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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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