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mmu_circRyk_556
Basic information of circular RNA
PanCircBase ID:
mmu_circRyk_556
mm39_Chr. Position ID:
chr9|102739072|102753082|+
Gene name:
Ryk
Transcript:
ENSMUST00000175883.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
2,3,4,5,6
Exon/intron offsets:
0,5681,7400,9854,13865
Genomic length:
14010
Exon/intron sizes in nt:
1,22,10,01,35,54,145
Flanking exon/introns:
chr9:102712438-102739072|chr9:102753082-102758852
Splice length:
556
Other database IDs:
circBase: mmu_circ_0015186, CIRCpedia: MMU_CIRCpedia_789, circAtlas: mmu-Ryk_0001
circAtlas: hsa-RYK_0003, CIRCpedia: HSA_CIRCpedia_43649
Human Ortholog IDs:
Mature spliced Sequence:
GTCTTGATGCAGAGCTTTACTATGTGAGAAATGACCTCATCAGTCACTACGCTCTGTCCTTTAACCTGCTAGTGCCCAGTGAGACAAACTTCCTGCACTTCACTTGGCATGCAAAGTCCAAGGTTGAATATAAGCTGGGATTCCAAGTAGACAACTTTGTGGCTATGGGCATGCCCCAGGTCAATATTTCTGCTCAAGGGGAGGTCCCACGCACTTTATCAGTGTTTCGGGTCGAGCTTTCTTGTACCGGCAAAGTCGACTCTGAAGTCATGATTCTAATGCAGCTCAATCTGACAGTGAATTCCTCAAAAAATTTTACAGTTTTAAATTTTAAACGAAGGAAAATGTGCTACAAAAAACTTGAAGAAGTAAAAACTTCAGCCTTGGACAAAAACACTAGCAGAACTATTTATGACCCTGTCCATGCAGCGCCAACGACTTCCACGCGTGTGTTTTACATCAGTGTAGGGGTTTGCTGTGCAGTGATATTTCTTGTAGCAATAATATTAGCCGTTTTGCACCTTCATAGCATGAAAAGGATTGAACTGGATGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TAGGGGTTTGCTGTGCAGTG
60.54
GTCTCACTGGGCACTAGCAG
60.11
176
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTAGGGGTTTGCTGTGCAG
60.54
GTCTCACTGGGCACTAGCAG
60.11
178
PCR template sequence:
ACATCAGTGTAGGGGTTTGCTGTGCAGTGATATTTCTTGTAGCAATAATATTAGCCGTTTTGCACCTTCATAGCATGAAAAGGATTGAACTGGATGACAGGTCTTGATGCAGAGCTTTACTATGTGAGAAATGACCTCATCAGTCACTACGCTCTGTCCTTTAACCTGCTAGTGCCCAGTGAGACAAACTTCCTGCACTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-382-5p(2), mmu-miR-137-3p(1), mmu-miR-217-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AACTGGATGACAGGTCTTGATGCAGA
siRNA sets
ATCAAGACCTGTCATCCAG,TCTGCATCAAGACCTGTCA,CATCAAGACCTGTCATCCA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCRYK_556_ORF_1
0.9567
0.055860153
0.687136279
561
ORF sequence:
ATGACAGGTCTTGATGCAGAGCTTTACTATGTGAGAAATGACCTCATCAGTCACTACGCTCTGTCCTTTAACCTGCTAGTGCCCAGTGAGACAAACTTCCTGCACTTCACTTGGCATGCAAAGTCCAAGGTTGAATATAAGCTGGGATTCCAAGTAGACAACTTTGTGGCTATGGGCATGCCCCAGGTCAATATTTCTGCTCAAGGGGAGGTCCCACGCACTTTATCAGTGTTTCGGGTCGAGCTTTCTTGTACCGGCAAAGTCGACTCTGAAGTCATGATTCTAATGCAGCTCAATCTGACAGTGAATTCCTCAAAAAATTTTACAGTTTTAAATTTTAAACGAAGGAAAATGTGCTACAAAAAACTTGAAGAAGTAAAAACTTCAGCCTTGGACAAAAACACTAGCAGAACTATTTATGACCCTGTCCATGCAGCGCCAACGACTTCCACGCGTGTGTTTTACATCAGTGTAGGGGTTTGCTGTGCAGTGATATTTCTTGTAGCAATAATATTAGCCGTTTTGCACCTTCATAGCATGAAAAGGATTGAACTGGATGAC
Peptide sequence:
MTGLDAELYYVRNDLISHYALSFNLLVPSETNFLHFTWHAKSKVEYKLGFQVDNFVAMGMPQVNISAQGEVPRTLSVFRVELSCTGKVDSEVMILMQLNLTVNSSKNFTVLNFKRRKMCYKKLEEVKTSALDKNTSRTIYDPVHAAPTTSTRVFYISVGVCCAVIFLVAIILAVLHLHSMKRIELDD
IRESfinder result
IRESfinder score
0.683935779
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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