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mmu_circA1cf_404
Basic information of circular RNA
PanCircBase ID:
mmu_circA1cf_404
mm39_Chr. Position ID:
chr19|31895283|31898386|+
Gene name:
A1cf
Transcript:
ENSMUST00000224564.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
5,6
Exon/intron offsets:
0,2938
Genomic length:
3103
Exon/intron sizes in nt:
239,165
Flanking exon/introns:
chr19:31888636-31895283|chr19:31898386-31904507
Splice length:
404
Other database IDs:
CIRCpedia: HSA_CIRCpedia_369745
Human Ortholog IDs:
Mature spliced Sequence:
GACTGGCCGTCTCTTGGGAGTCTGTGCCAGTGTGGACAATTGCCGATTGTTTGTGGGAGGAATCCCCAAAACCAAAAAGAGGGAAGAAATCTTATCAGAGATGAAAAAAGTCACAGAAGGAGTTGTTGATGTCATTGTCTACCCAAGTGCTGCTGATAAAACCAAAAACCGGGGATTTGCCTTTGTGGAATATGAGAGTCACCGAGCAGCCGCCATGGCTAGGCGGAGGCTGCTGCCAGGAAGAATTCAGTTGTGGGGACATCCTATTGCAGTAGACTGGGCAGAACCAGAAGTTGAAGTTGATGAGGACACAATGTCTTCCGTGAAAATCCTGTACGTAAGGAACCTTATGCTGTCTACCTCGGAAGAAATGATTGAAAAGGAATTCAACAGTATTAAACCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGGACACAATGTCTTCCGTGA
59.31
GCAATTGTCCACACTGGCAC
60.32
142
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGGACACAATGTCTTCCGTGA
59.31
TCCTCCCACAAACAATCGGC
60.61
160
PCR template sequence:
GAGGACACAATGTCTTCCGTGAAAATCCTGTACGTAAGGAACCTTATGCTGTCTACCTCGGAAGAAATGATTGAAAAGGAATTCAACAGTATTAAACCAGGACTGGCCGTCTCTTGGGAGTCTGTGCCAGTGTGGACAATTGCCGATTGTTTGTGGGAGGAATCCCCAAAACCAAAAAGAGGGAAGAAATCTTATCAGAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-16-5p(1), mmu-miR-7b-5p(1), mmu-miR-429-3p(1), mmu-let-7c-5p(1), mmu-miR-7a-5p(1), mmu-miR-29b-1-5p(1), mmu-miR-182-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGTATTAAACCAGGACTGGCCGTCTC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCA1CF_404_ORF_1
0.87
0.13876783
0.466923171
408
ORF sequence:
ATGAAAAAAGTCACAGAAGGAGTTGTTGATGTCATTGTCTACCCAAGTGCTGCTGATAAAACCAAAAACCGGGGATTTGCCTTTGTGGAATATGAGAGTCACCGAGCAGCCGCCATGGCTAGGCGGAGGCTGCTGCCAGGAAGAATTCAGTTGTGGGGACATCCTATTGCAGTAGACTGGGCAGAACCAGAAGTTGAAGTTGATGAGGACACAATGTCTTCCGTGAAAATCCTGTACGTAAGGAACCTTATGCTGTCTACCTCGGAAGAAATGATTGAAAAGGAATTCAACAGTATTAAACCAGGACTGGCCGTCTCTTGGGAGTCTGTGCCAGTGTGGACAATTGCCGATTGTTTGTGGGAGGAATCCCCAAAACCAAAAAGAGGGAAGAAATCTTATCAGAGATGA
Peptide sequence:
MKKVTEGVVDVIVYPSAADKTKNRGFAFVEYESHRAAAMARRRLLPGRIQLWGHPIAVDWAEPEVEVDEDTMSSVKILYVRNLMLSTSEEMIEKEFNSIKPGLAVSWESVPVWTIADCLWEESPKPKRGKKSYQR
IRESfinder result
IRESfinder score
0.492728047
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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