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mmu_circAtp11b_536
Basic information of circular RNA
PanCircBase ID:
mmu_circAtp11b_536
mm39_Chr. Position ID:
chr3|35842235|35854714|+
Gene name:
Atp11b
Transcript:
ENSMUST00000200445.5
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
5,6,7,8,9,10
Exon/intron offsets:
0,339,1471,7672,10507,12397
Genomic length:
12479
Exon/intron sizes in nt:
108,129,104,48,65,82
Flanking exon/introns:
chr3:35838736-35842235|chr3:35854714-35859882
Splice length:
536
Other database IDs:
circAtlas: mmu-Atp11b_0001
circBase: hsa_circ_0122893, circAtlas: hsa-ATP11B_0001, CIRCpedia: HSA_CIRCpedia_106017
Human Ortholog IDs:
Mature spliced Sequence:
GGTTATGAAGACTGGTTACGCCATAACTCAGATAATGAAGTAAACGGAGCTCCTGTCTATGTTGTCAGAAGTGGGGGGCTTGTAAAAACTCGATCCAAAAACATTCGGGTGGGTGATATTGTTCGTATAGCCAAAGATGAAATTTTTCCTGCAGATTTGGTGCTTCTGTCCTCAGATCGACTTGATGGTTCATGTCATGTGACAACTGCTAGTTTGGATGGAGAGACAAACCTAAAGACACATGTGTCAGTTCCAGAAACAGCAGTATTACAAACAGTTGCCAACTTGGACAGTCTCATAGCTGTAATAGAATGCCAACAGCCAGAAGCAGATTTATACAGATTTATGGGACGAATGATAATAACTCAACAAATGGAAGAAATTGTAAGACCTCTGGGACCAGAGAGTCTCTTGCTTCGTGGAGCCAGATTAAAAAATACAAAAGAAATTTTTGGTGTGGCTGTATACACTGGAATGGAAACTAAGATGGCACTAAATTACAAGAGCAAGTCACAGAAAAGATCTGCAGTAGAAAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTGTGGCTGTATACACTGG
59.72
CAACATAGACAGGAGCTCCGT
59.52
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGGTGTGGCTGTATACACTGG
59.72
ACAACATAGACAGGAGCTCCG
59.52
149
PCR template sequence:
ATACAAAAGAAATTTTTGGTGTGGCTGTATACACTGGAATGGAAACTAAGATGGCACTAAATTACAAGAGCAAGTCACAGAAAAGATCTGCAGTAGAAAAGGTTATGAAGACTGGTTACGCCATAACTCAGATAATGAAGTAAACGGAGCTCCTGTCTATGTTGTCAGAAGTGGGGGGCTTGTAAAAACTCGATCCAAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-9-5p(1), mmu-miR-199a-5p(1), mmu-miR-429-3p(1), mmu-miR-200b-3p(1), mmu-miR-149-5p(1), mmu-miR-182-5p(1), mmu-miR-5101(1), mmu-miR-539-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CTGCAGTAGAAAAGGTTATGAAGACT
siRNA sets
ATAACCTTTTCTACTGCAG, TCATAACCTTTTCTACTGC, CTTCATAACCTTTTCTACT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCATP11B_536_ORF_1
0.9929
-0.014797922
0.14263137
234
ORF sequence:
ATGGGACGAATGATAATAACTCAACAAATGGAAGAAATTGTAAGACCTCTGGGACCAGAGAGTCTCTTGCTTCGTGGAGCCAGATTAAAAAATACAAAAGAAATTTTTGGTGTGGCTGTATACACTGGAATGGAAACTAAGATGGCACTAAATTACAAGAGCAAGTCACAGAAAAGATCTGCAGTAGAAAAGGTTATGAAGACTGGTTACGCCATAACTCAGATAATGAAGTAA
Peptide sequence:
MGRMIITQQMEEIVRPLGPESLLLRGARLKNTKEIFGVAVYTGMETKMALNYKSKSQKRSAVEKVMKTGYAITQIMK
IRESfinder result
IRESfinder score
0.564143011
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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