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mmu_circAtxn2_602
Basic information of circular RNA
PanCircBase ID:
mmu_circAtxn2_602
mm39_Chr. Position ID:
chr5|121934435|121941143|+
Gene name:
Atxn2
Transcript:
ENSMUST00000051950.14
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
16,17,18,19,20
Exon/intron offsets:
0,850,1352,5708,6575
Genomic length:
6708
Exon/intron sizes in nt:
64,15,36,71,85,133
Flanking exon/introns:
chr5:121933311-121934435|chr5:121941143-121944284
Splice length:
602
Other database IDs:
circAtlas: mmu-Atxn2_0012
Human Ortholog IDs:
Mature spliced Sequence:
GCAGGTTAGGAAATCGACATTGAATCCCAATGCAAAGGAGTTCAACCCTCGTTCTTTCTCTCAGCCAAAGCCTTCTACTACCCCAACGTCACCTCGGCCTCAAGCACAACCCAGCCCATCTATGGTGGGTCATCAGCAGCCAGCTCCAGTGTACACTCAGCCTGTGTGCTTCGCACCCAATATGATGTATCCCGTCCCAGTGAGCCCGGGCGTACAACCTTTATACCCAATACCTATGACGCCCATGCCTGTGAACCAAGCCAAGACATATAGAGCAGGTAAAGTACCAAATATGCCCCAACAGCGACAAGACCAACATCATCAAAGCACCATGATGCACCCAGCCTCCGCGGCAGGGCCACCCATCGTAGCCACCCCGCCCGCTTACTCCACTCAGTACGTTGCCTACAGCCCTCAGCAGTTTCCCAATCAGCCTTTGGTCCAGCATGTGCCGCATTATCAGTCTCAGCATCCTCATGTGTACAGTCCTGTCATACAAGGTAATGCCAGGATGATGGCACCACCAGCACATGCTCAGCCTGGTTTAGTGTCTTCTTCAGCTGCTCAGTTCGGGGCTCACGAGCAGACGCACGCCATGTATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTTCAGCTGCTCAGTTCGG
60.04
AGGTGACGTTGGGGTAGTAGA
59.92
143
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTTCAGCTGCTCAGTTCGG
60.04
CGAGGTGACGTTGGGGTAG
59.79
145
PCR template sequence:
AATGCCAGGATGATGGCACCACCAGCACATGCTCAGCCTGGTTTAGTGTCTTCTTCAGCTGCTCAGTTCGGGGCTCACGAGCAGACGCACGCCATGTATGGCAGGTTAGGAAATCGACATTGAATCCCAATGCAAAGGAGTTCAACCCTCGTTCTTTCTCTCAGCCAAAGCCTTCTACTACCCCAACGTCACCTCGGCCT
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-33-5p(1), mmu-miR-138-5p(1), mmu-miR-218-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CACGCCATGTATGGCAGGTTAGGAAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATXN2_602_ORF_1
1.1598
0.11851687
0.732465748
504
ORF sequence:
ATGGTGGGTCATCAGCAGCCAGCTCCAGTGTACACTCAGCCTGTGTGCTTCGCACCCAATATGATGTATCCCGTCCCAGTGAGCCCGGGCGTACAACCTTTATACCCAATACCTATGACGCCCATGCCTGTGAACCAAGCCAAGACATATAGAGCAGGTAAAGTACCAAATATGCCCCAACAGCGACAAGACCAACATCATCAAAGCACCATGATGCACCCAGCCTCCGCGGCAGGGCCACCCATCGTAGCCACCCCGCCCGCTTACTCCACTCAGTACGTTGCCTACAGCCCTCAGCAGTTTCCCAATCAGCCTTTGGTCCAGCATGTGCCGCATTATCAGTCTCAGCATCCTCATGTGTACAGTCCTGTCATACAAGGTAATGCCAGGATGATGGCACCACCAGCACATGCTCAGCCTGGTTTAGTGTCTTCTTCAGCTGCTCAGTTCGGGGCTCACGAGCAGACGCACGCCATGTATGGCAGGTTAGGAAATCGACATTGA
Peptide sequence:
MVGHQQPAPVYTQPVCFAPNMMYPVPVSPGVQPLYPIPMTPMPVNQAKTYRAGKVPNMPQQRQDQHHQSTMMHPASAAGPPIVATPPAYSTQYVAYSPQQFPNQPLVQHVPHYQSQHPHVYSPVIQGNARMMAPPAHAQPGLVSSSAAQFGAHEQTHAMYGRLGNRH
IRESfinder result
IRESfinder score
0.469061395
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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