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mmu_circRbm5_827
Basic information of circular RNA
PanCircBase ID:
mmu_circRbm5_827
mm39_Chr. Position ID:
chr9|107626906|107631687|-
Gene name:
Rbm5
Transcript:
ENSMUST00000182659.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
9
Exon/intron indexes:
17,16,15,14,13,12,11,10,9
Exon/intron offsets:
0,300,755,2011,2168,2403,3269,4314,4715
Genomic length:
4781
Exon/intron sizes in nt:
92,85,86,73,78,88,98,161,66
Flanking exon/introns:
chr9:107623379-107626906|chr9:107631687-107633051
Splice length:
827
Other database IDs:
circAtlas: mmu-Rbm5_0009
circAtlas: hsa-RBM5_0007, CIRCpedia: HSA_CIRCpedia_46199
Human Ortholog IDs:
Mature spliced Sequence:
ACTCTGAACAGGAAGTGCCCCCCGGAACCACAGAGTCTGCTCAGTCCGTGGATTACTACTGTGATACTATCATTCTTCGGAACATAGCTCCGCACACTGTGGTGGATTCCATCATGACAGCCCTATCTCCCTATGCTTCCTTAGCTGTCAATAACATTCGCCTCATAAAAGACAAACAGACACAACAGAACAGAGGGTTTGCATTTGTGCAGCTATCTTCTGCAATGGATGCCTCTCAGCTGCTTCAGATATTACAGAGTCTCCATCCTCCATTGAAAATTGATGGGAAAACTATTGGAGTTGATTTTGCAAAAAGTGCCAGAAAAGATTTGGTCCTTCCAGATGGTAACCGAGTCAGCGCCTTCTCTGTAGCTAGTACAGCCATTGCTGCTGCTCAGTGGTCATCCACTCAGTCTCAAAGTGGTGAAGGAGGCAGTGTTGACTACAGTTACATGCAGCCAGGCCAGGATGGCTACACACAGTACACTCAATACTCACAGGATTACCAGCAGTTTTATCAGCAGCAAGCTGGAGGGCTGGAGTCTGATACATCAGCTACATCAGGCACCACAGTGACTACCACCTCAGCAGCTGTAGTATCCCAAAGTCCCCAACTCTATAATCAGACCTCCAACCCACCTGGCTCTCCGACTGAGGAAGCACAGCCTAGCACTAGCACAAGTACACAGGCCCCCGCTGCTTCCCCTACTGGTGTAGTTCCTGGTACCAAGTATGCAGTACCTGACACGTCTACTTATCAATATGATGAATCATCAGGATATTATTATGATCCTACAACAGGGCTCTACTATGACCCTAACTCACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCAGTACCTGACACGTCT
58.74
CACGGACTGAGCAGACTCTG
60.11
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCAGTACCTGACACGTCT
58.74
AATCCACGGACTGAGCAGAC
59.75
149
PCR template sequence:
CAAGTATGCAGTACCTGACACGTCTACTTATCAATATGATGAATCATCAGGATATTATTATGATCCTACAACAGGGCTCTACTATGACCCTAACTCACAGACTCTGAACAGGAAGTGCCCCCCGGAACCACAGAGTCTGCTCAGTCCGTGGATTACTACTGTGATACTATCATTCTTCGGAACATAGCTCCGCACACTGT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
14
Interacting miRNAs (#binding sites)
mmu-miR-15a-5p(1), mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-298-5p(1), mmu-miR-128-3p(1), mmu-miR-503-5p(1), mmu-miR-433-3p(1), mmu-miR-129-5p(1), mmu-miR-5101(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CCCTAACTCACAGACTCTGAACAGGA
siRNA sets
CAGAGTCTGTGAGTTAGGG, TCAGAGTCTGTGAGTTAGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRBM5_827_ORF_1
1.0747
0.100936889
0.948327092
801
ORF sequence:
ATGACAGCCCTATCTCCCTATGCTTCCTTAGCTGTCAATAACATTCGCCTCATAAAAGACAAACAGACACAACAGAACAGAGGGTTTGCATTTGTGCAGCTATCTTCTGCAATGGATGCCTCTCAGCTGCTTCAGATATTACAGAGTCTCCATCCTCCATTGAAAATTGATGGGAAAACTATTGGAGTTGATTTTGCAAAAAGTGCCAGAAAAGATTTGGTCCTTCCAGATGGTAACCGAGTCAGCGCCTTCTCTGTAGCTAGTACAGCCATTGCTGCTGCTCAGTGGTCATCCACTCAGTCTCAAAGTGGTGAAGGAGGCAGTGTTGACTACAGTTACATGCAGCCAGGCCAGGATGGCTACACACAGTACACTCAATACTCACAGGATTACCAGCAGTTTTATCAGCAGCAAGCTGGAGGGCTGGAGTCTGATACATCAGCTACATCAGGCACCACAGTGACTACCACCTCAGCAGCTGTAGTATCCCAAAGTCCCCAACTCTATAATCAGACCTCCAACCCACCTGGCTCTCCGACTGAGGAAGCACAGCCTAGCACTAGCACAAGTACACAGGCCCCCGCTGCTTCCCCTACTGGTGTAGTTCCTGGTACCAAGTATGCAGTACCTGACACGTCTACTTATCAATATGATGAATCATCAGGATATTATTATGATCCTACAACAGGGCTCTACTATGACCCTAACTCACAGACTCTGAACAGGAAGTGCCCCCCGGAACCACAGAGTCTGCTCAGTCCGTGGATTACTACTGTGATACTATCATTCTTCGGAACATAG
Peptide sequence:
MTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQILQSLHPPLKIDGKTIGVDFAKSARKDLVLPDGNRVSAFSVASTAIAAAQWSSTQSQSGEGGSVDYSYMQPGQDGYTQYTQYSQDYQQFYQQQAGGLESDTSATSGTTVTTTSAAVVSQSPQLYNQTSNPPGSPTEEAQPSTSTSTQAPAASPTGVVPGTKYAVPDTSTYQYDESSGYYYDPTTGLYYDPNSQTLNRKCPPEPQSLLSPWITTVILSFFGT
IRESfinder result
IRESfinder score
0.602022648
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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