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mmu_circRaf1_536
Basic information of circular RNA
PanCircBase ID:
mmu_circRaf1_536
mm39_Chr. Position ID:
chr6|115599837|115603927|-
Gene name:
Raf1
Transcript:
ENSMUST00000130528.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
7,6,5,4,3
Exon/intron offsets:
0,587,3414,3835,4062
Genomic length:
4090
Exon/intron sizes in nt:
177,85,118,128,28
Flanking exon/introns:
chr6:115598823-115599837|chr6:115603927-115609857
Splice length:
536
Other database IDs:
circAtlas: mmu-Raf1_0007
circBase: hsa_circ_0064361, circAtlas: hsa-RAF1_0010
Human Ortholog IDs:
Mature spliced Sequence:
GATGCAATTCGAAGTCACAGTGAATCAGCCTCACCTTCAGCCCTGTCCAGCAGCCCAAACAACCTGAGTCCAACAGGCTGGTCACAGCCCAAAACCCCTGTGCCAGCACAAAGAGAGCGGGCACCAGGATCTGGGACCCAGGAAAAAAACAAAATTAGGCCTCGTGGGCAGAGAGACTCGAGTTATTACTGGGAAATAGAAGCCAGTGAGGTGATGCTGTCTACTCGGATCGGGTCAGGTTCCTTTGGCACTGTGTACAAGGGCAAGTGGCATGGAGATGTTGCAGTAAAGATCCTAAAGGTGGTTGACCCAACTCCAGAGCAACTTCAGGCCTTCAGGAACGAGGTGGCTGTTTTGCGCAAAACACGGCATGTTAACATCCTGCTGTTCATGGGGTACATGACAAAGGACAACCTGGCGATTGTGACTCAGTGGTGTGAAGGCAGCAGTCTCTACAAACACCTGCATGTCCAGGAGACCAAATTCCAGATGTTCCAGCTAATTGACATTGCCCGACAGACAGCTCAGGGAATGGA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCATGTCCAGGAGACCAA
59.67
GGACTCAGGTTGTTTGGGCT
60.18
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCATGTCCAGGAGACCAA
59.67
GACCAGCCTGTTGGACTCAG
60.32
157
PCR template sequence:
GTGAAGGCAGCAGTCTCTACAAACACCTGCATGTCCAGGAGACCAAATTCCAGATGTTCCAGCTAATTGACATTGCCCGACAGACAGCTCAGGGAATGGAGATGCAATTCGAAGTCACAGTGAATCAGCCTCACCTTCAGCCCTGTCCAGCAGCCCAAACAACCTGAGTCCAACAGGCTGGTCACAGCCCAAAACCCCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-27b-3p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-205-5p(1), mmu-miR-351-5p(1), mmu-miR-34b-5p(1), mmu-miR-5101(1), mmu-miR-1199-5p(1), mmu-miR-670-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTCAGGGAATGGAGATGCAATTCGAA
siRNA sets
GAATTGCATCTCCATTCCC, AATTGCATCTCCATTCCCT, ATTGCATCTCCATTCCCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRAF1_536_ORF_1
1.115
0.297146965
0.697328012
390
ORF sequence:
ATGCTGTCTACTCGGATCGGGTCAGGTTCCTTTGGCACTGTGTACAAGGGCAAGTGGCATGGAGATGTTGCAGTAAAGATCCTAAAGGTGGTTGACCCAACTCCAGAGCAACTTCAGGCCTTCAGGAACGAGGTGGCTGTTTTGCGCAAAACACGGCATGTTAACATCCTGCTGTTCATGGGGTACATGACAAAGGACAACCTGGCGATTGTGACTCAGTGGTGTGAAGGCAGCAGTCTCTACAAACACCTGCATGTCCAGGAGACCAAATTCCAGATGTTCCAGCTAATTGACATTGCCCGACAGACAGCTCAGGGAATGGAGATGCAATTCGAAGTCACAGTGAATCAGCCTCACCTTCAGCCCTGTCCAGCAGCCCAAACAACCTGA
Peptide sequence:
MLSTRIGSGSFGTVYKGKWHGDVAVKILKVVDPTPEQLQAFRNEVAVLRKTRHVNILLFMGYMTKDNLAIVTQWCEGSSLYKHLHVQETKFQMFQLIDIARQTAQGMEMQFEVTVNQPHLQPCPAAQTT
IRESfinder result
IRESfinder score
0.500559161
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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