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mmu_ciNcl_176
Basic information of circular RNA
PanCircBase ID:
mmu_ciNcl_176
mm39_Chr. Position ID:
chr1|86283916|86284092|-
Gene name:
Ncl
Transcript:
ENSMUST00000027438.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
5
Exon/intron offsets:
0
Genomic length:
176
Exon/intron sizes in nt:
176
Flanking exon/introns:
chr1:86283915-86284092
Splice length:
176
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGCCTGCAAAACTGGGGAAACAGATCAGAGTAGCACTAGCACAAGTGATGAGTGACAAAGGGACTTAATACTGAACCATGGGGTTGAAATGAAATATGCTGATGTGCTTTATAGTTTATGATGAAATTTGTTGTGTGCTTAAGTGGGCTGAAAGTTCATTTTTTGTGTGTGCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGTGCTTAAGTGGGCTGA
59.53
ACCCCATGGTTCAGTATTAAGTCC
60.08
129
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTGTGCTTAAGTGGGCTGA
59.53
CCCATGGTTCAGTATTAAGTCCCT
59.83
127
PCR template sequence:
GAAATGAAATATGCTGATGTGCTTTATAGTTTATGATGAAATTTGTTGTGTGCTTAAGTGGGCTGAAAGTTCATTTTTTGTGTGTGCAGTAAGCCTGCAAAACTGGGGAAACAGATCAGAGTAGCACTAGCACAAGTGATGAGTGACAAAGGGACTTAATACTGAACCATGGGGTT
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-211-5p(1), mmu-miR-204-5p(1), mmu-miR-340-5p(1)
siRNAs for circular RNA silencing
Junction sequence
TTTTGTGTGTGCAGTAAGCCTGCAAA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CINCL_176_ORF_1
0.4033
-0.37350366
0.005454677
114
ORF sequence:
ATGCTGATGTGCTTTATAGTTTATGATGAAATTTGTTGTGTGCTTAAGTGGGCTGAAAGTTCATTTTTTGTGTGTGCAGTAAGCCTGCAAAACTGGGGAAACAGATCAGAGTAG
Peptide sequence:
MLMCFIVYDEICCVLKWAESSFFVCAVSLQNWGNRSE
IRESfinder result
IRESfinder score
0.735656195
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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