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mmu_circCarf_916
Basic information of circular RNA
PanCircBase ID:
mmu_circCarf_916
mm39_Chr. Position ID:
chr1|60171002|60185331|+
Gene name:
Carf
Transcript:
ENSMUST00000130075.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
10,11,12,13,14,15
Exon/intron offsets:
0,4420,7356,9491,12150,14265
Genomic length:
14329
Exon/intron sizes in nt:
190,121,144,234,163,64
Flanking exon/introns:
chr1:60167232-60171002|chr1:60185331-60186526
Splice length:
916
Other database IDs:
circAtlas: hsa-CARF_0040, CIRCpedia: HSA_CIRCpedia_93363
Human Ortholog IDs:
Mature spliced Sequence:
AAAATTGGAGATTCCTACCGTGGCTACTGTGTAAGTGAGACTGAATTAGAAAGTGTCCTAACTTTTCACAAGCAGCAAACACAGACTGTCTGGGGTACTCGCCAGTCTCCAAGCCCAGCCAAACCTGCCACACGCTTGATGTGGAAGTCTCAGTATGTCCCATATGACGGAATCCCATTTGTCAATGCAGGAAGTCGAGCTGTGGTAATGGAGTGTCAGTATGGACCAAGGAGAAAAGGTTTTCAGTTAAAAAAAATCAGTGAGCAAGAAAGTAGGTCTTGTCATCTCTATAAAGCTACTTGTCCAGCCAGGATATACATTAAAAAGGTACAGAAATTTCCTGAATATAGAGTACCTACAGACCCCCAAATTGACAGGAAGATAATCAGACTGGAGCAGGAGAAAGCCTTCACTATGCTGAAGAAGAACCTGATGGATGCTGGTGGTGTACTTCGATGGTATGTGCAGTTACCTACACAGCAAGCTCATCAGTATCATGAATCAGAGACTCCTGGTGTCCCTTTGTCACCGTCACCTTTTCCTATGTCTCCTCTTGAAGAAGAGGAAGCTATAGTCAGAGATGAGAACTGTGCGTTGCCCTCTCGTCTCCACCCGCAAGTAGCGCATAAGATTCAGGAACTAGTGTCACAGGGAGTAGGACAAGTGTATGCAGTAAGGAAGCAGCTAAGAAAATTTGTGGAAAGAGAACTGTTCAAACCTGATGAGATACCTGAAAGACATAATTTATCTTATTTTCCAACTGTAAATGATATAAAAAATCATATCCATGAGGTACAGAAATCCTTGAGGACTGGAGATGTGGTATATAACTCAGAGATTATTCCAGCAACGCTTCAGTGGACGACAGATAGTGGGAACATCCTCAGAGAGACTGTAACAGTTACATTTGCAGAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CGCTTCAGTGGACGACAGAT
60.11
CCCAGACAGTCTGTGTTTGC
59.05
160
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGCTTCAGTGGACGACAGAT
60.11
CAGACAGTCTGTGTTTGCTGC
60
158
PCR template sequence:
GATGTGGTATATAACTCAGAGATTATTCCAGCAACGCTTCAGTGGACGACAGATAGTGGGAACATCCTCAGAGAGACTGTAACAGTTACATTTGCAGAAGAAAATTGGAGATTCCTACCGTGGCTACTGTGTAAGTGAGACTGAATTAGAAAGTGTCCTAACTTTTCACAAGCAGCAAACACAGACTGTCTGGGGTACTC
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-452-3p(2), mmu-miR-434-5p(1), mmu-miR-411-3p(1), mmu-miR-541-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACATTTGCAGAAGAAAATTGGAGATT
siRNA sets
ATCTCCAATTTTCTTCTGC,AATCTCCAATTTTCTTCTG,AATTTTCTTCTGCAAATGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCARF_916_ORF_1
0.943
0.007572575
0.915846334
816
ORF sequence:
ATGTGGAAGTCTCAGTATGTCCCATATGACGGAATCCCATTTGTCAATGCAGGAAGTCGAGCTGTGGTAATGGAGTGTCAGTATGGACCAAGGAGAAAAGGTTTTCAGTTAAAAAAAATCAGTGAGCAAGAAAGTAGGTCTTGTCATCTCTATAAAGCTACTTGTCCAGCCAGGATATACATTAAAAAGGTACAGAAATTTCCTGAATATAGAGTACCTACAGACCCCCAAATTGACAGGAAGATAATCAGACTGGAGCAGGAGAAAGCCTTCACTATGCTGAAGAAGAACCTGATGGATGCTGGTGGTGTACTTCGATGGTATGTGCAGTTACCTACACAGCAAGCTCATCAGTATCATGAATCAGAGACTCCTGGTGTCCCTTTGTCACCGTCACCTTTTCCTATGTCTCCTCTTGAAGAAGAGGAAGCTATAGTCAGAGATGAGAACTGTGCGTTGCCCTCTCGTCTCCACCCGCAAGTAGCGCATAAGATTCAGGAACTAGTGTCACAGGGAGTAGGACAAGTGTATGCAGTAAGGAAGCAGCTAAGAAAATTTGTGGAAAGAGAACTGTTCAAACCTGATGAGATACCTGAAAGACATAATTTATCTTATTTTCCAACTGTAAATGATATAAAAAATCATATCCATGAGGTACAGAAATCCTTGAGGACTGGAGATGTGGTATATAACTCAGAGATTATTCCAGCAACGCTTCAGTGGACGACAGATAGTGGGAACATCCTCAGAGAGACTGTAACAGTTACATTTGCAGAAGAAAATTGGAGATTCCTACCGTGGCTACTGTGTAAGTGA
Peptide sequence:
MWKSQYVPYDGIPFVNAGSRAVVMECQYGPRRKGFQLKKISEQESRSCHLYKATCPARIYIKKVQKFPEYRVPTDPQIDRKIIRLEQEKAFTMLKKNLMDAGGVLRWYVQLPTQQAHQYHESETPGVPLSPSPFPMSPLEEEEAIVRDENCALPSRLHPQVAHKIQELVSQGVGQVYAVRKQLRKFVERELFKPDEIPERHNLSYFPTVNDIKNHIHEVQKSLRTGDVVYNSEIIPATLQWTTDSGNILRETVTVTFAEENWRFLPWLLCK
IRESfinder result
IRESfinder score
0.596728994
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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