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mmu_circUxs1_905
Basic information of circular RNA
PanCircBase ID:
mmu_circUxs1_905
mm39_Chr. Position ID:
chr1|43794858|43844834|-
Gene name:
Uxs1
Transcript:
ENSMUST00000126008.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
11
Exon/intron indexes:
13,12,11,10,9,8,7,6,5,4,3
Exon/intron offsets:
0,1273,4822,9191,15982,19118,24366,34765,41546,49654,49927
Genomic length:
49976
Exon/intron sizes in nt:
58,61,44,120,122,60,105,181,61,44,49
Flanking exon/introns:
chr1:43792980-43794858|chr1:43844834-43846509
Splice length:
905
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_363928
Human Ortholog IDs:
Mature spliced Sequence:
GTCTATCCAGGAAAATGGAGAACTAAAGATCGAAAGCAAGATTGAAGAGATTGTTGAACCATTAAGAGAGAAAATCAGAGATTTGGAAAAAAGTTTTACCCAGAAATACCCGCCTGTAAAGTTTTTATCAGAAAAGGACCGGAAAAGGATTTTGATCACTGGAGGTGCAGGCTTTGTGGGCTCCCATCTAACTGACAAACTCATGATGGATGGCCATGAGGTGACCGTGGTGGACAACTTCTTCACAGGCAGGAAGAGAAATGTGGAACACTGGATTGGCCATGAGAACTTCGAGCTGATTAACCATGATGTGGTCGAGCCGCTCTACATAGAAGTTGACCAGATATATCATCTGGCATCTCCAGCCTCCCCACCAAACTACATGTACAACCCCATCAAGACACTGAAGACTAATACAATTGGAACACTAAACATGTTGGGATTGGCAAAGCGCGTGGGTGCCCGTCTGCTCTTGGCCTCCACTTCCGAGGTATATGGAGATCCTGAGGTCCACCCTCAAAGTGAGGACTACTGGGGCCATGTGAATCCCATAGGACCCCGAGCCTGCTATGATGAGGGCAAACGTGTTGCAGAGACCATGTGCTATGCCTACATGAAGCAGGAAGGTGTGGAAGTACGGGTGGCAAGGATCTTCAACACCTTTGGGCCGAGAATGCACATGAATGATGGGCGGGTGGTCAGCAACTTCATCTTACAAGCACTACAAGGGGAGCCACTCACAGTCTATGGCTCTGGGTCTCAGACACGGGCATTCCAGTACGTAAGTGATCTGGTGAATGGCCTGGTAGCACTGATGAACAGCAATGTCAGCAGTCCTGTCAACTTGGGAAATCCAGAAGAACACACAATCCTGGAATTTGCTCAGTTAATTAAAAACCTTGTTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACAGCAATGTCAGCAGTCCT
59.6
ACAATCTCTTCAATCTTGCTTTCGA
59.3
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCAATGTCAGCAGTCCTGT
59.6
GGTTCAACAATCTCTTCAATCTTGC
59.14
145
PCR template sequence:
GTAGCACTGATGAACAGCAATGTCAGCAGTCCTGTCAACTTGGGAAATCCAGAAGAACACACAATCCTGGAATTTGCTCAGTTAATTAAAAACCTTGTTGGTCTATCCAGGAAAATGGAGAACTAAAGATCGAAAGCAAGATTGAAGAGATTGTTGAACCATTAAGAGAGAAAATCAGAGATTTGGAAAAAAGTTTTACC
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-199a-5p(1), mmu-miR-136-5p(1), mmu-miR-382-3p(1), mmu-miR-199b-3p(1), mmu-miR-199a-3p(1), mmu-miR-382-5p(1), mmu-miR-362-5p(1), mmu-miR-99a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAAAACCTTGTTGGTCTATCCAGGAA
siRNA sets
CTGGATAGACCAACAAGGT, CCTGGATAGACCAACAAGG, TTCCTGGATAGACCAACAA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCUXS1_905_ORF_1
1.1744
0.29161136
0.966155065
729
ORF sequence:
ATGATGGATGGCCATGAGGTGACCGTGGTGGACAACTTCTTCACAGGCAGGAAGAGAAATGTGGAACACTGGATTGGCCATGAGAACTTCGAGCTGATTAACCATGATGTGGTCGAGCCGCTCTACATAGAAGTTGACCAGATATATCATCTGGCATCTCCAGCCTCCCCACCAAACTACATGTACAACCCCATCAAGACACTGAAGACTAATACAATTGGAACACTAAACATGTTGGGATTGGCAAAGCGCGTGGGTGCCCGTCTGCTCTTGGCCTCCACTTCCGAGGTATATGGAGATCCTGAGGTCCACCCTCAAAGTGAGGACTACTGGGGCCATGTGAATCCCATAGGACCCCGAGCCTGCTATGATGAGGGCAAACGTGTTGCAGAGACCATGTGCTATGCCTACATGAAGCAGGAAGGTGTGGAAGTACGGGTGGCAAGGATCTTCAACACCTTTGGGCCGAGAATGCACATGAATGATGGGCGGGTGGTCAGCAACTTCATCTTACAAGCACTACAAGGGGAGCCACTCACAGTCTATGGCTCTGGGTCTCAGACACGGGCATTCCAGTACGTAAGTGATCTGGTGAATGGCCTGGTAGCACTGATGAACAGCAATGTCAGCAGTCCTGTCAACTTGGGAAATCCAGAAGAACACACAATCCTGGAATTTGCTCAGTTAATTAAAAACCTTGTTGGTCTATCCAGGAAAATGGAGAACTAA
Peptide sequence:
MMDGHEVTVVDNFFTGRKRNVEHWIGHENFELINHDVVEPLYIEVDQIYHLASPASPPNYMYNPIKTLKTNTIGTLNMLGLAKRVGARLLLASTSEVYGDPEVHPQSEDYWGHVNPIGPRACYDEGKRVAETMCYAYMKQEGVEVRVARIFNTFGPRMHMNDGRVVSNFILQALQGEPLTVYGSGSQTRAFQYVSDLVNGLVALMNSNVSSPVNLGNPEEHTILEFAQLIKNLVGLSRKMEN
IRESfinder result
IRESfinder score
0.463358937
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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