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mmu_circAtxn2_306

Basic information of circular RNA
PanCircBase ID:

mmu_circAtxn2_306

mm39_Chr. Position ID:

chr5|121923277|121923929|+

Gene name:

Atxn2

Transcript:

ENSMUST00000051950.14

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

2

Exon/intron indexes:

12,13

Exon/intron offsets:

0,544

Genomic length:

652

Exon/intron sizes in nt:

1,98,108

Flanking exon/introns:

chr5:121922102-121923277|chr5:121923929-121924396

Splice length:

306

Other database IDs:

Human Ortholog IDs:
Mature spliced Sequence:

TTCCAAGGTTATCTCCCAAAACTCACAGACCCAGGTCTCCCAGGCAGAGCAGCATTGGAAACTCTCCCAGCGGGCCTGTGCTTGCTTCTCCCCAAGCTGGCATCATCCCTGCAGAAGCCGTTTCCATGCCTGTTCCCGCCGCATCTCCGACTCCTGCCAGCCCTGCATCCAACAGAGCACTGACCCCATCTATTGAGGCAAAAGATTCCAGGCTTCAAGATCAGAGGCAGAACTCTCCTGCAGGGAGTAAAGAAAATGTTAAAGCAAGTGAAACATCACCTAGCTTTTCAAAAGCTGACAACAAAG

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

CAGGCTTCAAGATCAGAGGCA

60.07

GTTTCCAATGCTGCTCTGCC

60.11

160

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

CAGGCTTCAAGATCAGAGGCA

60.07

TTTCCAATGCTGCTCTGCCT

60.25

159

PCR template sequence:

TCCAGGCTTCAAGATCAGAGGCAGAACTCTCCTGCAGGGAGTAAAGAAAATGTTAAAGCAAGTGAAACATCACCTAGCTTTTCAAAAGCTGACAACAAAGTTCCAAGGTTATCTCCCAAAACTCACAGACCCAGGTCTCCCAGGCAGAGCAGCATTGGAAACTCTCCCAGCGGGCCTGTGCTTGCTTCTCCCCAAGCTGG

Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs

NA

Interacting miRNAs (#binding sites)

NA

siRNAs for circular RNA silencing
Junction sequence

GCTGACAACAAAGTTCCAAGGTTATC

siRNA sets

TAACCTTGGAACTTTGTTG,AACCTTGGAACTTTGTTGT,GATAACCTTGGAACTTTGT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCATXN2_306_ORF_1

1.075

0.032843709

0.594626831

486

ORF sequence:

ATGCCTGTTCCCGCCGCATCTCCGACTCCTGCCAGCCCTGCATCCAACAGAGCACTGACCCCATCTATTGAGGCAAAAGATTCCAGGCTTCAAGATCAGAGGCAGAACTCTCCTGCAGGGAGTAAAGAAAATGTTAAAGCAAGTGAAACATCACCTAGCTTTTCAAAAGCTGACAACAAAGTTCCAAGGTTATCTCCCAAAACTCACAGACCCAGGTCTCCCAGGCAGAGCAGCATTGGAAACTCTCCCAGCGGGCCTGTGCTTGCTTCTCCCCAAGCTGGCATCATCCCTGCAGAAGCCGTTTCCATGCCTGTTCCCGCCGCATCTCCGACTCCTGCCAGCCCTGCATCCAACAGAGCACTGACCCCATCTATTGAGGCAAAAGATTCCAGGCTTCAAGATCAGAGGCAGAACTCTCCTGCAGGGAGTAAAGAAAATGTTAAAGCAAGTGAAACATCACCTAGCTTTTCAAAAGCTGACAACAAA

Peptide sequence:

MPVPAASPTPASPASNRALTPSIEAKDSRLQDQRQNSPAGSKENVKASETSPSFSKADNKVPRLSPKTHRPRSPRQSSIGNSPSGPVLASPQAGIIPAEAVSMPVPAASPTPASPASNRALTPSIEAKDSRLQDQRQNSPAGSKENVKASETSPSFSKADNK

IRESfinder result

IRESfinder score

0.704782788

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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Institute of Life sciences, Bhubaneswar, India

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