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mmu_circZfp280d_663
Basic information of circular RNA
PanCircBase ID:
mmu_circZfp280d_663
mm39_Chr. Position ID:
chr9|72219359|72229892|+
Gene name:
Zfp280d
Transcript:
ENSMUST00000184036.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
7,8,9,10
Exon/intron offsets:
0,573,7014,10375
Genomic length:
10533
Exon/intron sizes in nt:
1,71,11,02,24,158
Flanking exon/introns:
chr9:72215350-72219359|chr9:72229892-72230281
Splice length:
663
Other database IDs:
circAtlas: mmu-Zfp280d_0089
circBase: hsa_circ_0103973, circAtlas: hsa-ZNF280D_0044, CIRCpedia: HSA_CIRCpedia_130719
Human Ortholog IDs:
Mature spliced Sequence:
GTTTGAATGAAACTTCATTTTTATCAAAACGTCCTTCTGGTTCTGACATAAGCAGTGTTAACCCAAAAAAGCCTAAACCCAGTGAAAATACTTCTGGAATAGATGCCTCTTCTGTAATCTCTTCAGAAAAGTCCCCATCAGTGATATCTCTCCAAGTGGTGCCATCGCAAGGTGCAAATTGTTCATCAAGTCAATCTAAAAATGGAACAACTTTTCCAAGAGCATGTCCCAAGTGTGATATTCACTTCAATCTTTTGGATCCTCTAAAAAATCACATGACGTATTGTTGTCCAGACATGATAAATAACTTTTTGGGATTGACTAAAGCAGACAATTTAAATTCAGCAAATGAAGCTAAGACTCTTGAATCAGAGAAAGGAAAATTGATAATGTTAGTTAATGACTTTTATTACGGAAAACATGAAGGAGACGTCCTGGAAGAACAGAAGACTCATACAACCTTTAAGTGCTTCAGTTGCTTAAAAGTTCTCAAAAATAATATTAGGTTTATGAACCACATGAAGCACCATTTGGAGCTCGAGAAGCAGAGCAGCGAGAGCTGGGAGAAGCACACCACGTGCCAGCACTGCTACCGGCAGTTCCCCACGCCCTTCCAGCTCCAGTGCCACATCGAGAGCACCCACACTCCTCATGAGTTCTCCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CACCACGTGCCAGCACTG
61.65
TGTCAGAACCAGAAGGACGT
58.59
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTCCAGTGCCACATCGAGAG
60.18
TCCAGAAGTATTTTCACTGGGT
57.01
144
PCR template sequence:
GAGAAGCACACCACGTGCCAGCACTGCTACCGGCAGTTCCCCACGCCCTTCCAGCTCCAGTGCCACATCGAGAGCACCCACACTCCTCATGAGTTCTCCAGTTTGAATGAAACTTCATTTTTATCAAAACGTCCTTCTGGTTCTGACATAAGCAGTGTTAACCCAAAAAAGCCTAAACCCAGTGAAAATACTTCTGGAAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-205-5p(1), mmu-miR-382-5p(1), mmu-miR-207(1), mmu-miR-3105-3p(1), mmu-miR-574-5p(1)
siRNAs for circular RNA silencing
Junction sequence
CATGAGTTCTCCAGTTTGAATGAAAC
siRNA sets
TTCAAACTGGAGAACTCAT,CATTCAAACTGGAGAACTC,ATTCAAACTGGAGAACTCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCZFP280D_663_ORF_1
0.7006
0.040776118
0.977524591
1050
ORF sequence:
ATGACGTATTGTTGTCCAGACATGATAAATAACTTTTTGGGATTGACTAAAGCAGACAATTTAAATTCAGCAAATGAAGCTAAGACTCTTGAATCAGAGAAAGGAAAATTGATAATGTTAGTTAATGACTTTTATTACGGAAAACATGAAGGAGACGTCCTGGAAGAACAGAAGACTCATACAACCTTTAAGTGCTTCAGTTGCTTAAAAGTTCTCAAAAATAATATTAGGTTTATGAACCACATGAAGCACCATTTGGAGCTCGAGAAGCAGAGCAGCGAGAGCTGGGAGAAGCACACCACGTGCCAGCACTGCTACCGGCAGTTCCCCACGCCCTTCCAGCTCCAGTGCCACATCGAGAGCACCCACACTCCTCATGAGTTCTCCAGTTTGAATGAAACTTCATTTTTATCAAAACGTCCTTCTGGTTCTGACATAAGCAGTGTTAACCCAAAAAAGCCTAAACCCAGTGAAAATACTTCTGGAATAGATGCCTCTTCTGTAATCTCTTCAGAAAAGTCCCCATCAGTGATATCTCTCCAAGTGGTGCCATCGCAAGGTGCAAATTGTTCATCAAGTCAATCTAAAAATGGAACAACTTTTCCAAGAGCATGTCCCAAGTGTGATATTCACTTCAATCTTTTGGATCCTCTAAAAAATCACATGACGTATTGTTGTCCAGACATGATAAATAACTTTTTGGGATTGACTAAAGCAGACAATTTAAATTCAGCAAATGAAGCTAAGACTCTTGAATCAGAGAAAGGAAAATTGATAATGTTAGTTAATGACTTTTATTACGGAAAACATGAAGGAGACGTCCTGGAAGAACAGAAGACTCATACAACCTTTAAGTGCTTCAGTTGCTTAAAAGTTCTCAAAAATAATATTAGGTTTATGAACCACATGAAGCACCATTTGGAGCTCGAGAAGCAGAGCAGCGAGAGCTGGGAGAAGCACACCACGTGCCAGCACTGCTACCGGCAGTTCCCCACGCCCTTCCAGCTCCAGTGCCACATCGAGAGCACCCACACTCCTCATGAGTTCTCC
Peptide sequence:
MTYCCPDMINNFLGLTKADNLNSANEAKTLESEKGKLIMLVNDFYYGKHEGDVLEEQKTHTTFKCFSCLKVLKNNIRFMNHMKHHLELEKQSSESWEKHTTCQHCYRQFPTPFQLQCHIESTHTPHEFSSLNETSFLSKRPSGSDISSVNPKKPKPSENTSGIDASSVISSEKSPSVISLQVVPSQGANCSSSQSKNGTTFPRACPKCDIHFNLLDPLKNHMTYCCPDMINNFLGLTKADNLNSANEAKTLESEKGKLIMLVNDFYYGKHEGDVLEEQKTHTTFKCFSCLKVLKNNIRFMNHMKHHLELEKQSSESWEKHTTCQHCYRQFPTPFQLQCHIESTHTPHEFS
IRESfinder result
IRESfinder score
0.704108096
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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