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mmu_circAtxn2_913
Basic information of circular RNA
PanCircBase ID:
mmu_circAtxn2_913
mm39_Chr. Position ID:
chr5|121933000|121941143|+
Gene name:
Atxn2
Transcript:
ENSMUST00000051950.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
15,16,17,18,19,20
Exon/intron offsets:
0,1435,2285,2787,7143,8010
Genomic length:
8143
Exon/intron sizes in nt:
3,11,64,15,36,71,85,130
Flanking exon/introns:
chr5:121924467-121933000|chr5:121941143-121944284
Splice length:
913
Other database IDs:
CIRCpedia: MMU_CIRCpedia_5607, circAtlas: mmu-Atxn2_0007
Human Ortholog IDs:
Mature spliced Sequence:
TTACAGCCAAGCTCTACATCTGAATCTATGGATCAACTACTAAGCAAAAATAGAGAAGGAGAAAAGTCACGAGATTTGATTAAAGATAAAACGGAAGCAAGTGCTAAGGATAGTTTCATTGACAGCAGCAGCAGCAGCAGCAACTGTACCAGTGGCAGCAGCAAGACCAACAGCCCTAGCATCTCCCCTTCCATGCTTAGTAATGCAGAGCACAAGAGGGGGCCTGAGGTCACATCCCAAGGGGTGCAGACTTCCAGCCCAGCCTGCAAACAAGAGAAGGATGACAGAGAAGAGAAGAAAGACACAACAGAGCAGGTTAGGAAATCGACATTGAATCCCAATGCAAAGGAGTTCAACCCTCGTTCTTTCTCTCAGCCAAAGCCTTCTACTACCCCAACGTCACCTCGGCCTCAAGCACAACCCAGCCCATCTATGGTGGGTCATCAGCAGCCAGCTCCAGTGTACACTCAGCCTGTGTGCTTCGCACCCAATATGATGTATCCCGTCCCAGTGAGCCCGGGCGTACAACCTTTATACCCAATACCTATGACGCCCATGCCTGTGAACCAAGCCAAGACATATAGAGCAGGTAAAGTACCAAATATGCCCCAACAGCGACAAGACCAACATCATCAAAGCACCATGATGCACCCAGCCTCCGCGGCAGGGCCACCCATCGTAGCCACCCCGCCCGCTTACTCCACTCAGTACGTTGCCTACAGCCCTCAGCAGTTTCCCAATCAGCCTTTGGTCCAGCATGTGCCGCATTATCAGTCTCAGCATCCTCATGTGTACAGTCCTGTCATACAAGGTAATGCCAGGATGATGGCACCACCAGCACATGCTCAGCCTGGTTTAGTGTCTTCTTCAGCTGCTCAGTTCGGGGCTCACGAGCAGACGCACGCCATGTATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCTCAGCCTGGTTTAGTGT
59.24
TCTCGTGACTTTTCTCCTTCTCT
58.85
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTCAGCCTGGTTTAGTGTCT
60
TCTCGTGACTTTTCTCCTTCTCT
58.85
144
PCR template sequence:
AATGCCAGGATGATGGCACCACCAGCACATGCTCAGCCTGGTTTAGTGTCTTCTTCAGCTGCTCAGTTCGGGGCTCACGAGCAGACGCACGCCATGTATGTTACAGCCAAGCTCTACATCTGAATCTATGGATCAACTACTAAGCAAAAATAGAGAAGGAGAAAAGTCACGAGATTTGATTAAAGATAAAACGGAAGCAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-33-5p(1), mmu-miR-138-5p(1), mmu-miR-431-5p(1), mmu-miR-218-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CACGCCATGTATGTTACAGCCAAGCT
siRNA sets
TTGGCTGTAACATACATGG, CTTGGCTGTAACATACATG, CTGTAACATACATGGCGTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATXN2_913_ORF_1
0.9752
0.167730195
0.978468054
915
ORF sequence:
ATGTTACAGCCAAGCTCTACATCTGAATCTATGGATCAACTACTAAGCAAAAATAGAGAAGGAGAAAAGTCACGAGATTTGATTAAAGATAAAACGGAAGCAAGTGCTAAGGATAGTTTCATTGACAGCAGCAGCAGCAGCAGCAACTGTACCAGTGGCAGCAGCAAGACCAACAGCCCTAGCATCTCCCCTTCCATGCTTAGTAATGCAGAGCACAAGAGGGGGCCTGAGGTCACATCCCAAGGGGTGCAGACTTCCAGCCCAGCCTGCAAACAAGAGAAGGATGACAGAGAAGAGAAGAAAGACACAACAGAGCAGGTTAGGAAATCGACATTGAATCCCAATGCAAAGGAGTTCAACCCTCGTTCTTTCTCTCAGCCAAAGCCTTCTACTACCCCAACGTCACCTCGGCCTCAAGCACAACCCAGCCCATCTATGGTGGGTCATCAGCAGCCAGCTCCAGTGTACACTCAGCCTGTGTGCTTCGCACCCAATATGATGTATCCCGTCCCAGTGAGCCCGGGCGTACAACCTTTATACCCAATACCTATGACGCCCATGCCTGTGAACCAAGCCAAGACATATAGAGCAGGTAAAGTACCAAATATGCCCCAACAGCGACAAGACCAACATCATCAAAGCACCATGATGCACCCAGCCTCCGCGGCAGGGCCACCCATCGTAGCCACCCCGCCCGCTTACTCCACTCAGTACGTTGCCTACAGCCCTCAGCAGTTTCCCAATCAGCCTTTGGTCCAGCATGTGCCGCATTATCAGTCTCAGCATCCTCATGTGTACAGTCCTGTCATACAAGGTAATGCCAGGATGATGGCACCACCAGCACATGCTCAGCCTGGTTTAGTGTCTTCTTCAGCTGCTCAGTTCGGGGCTCACGAGCAGACGCACGCCATGTAT
Peptide sequence:
MLQPSSTSESMDQLLSKNREGEKSRDLIKDKTEASAKDSFIDSSSSSSNCTSGSSKTNSPSISPSMLSNAEHKRGPEVTSQGVQTSSPACKQEKDDREEKKDTTEQVRKSTLNPNAKEFNPRSFSQPKPSTTPTSPRPQAQPSPSMVGHQQPAPVYTQPVCFAPNMMYPVPVSPGVQPLYPIPMTPMPVNQAKTYRAGKVPNMPQQRQDQHHQSTMMHPASAAGPPIVATPPAYSTQYVAYSPQQFPNQPLVQHVPHYQSQHPHVYSPVIQGNARMMAPPAHAQPGLVSSSAAQFGAHEQTHAMY
IRESfinder result
IRESfinder score
0.497507772
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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