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AAATTCCCTGAGTTTCTTCCA
55
GAAGCAGCCACTAGCCATGA
60.11
140
PCR template sequence:
CAATCAAGCGTCCATAAAATATTTTATTGAGTGGCTTATTATATTGATTCTTCATAAATTCCCTGAGTTTCTTCCAAAGTTCTGGGCGTGTTTTTCTTACATTATGTGCAAGATGATTGAAATGTCCTCCATAAAATCAGGTGTCTTCAATATTCTGATACGTCACTGCTGCCAGTCATGGCTAGTGGCTGCTTCCGGCG
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-200a-3p(1), mmu-miR-7b-5p(1), mmu-miR-31-5p(1), mmu-miR-335-5p(1), mmu-miR-7a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GTGTTTTTCTTACATTATGTGCAAGA
siRNA sets
CATAATGTAAGAAAAACAC, ACATAATGTAAGAAAAACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTARBP1_645_ORF_1
1.0041
0.104904559
0.998185867
1287
ORF sequence:
ATGTGCAAGATGATTGAAATGTCCTCCATAAAATCAGGTGTCTTCAATATTCTGATACGTCACTGCTGCCAGTCATGGCTAGTGGCTGCTTCCGGCGTGTCCCAGGGGTCATTCTCCAGTGCTAAGGATTACAGTGAACTTGTCCTGGAGGCTTGCGTGTTTGGAACAGTGTTTAGGCGCGATCAGAGACTTATTCAGGATGTCCAAACCTTCATAGAAAACCTTGGACAAGGCTGTGCAGCAAACGTCATCATTGAGAATGCTAAGAGAGAAGATTATTACGTGAGAATCTGTGCCATCAAATTCTTGTGTCTGCTAGATGGCTCCGATGTGTCCCACAAGTTGTTCTTAGAAGCTCTTGCCATCAAGCTCTTGGATAAGGATGAGTCAGCATCCAGGTCCAGAACTCGATACCATGAGAACTCCCTCCAGCACCGGGTGAAGAACCGTGTGTGGCAGACTCTGCTTGTCCTCTTCCCTGCATTTGATCAGAACTTCTTACATGGAATTATTGATAAGGTCTTTCACGCTGGCTTCACCAACAATCAAGCGTCCATAAAATATTTTATTGAGTGGCTTATTATATTGATTCTTCATAAATTCCCTGAGTTTCTTCCAAAGTTCTGGGCGTGTTTTTCTTACATTATGTGCAAGATGATTGAAATGTCCTCCATAAAATCAGGTGTCTTCAATATTCTGATACGTCACTGCTGCCAGTCATGGCTAGTGGCTGCTTCCGGCGTGTCCCAGGGGTCATTCTCCAGTGCTAAGGATTACAGTGAACTTGTCCTGGAGGCTTGCGTGTTTGGAACAGTGTTTAGGCGCGATCAGAGACTTATTCAGGATGTCCAAACCTTCATAGAAAACCTTGGACAAGGCTGTGCAGCAAACGTCATCATTGAGAATGCTAAGAGAGAAGATTATTACGTGAGAATCTGTGCCATCAAATTCTTGTGTCTGCTAGATGGCTCCGATGTGTCCCACAAGTTGTTCTTAGAAGCTCTTGCCATCAAGCTCTTGGATAAGGATGAGTCAGCATCCAGGTCCAGAACTCGATACCATGAGAACTCCCTCCAGCACCGGGTGAAGAACCGTGTGTGGCAGACTCTGCTTGTCCTCTTCCCTGCATTTGATCAGAACTTCTTACATGGAATTATTGATAAGGTCTTTCACGCTGGCTTCACCAACAATCAAGCGTCCATAAAATATTTTATTGAGTGGCTTATTATATTGATTCTTCATAAATTCCCTGAGTTTCTTCCAAAGTTCTGGGCGTGTTTTTCTTAC
Peptide sequence:
MCKMIEMSSIKSGVFNILIRHCCQSWLVAASGVSQGSFSSAKDYSELVLEACVFGTVFRRDQRLIQDVQTFIENLGQGCAANVIIENAKREDYYVRICAIKFLCLLDGSDVSHKLFLEALAIKLLDKDESASRSRTRYHENSLQHRVKNRVWQTLLVLFPAFDQNFLHGIIDKVFHAGFTNNQASIKYFIEWLIILILHKFPEFLPKFWACFSYIMCKMIEMSSIKSGVFNILIRHCCQSWLVAASGVSQGSFSSAKDYSELVLEACVFGTVFRRDQRLIQDVQTFIENLGQGCAANVIIENAKREDYYVRICAIKFLCLLDGSDVSHKLFLEALAIKLLDKDESASRSRTRYHENSLQHRVKNRVWQTLLVLFPAFDQNFLHGIIDKVFHAGFTNNQASIKYFIEWLIILILHKFPEFLPKFWACFSY
IRESfinder result
IRESfinder score
0.704038195
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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