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mmu_ciRad23b_1166
Basic information of circular RNA
PanCircBase ID:
mmu_ciRad23b_1166
mm39_Chr. Position ID:
chr4|55366858|55368024|+
Gene name:
Rad23b
Transcript:
ENSMUST00000030134.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
2
Exon/intron offsets:
0
Genomic length:
1166
Exon/intron sizes in nt:
1166
Flanking exon/introns:
chr4:55366858-55368044
Splice length:
1166
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTATGAATTCAATTCTGAAATGAATTGCCATTTCTTGCCTATTTATTGTCTTAGTTTTAGAAATGTTATCTTAGAAAAGACAGTATTTTCCAGTTGATTCTGTCAGAAACAAGACTGTAGATAACAGGAGTGGAAACAGGTATTTATGGTTTAATACTCAGTCTTCTCTTTACACATTTTCCTTTTGCTCCATGGAGTGATGTTCCTTAGTCTGTGAGCATTGTGGCTGACTTCTGTGCCGTTCAGAAACTGAGCACCATTATTTTAATCTATTAGTAAAGTATGTACTAGTTCACTAATGTGCATGAAATTGTTCCTGTCAAAGAAAATCAGTATGTATTTCTAAACTACCAAAGTAAAAGAATCAAAGTTTGTTGTATTTCAGACATCAAAAGACCTTCATGGTAGTATCAAAAACAAAAAGACCCAAACAAACAAAAAACCAAATTATATAGAATACTTTGAAATTAATAATTAAAAGAGGCCCAAATAGAAAAATGCCCAAGAGTATGACTAGGAAATTGCAAATTTAATTAGCATCATTAATAACCCAGGAAAATAGACTTGATAGCCTCTTGCTGGGCATGGTGGCACATGCCTTTAATCCCAGCACTTTGGAGGCAGGTGGATCTGATCTAAGTGTGTCCTTGAGAGTCTTCCCCTTTCTTATGTATTATGCTTTCTTTCTGCAAGGTTTTGTTTGCTCACTTGGCTTGTTTTGTTTATAAGTATTTTGCTTTTACAACATTGGAACATCTCTGCTTCATCAAGTGTTTGATATTTGAAAATAAGAAGTTGTTCATTCCTTCTATCAGGGAAAAAAATACTTATTTCCCAAAGGTGCCTAGGCAATTGAAATGTTTAATTTTCTTTGCCTTTAAGATATCCTTGTTTTCAGGACTTACTTCAAATTTCTTTGTCTAATAAATCTTTAATACAGTTAGTTAATAAATTAAAAACTAAATCAATTGGTGTTTTATATACTGAAGATGTTAGACATTTTCTTGTAAGACATCTGTGCTTTTAAAGTAGTACATGTCTGTTTATATATTTATCTTATCTGGTTGTTAAAGGGTTTTTTAGAAGTTTTACTTGGTAGAATTAATGTTGCCAAAAAAGTAAGAGTAGTTTCTTTGTAAGAAGAAGCTTAATATGTCTTTAACATT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTTGGTAGAATTAATGTTGCCA
56.42
TCAACTGGAAAATACTGTCTTTTCT
56.88
173
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTTGGTAGAATTAATGTTGCCA
56.42
TCAACTGGAAAATACTGTCTTTTC
55.57
173
PCR template sequence:
GTTAAAGGGTTTTTTAGAAGTTTTACTTGGTAGAATTAATGTTGCCAAAAAAGTAAGAGTAGTTTCTTTGTAAGAAGAAGCTTAATATGTCTTTAACATTGTATGAATTCAATTCTGAAATGAATTGCCATTTCTTGCCTATTTATTGTCTTAGTTTTAGAAATGTTATCTTAGAAAAGACAGTATTTTCCAGTTGATTC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
19
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-20b-5p(1), mmu-miR-106a-5p(1), mmu-miR-93-5p(1), mmu-miR-20a-5p(1), mmu-miR-17-5p(1), mmu-miR-7b-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-31-5p(1), mmu-miR-106b-5p(1), mmu-miR-139-5p(1), mmu-miR-495-3p(1), mmu-miR-182-5p(1), mmu-miR-511-3p(1), mmu-miR-5101(1), mmu-miR-369-3p(1), mmu-miR-3065-5p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TGTCTTTAACATTGTATGAATTCAAT
siRNA sets
ATTCATACAATGTTAAAGA, AATTCATACAATGTTAAAG, ATTGAATTCATACAATGTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRAD23B_1166_ORF_5
0.4092
-0.482163763
0.003311593
111
ORF sequence:
ATGTCTTTAACATTGTATGAATTCAATTCTGAAATGAATTGCCATTTCTTGCCTATTTATTGTCTTAGTTTTAGAAATGTTATCTTAGAAAAGACAGTATTTTCCAGTTGA
Peptide sequence:
MSLTLYEFNSEMNCHFLPIYCLSFRNVILEKTVFSS
IRESfinder result
IRESfinder score
0.942440865
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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