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mmu_ciArhgap21_306
Basic information of circular RNA
PanCircBase ID:
mmu_ciArhgap21_306
mm39_Chr. Position ID:
chr2|20859858|20860164|-
Gene name:
Arhgap21
Transcript:
ENSMUST00000154230.9
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
22
Exon/intron offsets:
0
Genomic length:
306
Exon/intron sizes in nt:
306
Flanking exon/introns:
chr2:20859851-20860164
Splice length:
306
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGTATTGTCCACACGTGCTCGGCTGCTCTCATGTGAGACACAGCCTCCTTCCTGATGCCATGGCCATCTTGGTCTCCTGCTTAGTATGCTGTTACCAGCTTTGCACCCTGGATGCAGGCGGCTAGCCCCTCAGTTGCTGGCCTGATAAGAATATAACGATGGTGCCTACTTTACCATTAGTGACATCTAACCAATGCAAAATTAACCTTGTGCTCAATATAATACTGTATCTTTTACTAAATGTTGTTTAAAATTTTAAAAATGTTGCCTTTGAAGAGATGATGAAGAGCTCTCTGTTTGTTA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTTGTGCTCAATATAATACTGT
55.92
GGAAGGAGGCTGTGTCTCAC
60.04
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACCTTGTGCTCAATATAATACTGT
55.92
AGGAAGGAGGCTGTGTCTCA
60.18
155
PCR template sequence:
AACCTTGTGCTCAATATAATACTGTATCTTTTACTAAATGTTGTTTAAAATTTTAAAAATGTTGCCTTTGAAGAGATGATGAAGAGCTCTCTGTTTGTTAGTAAGTATTGTCCACACGTGCTCGGCTGCTCTCATGTGAGACACAGCCTCCTTCCTGATGCCATGGCCATCTTGGTCTCCTGCTTAGTATGCTGTTACCA
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-33-5p(1), mmu-miR-101b-3p(1), mmu-miR-320-3p(1), mmu-miR-495-3p(1), mmu-miR-194-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTCTGTTTGTTAGTAAGTATTGTCC
siRNA sets
AATACTTACTAACAAACAG, ATACTTACTAACAAACAGA, CAATACTTACTAACAAACA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIARHGAP21_306_ORF_1
0.718
-0.067760883
0.04330735
153
ORF sequence:
ATGATGAAGAGCTCTCTGTTTGTTAGTAAGTATTGTCCACACGTGCTCGGCTGCTCTCATGTGAGACACAGCCTCCTTCCTGATGCCATGGCCATCTTGGTCTCCTGCTTAGTATGCTGTTACCAGCTTTGCACCCTGGATGCAGGCGGCTAG
Peptide sequence:
MMKSSLFVSKYCPHVLGCSHVRHSLLPDAMAILVSCLVCCYQLCTLDAGG
IRESfinder result
IRESfinder score
0.678233474
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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