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mmu_circAtrx_1627

Basic information of circular RNA
PanCircBase ID:

mmu_circAtrx_1627

mm39_Chr. Position ID:

chrX|104874453|104894876|-

Gene name:

Atrx

Transcript:

ENSMUST00000113573.8

CircRNA type:

Exonic circular (circ)RNA

Exon/Intron count:

11

Exon/intron indexes:

25,24,23,22,21,20,19,18,17,16,15

Exon/intron offsets:

0,347,1599,5462,7391,8993,14649,14947,15838,16734,20189

Genomic length:

20423

Exon/intron sizes in nt:

1,73,80,13,11,18,17,61,00,00,00,00,00,00,00,000

Flanking exon/introns:

chrX:104869860-104874453|chrX:104894876-104895570

Splice length:

1627

Other database IDs:

circAtlas: mmu-Atrx_0088

Human Ortholog IDs:
Mature spliced Sequence:

AGCCATTCTGAGGAGGACAAGAAGGAAGGTGATGAGGAGGACGAGGAGGACGAGGACGAAGACGAGGAAGATGAAAATGATGATTCCAAGTCACCTGGAAAAGGCAGAAAGAAAATTCGGAAGATTCTTAAAGATGATAAACTAAGAACAGAAACACAGAATGCCCTTAAAGAAGAGGAAGAAAGGCGAAAACGTATTGCAGAGAGGGAACGTGAAAGGGAGAAATTGAGAGAGGTGATAGAAATTGAGGATGCTTCACCTACTAAGTGTCCAATAACAACCAAATTGGTTTTAGATGAAAATGAAGAGACCAAAGAACCGTTAGTGCAGGTTCATAGAAACATGGTTATAAAATTGAAACCCCATCAAGTAGATGGTGTTCAGTTTATGTGGGATTGCTGCTGTGAGTCTGTGGAAAAGACAAAGAAGTCCCCAGGTTCAGGATGTATTCTTGCCCACTGCATGGGCCTTGGTAAGACCCTCCAGGTGGTTAGTTTTCTTCACACAGTTCTTCTGTGTGACAAATTGGATTTCAGTACAGCTTTAGTGGTTTGTCCTCTTAACACTGCTTTGAATTGGATGAATGAATTTGAGAAGTGGCAGGAGGGATTAAATGATAATGAAAAACTTGAGGTATCTGAGTTAGCAACTGTGAAACGTCCTCAGGAGAGAAGTTATATGCTACAGAGATGGCAAGAAGATGGTGGTGTTATGATCATAGGGTATGAAATGTACAGAAATCTCGCTCAAGGAAGAAATGTGAAAAGTCGGAAACTTAAAGACATATTTAATAAAGCTTTAGTTGACCCAGGCCCTGATTTTGTTGTTTGTGATGAAGGCCATATTCTAAAAAATGAAGCATCTGCTGTTTCAAAAGCTATGAACTCTATAAAATCAAGGAGGAGGATTATTTTAACAGGAACACCACTTCAAAATAACCTAATTGAATATCATTGCATGGTTAACTTTATCAAGGAAAATTTGCTTGGATCCATCAAGGAATTCAGGAATAGATTTATAAATCCAATCCAAAATGGACAGTGTGCAGATTCTACCATGGTAGATGTGAGAGTGATGAAAAAACGTGCTCATATTCTCTATGAGATGTTAGCCGGATGTGTTCAGAGGAAAGATTACACAGCGCTAACAAAGTTCTTACCTCCAAAACATGAGTATGTGTTAGCTGTGAGAATGACTGCTATTCAGTGCAAGCTCTATCAATACTACTTAGATCACTTAACAGGTGTGGGCAATAGCACTGAAGGTGGAAGAGGAAAGGCAGGTGCAAAGCTTTTTCAAGATTTCCAAATGTTAAGTAGAATCTGGACTCATCCTTGGTGTTTGCAACTGGACTATATCAGCAAAGAAAATAAGGGTTATTTTGATGAAGATAGTATGGATGAATTTATAGCTTCAGATTCTGATGAAACCTCTAAGAGTTTAAGCTCAGATGAAAAGAAGAAACCAAAGGGGAAGAAGGGGAAAAAGGACAGCAGCTCAAGCGGAAGTGGCAGTGACAACGATGTTGAAGTCATCAAAGTCTGGAATTCAAGATCTCGAGGAGGTGGAGATGGCAACGTGGATGACACAGGAAATAACCCTTCAGTTTCTCTGAAGCTAGATGAAA

Divergent primers for circular RNA PCR

Primer Set-1

Forward primer
Tm
Reverse primer
Tm
Product size

TCTCGAGGAGGTGGAGATGG

60.11

CTTCCTCGTCTTCGTCCTCG

59.9

143

Primer Set-2

Forward primer
Tm
Reverse primer
Tm
Product size

TCTCGAGGAGGTGGAGATGG

60.11

TTCCTCGTCTTCGTCCTCGT

60.6

142

PCR template sequence:

GAAGTCATCAAAGTCTGGAATTCAAGATCTCGAGGAGGTGGAGATGGCAACGTGGATGACACAGGAAATAACCCTTCAGTTTCTCTGAAGCTAGATGAAAAGCCATTCTGAGGAGGACAAGAAGGAAGGTGATGAGGAGGACGAGGAGGACGAGGACGAAGACGAGGAAGATGAAAATGATGATTCCAAGTCACCTGGAA

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

13

Interacting miRNAs (#binding sites)

mmu-miR-335-3p(3), mmu-miR-211-5p(2), mmu-miR-320-3p(2), mmu-miR-9-5p(1), mmu-miR-27b-3p(1), mmu-miR-27a-3p(1), mmu-miR-205-5p(1), mmu-miR-322-5p(1), mmu-miR-377-3p(1), mmu-miR-673-5p(1), mmu-miR-3065-5p(1), mmu-miR-697(1), mmu-miR-490-3p(1)

siRNAs for circular RNA silencing
Junction sequence

AAGCTAGATGAAAAGCCATTCTGAGG

siRNA sets

GAATGGCTTTTCATCTAGC, TCAGAATGGCTTTTCATCT

Protein-coding potential of circular RNAs

CPAT analysis

CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length

CIRCATRX_1627_ORF_1

1.028

0.081099783

0.999833642

1632

ORF sequence:

ATGAAAAGCCATTCTGAGGAGGACAAGAAGGAAGGTGATGAGGAGGACGAGGAGGACGAGGACGAAGACGAGGAAGATGAAAATGATGATTCCAAGTCACCTGGAAAAGGCAGAAAGAAAATTCGGAAGATTCTTAAAGATGATAAACTAAGAACAGAAACACAGAATGCCCTTAAAGAAGAGGAAGAAAGGCGAAAACGTATTGCAGAGAGGGAACGTGAAAGGGAGAAATTGAGAGAGGTGATAGAAATTGAGGATGCTTCACCTACTAAGTGTCCAATAACAACCAAATTGGTTTTAGATGAAAATGAAGAGACCAAAGAACCGTTAGTGCAGGTTCATAGAAACATGGTTATAAAATTGAAACCCCATCAAGTAGATGGTGTTCAGTTTATGTGGGATTGCTGCTGTGAGTCTGTGGAAAAGACAAAGAAGTCCCCAGGTTCAGGATGTATTCTTGCCCACTGCATGGGCCTTGGTAAGACCCTCCAGGTGGTTAGTTTTCTTCACACAGTTCTTCTGTGTGACAAATTGGATTTCAGTACAGCTTTAGTGGTTTGTCCTCTTAACACTGCTTTGAATTGGATGAATGAATTTGAGAAGTGGCAGGAGGGATTAAATGATAATGAAAAACTTGAGGTATCTGAGTTAGCAACTGTGAAACGTCCTCAGGAGAGAAGTTATATGCTACAGAGATGGCAAGAAGATGGTGGTGTTATGATCATAGGGTATGAAATGTACAGAAATCTCGCTCAAGGAAGAAATGTGAAAAGTCGGAAACTTAAAGACATATTTAATAAAGCTTTAGTTGACCCAGGCCCTGATTTTGTTGTTTGTGATGAAGGCCATATTCTAAAAAATGAAGCATCTGCTGTTTCAAAAGCTATGAACTCTATAAAATCAAGGAGGAGGATTATTTTAACAGGAACACCACTTCAAAATAACCTAATTGAATATCATTGCATGGTTAACTTTATCAAGGAAAATTTGCTTGGATCCATCAAGGAATTCAGGAATAGATTTATAAATCCAATCCAAAATGGACAGTGTGCAGATTCTACCATGGTAGATGTGAGAGTGATGAAAAAACGTGCTCATATTCTCTATGAGATGTTAGCCGGATGTGTTCAGAGGAAAGATTACACAGCGCTAACAAAGTTCTTACCTCCAAAACATGAGTATGTGTTAGCTGTGAGAATGACTGCTATTCAGTGCAAGCTCTATCAATACTACTTAGATCACTTAACAGGTGTGGGCAATAGCACTGAAGGTGGAAGAGGAAAGGCAGGTGCAAAGCTTTTTCAAGATTTCCAAATGTTAAGTAGAATCTGGACTCATCCTTGGTGTTTGCAACTGGACTATATCAGCAAAGAAAATAAGGGTTATTTTGATGAAGATAGTATGGATGAATTTATAGCTTCAGATTCTGATGAAACCTCTAAGAGTTTAAGCTCAGATGAAAAGAAGAAACCAAAGGGGAAGAAGGGGAAAAAGGACAGCAGCTCAAGCGGAAGTGGCAGTGACAACGATGTTGAAGTCATCAAAGTCTGGAATTCAAGATCTCGAGGAGGTGGAGATGGCAACGTGGATGACACAGGAAATAACCCTTCAGTTTCTCTGAAGCTAGATGAA

Peptide sequence:

MKSHSEEDKKEGDEEDEEDEDEDEEDENDDSKSPGKGRKKIRKILKDDKLRTETQNALKEEEERRKRIAEREREREKLREVIEIEDASPTKCPITTKLVLDENEETKEPLVQVHRNMVIKLKPHQVDGVQFMWDCCCESVEKTKKSPGSGCILAHCMGLGKTLQVVSFLHTVLLCDKLDFSTALVVCPLNTALNWMNEFEKWQEGLNDNEKLEVSELATVKRPQERSYMLQRWQEDGGVMIIGYEMYRNLAQGRNVKSRKLKDIFNKALVDPGPDFVVCDEGHILKNEASAVSKAMNSIKSRRRIILTGTPLQNNLIEYHCMVNFIKENLLGSIKEFRNRFINPIQNGQCADSTMVDVRVMKKRAHILYEMLAGCVQRKDYTALTKFLPPKHEYVLAVRMTAIQCKLYQYYLDHLTGVGNSTEGGRGKAGAKLFQDFQMLSRIWTHPWCLQLDYISKENKGYFDEDSMDEFIASDSDETSKSLSSDEKKKPKGKKGKKDSSSSGSGSDNDVEVIKVWNSRSRGGGDGNVDDTGNNPSVSLKLDE

IRESfinder result

IRESfinder score

0.57854214

IRES/non IRES

IRES

riboCIRC information

riboCIRC ID

NA

NA

Evidence
Peptide sequence:

NA

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