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mmu_circArhgap21_476
Basic information of circular RNA
PanCircBase ID:
mmu_circArhgap21_476
mm39_Chr. Position ID:
chr2|20865996|20870201|-
Gene name:
Arhgap21
Transcript:
ENSMUST00000154230.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
14,13,12
Exon/intron offsets:
0,1894,4079
Genomic length:
4205
Exon/intron sizes in nt:
6,52,85,126
Flanking exon/introns:
chr2:20865918-20865996|chr2:20870201-20872612
Splice length:
476
Other database IDs:
circAtlas: mmu-Arhgap21_0074
Human Ortholog IDs:
Mature spliced Sequence:
ATTACAGACAGCCAGAAGTCATCAGAAGACTCTGGATCGAGAAAGGGTTCTTCCTCCGAGGTCTTCAGTGATGCAGCCCGAGAAGGCTGGCTCCAGTTCCGACCACTGGTCACCGATAAGGGCAAGAGAGTTGGTGGCAGTATTCGGCCATGGAAACAGATGTATGTTGTCCTTCGGGGCCACTCACTTTACTTGTACAAAGACAGAAGAGAGCAGACAACGCCATCAGAAGAAGAGCAGCCCATCAGTGTCAACGCTTGCCTGATAGACATCTCGTACAGTGAGACCAAGAGGCGGAATGTATTCCGACTTACCACGTCTGACTGTGAATGCTTGTTCCAGGCTGAAGACAGAGATGATATGTTATCATGGATCAAGACTATTCAGGAAAGTAGCAACCTAAATGAAGAGGACACTGGAGTTACCAACAGAGATCTAATTAGTCGAAGAATCAAAGAGTATAACAGTCTGCTGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGAAGAGGACACTGGAGTTACC
59.1
GGCTGCATCACTGAAGACCT
60.04
150
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGAAGAGGACACTGGAGTTACC
59.1
TGCATCACTGAAGACCTCGG
59.75
147
PCR template sequence:
AGACTATTCAGGAAAGTAGCAACCTAAATGAAGAGGACACTGGAGTTACCAACAGAGATCTAATTAGTCGAAGAATCAAAGAGTATAACAGTCTGCTGAGATTACAGACAGCCAGAAGTCATCAGAAGACTCTGGATCGAGAAAGGGTTCTTCCTCCGAGGTCTTCAGTGATGCAGCCCGAGAAGGCTGGCTCCAGTTCC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-200b-3p(1), mmu-miR-200c-3p(1), mmu-miR-382-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACAGTCTGCTGAGATTACAGACAGCC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCARHGAP21_476_ORF_1
0.5053
0.151741385
0.621183346
582
ORF sequence:
ATGTATGTTGTCCTTCGGGGCCACTCACTTTACTTGTACAAAGACAGAAGAGAGCAGACAACGCCATCAGAAGAAGAGCAGCCCATCAGTGTCAACGCTTGCCTGATAGACATCTCGTACAGTGAGACCAAGAGGCGGAATGTATTCCGACTTACCACGTCTGACTGTGAATGCTTGTTCCAGGCTGAAGACAGAGATGATATGTTATCATGGATCAAGACTATTCAGGAAAGTAGCAACCTAAATGAAGAGGACACTGGAGTTACCAACAGAGATCTAATTAGTCGAAGAATCAAAGAGTATAACAGTCTGCTGAGATTACAGACAGCCAGAAGTCATCAGAAGACTCTGGATCGAGAAAGGGTTCTTCCTCCGAGGTCTTCAGTGATGCAGCCCGAGAAGGCTGGCTCCAGTTCCGACCACTGGTCACCGATAAGGGCAAGAGAGTTGGTGGCAGTATTCGGCCATGGAAACAGATGTATGTTGTCCTTCGGGGCCACTCACTTTACTTGTACAAAGACAGAAGAGAGCAGACAACGCCATCAGAAGAAGAGCAGCCCATCAGTGTCAACGCTTGCCTGA
Peptide sequence:
MYVVLRGHSLYLYKDRREQTTPSEEEQPISVNACLIDISYSETKRRNVFRLTTSDCECLFQAEDRDDMLSWIKTIQESSNLNEEDTGVTNRDLISRRIKEYNSLLRLQTARSHQKTLDRERVLPPRSSVMQPEKAGSSSDHWSPIRARELVAVFGHGNRCMLSFGATHFTCTKTEESRQRHQKKSSPSVSTLA
IRESfinder result
IRESfinder score
0.442298705
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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