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mmu_circZmynd8_689
Basic information of circular RNA
PanCircBase ID:
mmu_circZmynd8_689
mm39_Chr. Position ID:
chr2|165675228|165688084|-
Gene name:
Zmynd8
Transcript:
ENSMUST00000177633.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
7
Exon/intron indexes:
10,9,8,7,6,5,4
Exon/intron offsets:
0,1581,3972,5503,6689,9455,12712
Genomic length:
12856
Exon/intron sizes in nt:
11,67,85,68,89,31,14,100
Flanking exon/introns:
chr2:165670609-165675228|chr2:165688084-165693919
Splice length:
689
Other database IDs:
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_354263
Human Ortholog IDs:
Mature spliced Sequence:
GACGGACGGAATGACTTCTATTGCTGGGTTTGTCACCGGGAAGGACAAGTCCTTTGCTGTGAGCTCTGTCCCCGGGTTTATCACGCTAAGTGTCTGAGACTGACATCGGAGCCAGAGGGGGACTGGTTTTGTCCTGAATGTGAGAAGATTACAGTAGCAGAATGCATCGAGACGCAGAGCAAAGCCATGACCATGCTGACCATTGAACAACTGTCCTACCTGCTCAAGTTTGCCATTCAGAAAATGAAGCAGCCAGGGACGGATGCATTCCAGAAGCCTGTTCCATTGGAGCAACACCCTGACTATGCAGAATATATTTTCCACCCCATGGACCTTTGTACATTGGAAAAGAATGCAAAAAAGAAGATGTACGGCTGCACAGAAGCCTTCCTGGCCGATGCCAAGTGGATCCTGCACAACTGCATTATTTATAATGGGGGAAATCACAAGTTGACGCAAATAGCAAAAGTCGTCATCAAAATCTGTGAGCACGAGATGAATGAAATCGAAGTCTGTCCAGAATGTTATCTTGCAGCTTGCCAAAAACGAGACAACTGGTTCTGTGAGCCCTGTAGCAATCCGCACCCTTTGGTCTGGGCAAAACTGAAAGGATTTCCATTCTGGCCAGCGAAAGCTCTGAGGGACAAAGACGGGCAGGTTGACGCCCGTTTCTTTGGACAACATGACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ATTTCCATTCTGGCCAGCGA
60.03
TTAGCGTGATAAACCCGGGG
59.82
167
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATTTCCATTCTGGCCAGCGA
60.03
GATAAACCCGGGGACAGAGC
60.18
160
PCR template sequence:
TGGTCTGGGCAAAACTGAAAGGATTTCCATTCTGGCCAGCGAAAGCTCTGAGGGACAAAGACGGGCAGGTTGACGCCCGTTTCTTTGGACAACATGACAGGACGGACGGAATGACTTCTATTGCTGGGTTTGTCACCGGGAAGGACAAGTCCTTTGCTGTGAGCTCTGTCCCCGGGTTTATCACGCTAAGTGTCTGAGAC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-181a-5p(1), mmu-let-7e-5p(1), mmu-miR-135a-5p(1), mmu-miR-149-5p(1), mmu-miR-153-3p(1), mmu-miR-182-5p(1), mmu-miR-129-5p(1), mmu-miR-452-3p(1), mmu-miR-1904(1)
siRNAs for circular RNA silencing
Junction sequence
GACAACATGACAGGACGGACGGAATG
siRNA sets
CATTCCGTCCGTCCTGTCA, ATTCCGTCCGTCCTGTCAT, TTCCGTCCGTCCTGTCATG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCZMYND8_689_ORF_1
1.087
0.20561299
0.871756128
600
ORF sequence:
ATGACCATGCTGACCATTGAACAACTGTCCTACCTGCTCAAGTTTGCCATTCAGAAAATGAAGCAGCCAGGGACGGATGCATTCCAGAAGCCTGTTCCATTGGAGCAACACCCTGACTATGCAGAATATATTTTCCACCCCATGGACCTTTGTACATTGGAAAAGAATGCAAAAAAGAAGATGTACGGCTGCACAGAAGCCTTCCTGGCCGATGCCAAGTGGATCCTGCACAACTGCATTATTTATAATGGGGGAAATCACAAGTTGACGCAAATAGCAAAAGTCGTCATCAAAATCTGTGAGCACGAGATGAATGAAATCGAAGTCTGTCCAGAATGTTATCTTGCAGCTTGCCAAAAACGAGACAACTGGTTCTGTGAGCCCTGTAGCAATCCGCACCCTTTGGTCTGGGCAAAACTGAAAGGATTTCCATTCTGGCCAGCGAAAGCTCTGAGGGACAAAGACGGGCAGGTTGACGCCCGTTTCTTTGGACAACATGACAGGACGGACGGAATGACTTCTATTGCTGGGTTTGTCACCGGGAAGGACAAGTCCTTTGCTGTGAGCTCTGTCCCCGGGTTTATCACGCTAAGTGTCTGA
Peptide sequence:
MTMLTIEQLSYLLKFAIQKMKQPGTDAFQKPVPLEQHPDYAEYIFHPMDLCTLEKNAKKKMYGCTEAFLADAKWILHNCIIYNGGNHKLTQIAKVVIKICEHEMNEIEVCPECYLAACQKRDNWFCEPCSNPHPLVWAKLKGFPFWPAKALRDKDGQVDARFFGQHDRTDGMTSIAGFVTGKDKSFAVSSVPGFITLSV
IRESfinder result
IRESfinder score
0.472909412
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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