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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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