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mmu_circDmxl1_1081
Basic information of circular RNA
PanCircBase ID:
mmu_circDmxl1_1081
mm39_Chr. Position ID:
chr18|50035327|50055782|+
Gene name:
Dmxl1
Transcript:
ENSMUST00000180611.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
27,28,29,30,31,32,33
Exon/intron offsets:
0,519,10382,15318,17627,18569,20337
Genomic length:
20455
Exon/intron sizes in nt:
1,28,24,91,55,14,38,62,00,000
Flanking exon/introns:
chr18:50031847-50035327|chr18:50055782-50064977
Splice length:
1081
Other database IDs:
circAtlas: mmu-Dmxl1_0023
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
TTCATTTCAAACAAATCAATTTACTGGAATGGTTTATCAAACAGTACTTCTTGCCCATCGGCATTCTTTGCGAACTGGAAGTTTGGATGAATCAGTAACTCCCAACACATCACCAGCTCAATGGCCAGGAATAAATTTTCTAATTCAGCTTTTGAATTCCTCTGGGGAAGAAGCTCAGTCAGGACTTACAGTCTTGCTTTGTGAAATTCTCACAGCAGTATATCTTAGTCTGTTCATTCATGGGCTGGCAACACACTCTAGTAATGAGCTATTTCGGATTGTAGCCCACCCCCTAAATGAAAAAATGTGGTCTGCAGTATTTGGTGGAGGAGCACATGTTCCCAGCAAAGGACAGGCAAACTCAAAAGCTTTATCTGTTGAAGGAGAAAAACAAAACAGACATATTAGTCCATCAAAAGTGTCTGCCAGAGAATCTCCTGTATCCTCTTCCTCTGGAAATCAGGAGCCACCTGCAGTCAAGGAGAAGTTCGTCCCGCCTGAACTAAGTATCTGGGACTACTTCATAGCCAAGCCTTTTCTACCACCTTCCCAAAGTAGAGCAGAGTATGATTCTGAGGAAAGTCTAGAAAGTGATGATGAAGAAGAAGAGGACGACGATGATGCTTTGCCTTCTGGTCTCCAGCTCCATGAGCATTCAAACTCAAATTCATTCAGTTGGTCTTTGATGAGATTGGCTATGGTCCAGTTGGTGCTCAACAATTTGAAGACTTTCTATCCCTTTGCAGGTCATGATCTTGCAGAACTACCAGTTAGTTCACCTCTTTGTCATGCAGTTCTAAAAACTCTTCAATGCTGGGAACAAGTTCTTCTCCGGCGACTTGAAATCCATGGTGGACCACCTCAAAACTATATCTCAAGTCACACTTCTGAGGAGAATGTGTCTGCAGGCCCTGCAATACTCCGTCACAAAGCTTTACTAGAACCTACAAACACTCCTTTCAAATCCAAAAATCATCTCGCACTATCTGTGAAGAGGCTTTGGCAGTACTTGGTGAAACAGGAAGAAATTCAAGAAACTTTTATCAGAAATATATTCACAAAGAAACGATGTCTAAATGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGAAGAGGCTTTGGCAGT
59.82
CCGATGGGCAAGAAGTACTGT
60.07
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGTGAAGAGGCTTTGGCA
59.53
CCGATGGGCAAGAAGTACTGT
60.07
157
PCR template sequence:
ACTATCTGTGAAGAGGCTTTGGCAGTACTTGGTGAAACAGGAAGAAATTCAAGAAACTTTTATCAGAAATATATTCACAAAGAAACGATGTCTAAATGAGTTCATTTCAAACAAATCAATTTACTGGAATGGTTTATCAAACAGTACTTCTTGCCCATCGGCATTCTTTGCGAACTGGAAGTTTGGATGAATCAGTAACT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
12
Interacting miRNAs (#binding sites)
mmu-miR-200c-3p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-216a-5p(1), mmu-miR-217-5p(1), mmu-miR-320-3p(1), mmu-miR-138-5p(1), mmu-miR-207(1), mmu-miR-350-3p(1), mmu-miR-574-5p(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ATGTCTAAATGAGTTCATTTCAAACA
siRNA sets
GAAATGAACTCATTTAGAC, TTGAAATGAACTCATTTAG, TGAAATGAACTCATTTAGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCDMXL1_1081_ORF_1
0.8279
-0.056426396
0.986122588
1143
ORF sequence:
ATGGTTTATCAAACAGTACTTCTTGCCCATCGGCATTCTTTGCGAACTGGAAGTTTGGATGAATCAGTAACTCCCAACACATCACCAGCTCAATGGCCAGGAATAAATTTTCTAATTCAGCTTTTGAATTCCTCTGGGGAAGAAGCTCAGTCAGGACTTACAGTCTTGCTTTGTGAAATTCTCACAGCAGTATATCTTAGTCTGTTCATTCATGGGCTGGCAACACACTCTAGTAATGAGCTATTTCGGATTGTAGCCCACCCCCTAAATGAAAAAATGTGGTCTGCAGTATTTGGTGGAGGAGCACATGTTCCCAGCAAAGGACAGGCAAACTCAAAAGCTTTATCTGTTGAAGGAGAAAAACAAAACAGACATATTAGTCCATCAAAAGTGTCTGCCAGAGAATCTCCTGTATCCTCTTCCTCTGGAAATCAGGAGCCACCTGCAGTCAAGGAGAAGTTCGTCCCGCCTGAACTAAGTATCTGGGACTACTTCATAGCCAAGCCTTTTCTACCACCTTCCCAAAGTAGAGCAGAGTATGATTCTGAGGAAAGTCTAGAAAGTGATGATGAAGAAGAAGAGGACGACGATGATGCTTTGCCTTCTGGTCTCCAGCTCCATGAGCATTCAAACTCAAATTCATTCAGTTGGTCTTTGATGAGATTGGCTATGGTCCAGTTGGTGCTCAACAATTTGAAGACTTTCTATCCCTTTGCAGGTCATGATCTTGCAGAACTACCAGTTAGTTCACCTCTTTGTCATGCAGTTCTAAAAACTCTTCAATGCTGGGAACAAGTTCTTCTCCGGCGACTTGAAATCCATGGTGGACCACCTCAAAACTATATCTCAAGTCACACTTCTGAGGAGAATGTGTCTGCAGGCCCTGCAATACTCCGTCACAAAGCTTTACTAGAACCTACAAACACTCCTTTCAAATCCAAAAATCATCTCGCACTATCTGTGAAGAGGCTTTGGCAGTACTTGGTGAAACAGGAAGAAATTCAAGAAACTTTTATCAGAAATATATTCACAAAGAAACGATGTCTAAATGAGTTCATTTCAAACAAATCAATTTACTGGAATGGTTTATCAAACAGTACTTCTTGCCCATCGGCATTCTTTGCGAACTGGAAGTTTGGATGA
Peptide sequence:
MVYQTVLLAHRHSLRTGSLDESVTPNTSPAQWPGINFLIQLLNSSGEEAQSGLTVLLCEILTAVYLSLFIHGLATHSSNELFRIVAHPLNEKMWSAVFGGGAHVPSKGQANSKALSVEGEKQNRHISPSKVSARESPVSSSSGNQEPPAVKEKFVPPELSIWDYFIAKPFLPPSQSRAEYDSEESLESDDEEEEDDDDALPSGLQLHEHSNSNSFSWSLMRLAMVQLVLNNLKTFYPFAGHDLAELPVSSPLCHAVLKTLQCWEQVLLRRLEIHGGPPQNYISSHTSEENVSAGPAILRHKALLEPTNTPFKSKNHLALSVKRLWQYLVKQEEIQETFIRNIFTKKRCLNEFISNKSIYWNGLSNSTSCPSAFFANWKFG
IRESfinder result
IRESfinder score
0.741525498
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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