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mmu_circAtxn10_420
Basic information of circular RNA
PanCircBase ID:
mmu_circAtxn10_420
mm39_Chr. Position ID:
chr15|85249477|85267185|+
Gene name:
Atxn10
Transcript:
ENSMUST00000163242.3
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
3,4,5,6
Exon/intron offsets:
0,10045,11267,17627
Genomic length:
17708
Exon/intron sizes in nt:
83,97,159,81
Flanking exon/introns:
chr15:85243846-85249477|chr15:85267185-85271191
Splice length:
420
Other database IDs:
CIRCpedia: MMU_CIRCpedia_214704, circAtlas: mmu-Atxn10_0012
circBase: hsa_circ_0063769, circAtlas: hsa-ATXN10_0015, CIRCpedia: HSA_CIRCpedia_37036
Human Ortholog IDs:
Mature spliced Sequence:
GAACCTGGATACGATCGGAGTTGCTGTTGATTTGGTTCTTCTCTTTCGTGAACTTCGGGTGGAACAAGACTCCTTGTTGACAGCTTTTCGATGTGGCCTGCAGTTTTTAGGCAACGTTGCCTCACGAAATGAAGAATCCCAGTCCATTGTTTGGGTCCACGCCTTCCCAGAACTCTTCATGTCTTGCTTGAACCATCCAGACAAAAAGATTGTTGCCTACTGTTCCATGATTCTGTTCACATCTCTTAATGCTGAAAGGATGAAAGACCTGGAAGAGAACCTCAATATTGCAATTAACGTCATAGAAGCTCACCAAAAGCACCCGGCGTCAGAGTGGCCGTTCTTGATTATTTCAGACCACTTTCTGAAAAGCCCGGAACTGGTGGAAGCTATGTATGGCAAACTCAGCAACCAGGAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTCAGAGTGGCCGTTCTTGA
59.97
GTTCCACCCGAAGTTCACGA
60.25
158
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGAAAAGCCCGGAACTGG
60.25
GGCCACATCGAAAAGCTGTC
59.83
155
PCR template sequence:
ACCCGGCGTCAGAGTGGCCGTTCTTGATTATTTCAGACCACTTTCTGAAAAGCCCGGAACTGGTGGAAGCTATGTATGGCAAACTCAGCAACCAGGAAAGGAACCTGGATACGATCGGAGTTGCTGTTGATTTGGTTCTTCTCTTTCGTGAACTTCGGGTGGAACAAGACTCCTTGTTGACAGCTTTTCGATGTGGCCTG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
1
Interacting miRNAs (#binding sites)
mmu-miR-320-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCAACCAGGAAAGGAACCTGGATACG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATXN10_420_ORF_1
1.1068
0.200911738
0.915268317
660
ORF sequence:
ATGTCTTGCTTGAACCATCCAGACAAAAAGATTGTTGCCTACTGTTCCATGATTCTGTTCACATCTCTTAATGCTGAAAGGATGAAAGACCTGGAAGAGAACCTCAATATTGCAATTAACGTCATAGAAGCTCACCAAAAGCACCCGGCGTCAGAGTGGCCGTTCTTGATTATTTCAGACCACTTTCTGAAAAGCCCGGAACTGGTGGAAGCTATGTATGGCAAACTCAGCAACCAGGAAAGGAACCTGGATACGATCGGAGTTGCTGTTGATTTGGTTCTTCTCTTTCGTGAACTTCGGGTGGAACAAGACTCCTTGTTGACAGCTTTTCGATGTGGCCTGCAGTTTTTAGGCAACGTTGCCTCACGAAATGAAGAATCCCAGTCCATTGTTTGGGTCCACGCCTTCCCAGAACTCTTCATGTCTTGCTTGAACCATCCAGACAAAAAGATTGTTGCCTACTGTTCCATGATTCTGTTCACATCTCTTAATGCTGAAAGGATGAAAGACCTGGAAGAGAACCTCAATATTGCAATTAACGTCATAGAAGCTCACCAAAAGCACCCGGCGTCAGAGTGGCCGTTCTTGATTATTTCAGACCACTTTCTGAAAAGCCCGGAACTGGTGGAAGCTATGTATGGCAAACTCAGCAACCAGGAA
Peptide sequence:
MSCLNHPDKKIVAYCSMILFTSLNAERMKDLEENLNIAINVIEAHQKHPASEWPFLIISDHFLKSPELVEAMYGKLSNQERNLDTIGVAVDLVLLFRELRVEQDSLLTAFRCGLQFLGNVASRNEESQSIVWVHAFPELFMSCLNHPDKKIVAYCSMILFTSLNAERMKDLEENLNIAINVIEAHQKHPASEWPFLIISDHFLKSPELVEAMYGKLSNQE
IRESfinder result
IRESfinder score
0.691205094
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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