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mmu_circTarbp1_495
Basic information of circular RNA
PanCircBase ID:
mmu_circTarbp1_495
mm39_Chr. Position ID:
chr8|127165541|127171064|-
Gene name:
Tarbp1
Transcript:
ENSMUST00000170518.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
21,20,19,18
Exon/intron offsets:
0,1951,5127,5332
Genomic length:
5523
Exon/intron sizes in nt:
11,11,21,72,191
Flanking exon/introns:
chr8:127163591-127165541|chr8:127171064-127173778
Splice length:
495
Other database IDs:
CIRCpedia: MMU_CIRCpedia_219069, circAtlas: mmu-Gm17296_0007
CIRCpedia: HSA_CIRCpedia_110784
Human Ortholog IDs:
Mature spliced Sequence:
ATTATGTGCAAGATGATTGAAATGTCCTCCATAAAATCAGGTGTCTTCAATATTCTGATACGTCACTGCTGCCAGTCATGGCTAGTGGCTGCTTCCGGCGTGTCCCAGGGGTCATTCTCCAGTGCTAAGGATTACAGTGAACTTGTCCTGGAGGCTTGCGTGTTTGGAACAGTGTTTAGGCGCGATCAGAGACTTATTCAGGATGTCCAAACCTTCATAGAAAACCTTGGACAAGGCTGTGCAGCAAACGTCATCATTGAGAATGCTAAGAGAGAAGATTATTACGTGAGAATCTGTGCCATCAAATTCTTGTGTCTGCTAGATGGCTCCGATGTGTCCCACAAGTTGTTCTTAGAAGCTCTTGCCATCAAGCTCTTGGATAAGGATGAGTCAGCATCCAGGTCCAGAACTCGATACCATGAGAACTCCCTCCAGCACCGGGTGAAGAACCGTGTGTGGCAGACTCTGCTTGTCCTCTTCCCTGCATTTGATCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CCATGAGAACTCCCTCCAGC
59.82
GAAGCAGCCACTAGCCATGA
60.11
174
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CCATGAGAACTCCCTCCAGC
59.82
ACTGGCAGCAGTGACGTATC
60.11
155
PCR template sequence:
ATCCAGGTCCAGAACTCGATACCATGAGAACTCCCTCCAGCACCGGGTGAAGAACCGTGTGTGGCAGACTCTGCTTGTCCTCTTCCCTGCATTTGATCAGATTATGTGCAAGATGATTGAAATGTCCTCCATAAAATCAGGTGTCTTCAATATTCTGATACGTCACTGCTGCCAGTCATGGCTAGTGGCTGCTTCCGGCG
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
TGCATTTGATCAGATTATGTGCAAGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCTARBP1_495_ORF_1
0.9172
0.200912474
0.987670577
987
ORF sequence:
ATGTGCAAGATGATTGAAATGTCCTCCATAAAATCAGGTGTCTTCAATATTCTGATACGTCACTGCTGCCAGTCATGGCTAGTGGCTGCTTCCGGCGTGTCCCAGGGGTCATTCTCCAGTGCTAAGGATTACAGTGAACTTGTCCTGGAGGCTTGCGTGTTTGGAACAGTGTTTAGGCGCGATCAGAGACTTATTCAGGATGTCCAAACCTTCATAGAAAACCTTGGACAAGGCTGTGCAGCAAACGTCATCATTGAGAATGCTAAGAGAGAAGATTATTACGTGAGAATCTGTGCCATCAAATTCTTGTGTCTGCTAGATGGCTCCGATGTGTCCCACAAGTTGTTCTTAGAAGCTCTTGCCATCAAGCTCTTGGATAAGGATGAGTCAGCATCCAGGTCCAGAACTCGATACCATGAGAACTCCCTCCAGCACCGGGTGAAGAACCGTGTGTGGCAGACTCTGCTTGTCCTCTTCCCTGCATTTGATCAGATTATGTGCAAGATGATTGAAATGTCCTCCATAAAATCAGGTGTCTTCAATATTCTGATACGTCACTGCTGCCAGTCATGGCTAGTGGCTGCTTCCGGCGTGTCCCAGGGGTCATTCTCCAGTGCTAAGGATTACAGTGAACTTGTCCTGGAGGCTTGCGTGTTTGGAACAGTGTTTAGGCGCGATCAGAGACTTATTCAGGATGTCCAAACCTTCATAGAAAACCTTGGACAAGGCTGTGCAGCAAACGTCATCATTGAGAATGCTAAGAGAGAAGATTATTACGTGAGAATCTGTGCCATCAAATTCTTGTGTCTGCTAGATGGCTCCGATGTGTCCCACAAGTTGTTCTTAGAAGCTCTTGCCATCAAGCTCTTGGATAAGGATGAGTCAGCATCCAGGTCCAGAACTCGATACCATGAGAACTCCCTCCAGCACCGGGTGAAGAACCGTGTGTGGCAGACTCTGCTTGTCCTCTTCCCTGCATTTGATCAG
Peptide sequence:
MCKMIEMSSIKSGVFNILIRHCCQSWLVAASGVSQGSFSSAKDYSELVLEACVFGTVFRRDQRLIQDVQTFIENLGQGCAANVIIENAKREDYYVRICAIKFLCLLDGSDVSHKLFLEALAIKLLDKDESASRSRTRYHENSLQHRVKNRVWQTLLVLFPAFDQIMCKMIEMSSIKSGVFNILIRHCCQSWLVAASGVSQGSFSSAKDYSELVLEACVFGTVFRRDQRLIQDVQTFIENLGQGCAANVIIENAKREDYYVRICAIKFLCLLDGSDVSHKLFLEALAIKLLDKDESASRSRTRYHENSLQHRVKNRVWQTLLVLFPAFDQ
IRESfinder result
IRESfinder score
0.516740715
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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