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mmu_circRbm17_380
Basic information of circular RNA
PanCircBase ID:
mmu_circRbm17_380
mm39_Chr. Position ID:
chr2|11592531|11595641|-
Gene name:
Rbm17
Transcript:
ENSMUST00000040314.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
9,8,7
Exon/intron offsets:
0,1207,2968
Genomic length:
3110
Exon/intron sizes in nt:
7,41,64,142
Flanking exon/introns:
chr2:11591776-11592531|chr2:11595641-11598218
Splice length:
380
Other database IDs:
CIRCpedia: MMU_CIRCpedia_39849, circAtlas: mmu-Rbm17_0008
Human Ortholog IDs:
Mature spliced Sequence:
TACCCCGCGATTTTCCTTATGAAGAGGACTCAAGACCGAGATCACAGTCTTCCAAAGCTGCTATTCCTCCCCCCGTGTATGAGGAGCCGGACAGACCAAGATCTCCAACAGGCCCCAGCAACTCCTTCCTTGCTAACATGGGTGGCACAGTGGCTCATAAGATTATGCAGAAGTATGGCTTCCGGGAAGGTCAGGGACTGGGGAAACACGAGCAAGGGCTGAGTACTGCATTGTCTGTGGAGAAGACCAGCAAGCGTGGCGGCAAGATCATTGTGGGGGATGCGACAGAGAAGGGCGAGGCTCAGGATGCATCCAAGAAGTCGGATTCAAATCCATTAACTGAAATTCTTAAGTGCCCTACTAAAGTGGTCTTGCTGAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GGATGCATCCAAGAAGTCGGA
60.13
TCTGTCCGGCTCCTCATACA
60.03
171
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGATGCATCCAAGAAGTCGGA
60.13
CTGTCCGGCTCCTCATACAC
59.9
170
PCR template sequence:
TGCGACAGAGAAGGGCGAGGCTCAGGATGCATCCAAGAAGTCGGATTCAAATCCATTAACTGAAATTCTTAAGTGCCCTACTAAAGTGGTCTTGCTGAGGTACCCCGCGATTTTCCTTATGAAGAGGACTCAAGACCGAGATCACAGTCTTCCAAAGCTGCTATTCCTCCCCCCGTGTATGAGGAGCCGGACAGACCAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-7b-5p(1), mmu-miR-7a-5p(1), mmu-miR-324-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GGTCTTGCTGAGGTACCCCGCGATTT
siRNA sets
AATCGCGGGGTACCTCAGC, AAATCGCGGGGTACCTCAG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRBM17_380_ORF_1
0.8634
0.174028443
0.601529149
465
ORF sequence:
ATGGGTGGCACAGTGGCTCATAAGATTATGCAGAAGTATGGCTTCCGGGAAGGTCAGGGACTGGGGAAACACGAGCAAGGGCTGAGTACTGCATTGTCTGTGGAGAAGACCAGCAAGCGTGGCGGCAAGATCATTGTGGGGGATGCGACAGAGAAGGGCGAGGCTCAGGATGCATCCAAGAAGTCGGATTCAAATCCATTAACTGAAATTCTTAAGTGCCCTACTAAAGTGGTCTTGCTGAGGTACCCCGCGATTTTCCTTATGAAGAGGACTCAAGACCGAGATCACAGTCTTCCAAAGCTGCTATTCCTCCCCCCGTGTATGAGGAGCCGGACAGACCAAGATCTCCAACAGGCCCCAGCAACTCCTTCCTTGCTAACATGGGTGGCACAGTGGCTCATAAGATTATGCAGAAGTATGGCTTCCGGGAAGGTCAGGGACTGGGGAAACACGAGCAAGGGCTGA
Peptide sequence:
MGGTVAHKIMQKYGFREGQGLGKHEQGLSTALSVEKTSKRGGKIIVGDATEKGEAQDASKKSDSNPLTEILKCPTKVVLLRYPAIFLMKRTQDRDHSLPKLLFLPPCMRSRTDQDLQQAPATPSLLTWVAQWLIRLCRSMASGKVRDWGNTSKG
IRESfinder result
IRESfinder score
0.424249383
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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