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mmu_circCdc23_282
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc23_282
mm39_Chr. Position ID:
chr18|34776851|34778161|-
Gene name:
Cdc23
Transcript:
ENSMUST00000025228.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
6,5,4
Exon/intron offsets:
0,226,1267
Genomic length:
1310
Exon/intron sizes in nt:
133,106,43
Flanking exon/introns:
chr18:34774703-34776851|chr18:34778161-34779954
Splice length:
282
Other database IDs:
CIRCpedia: MMU_CIRCpedia_226337, circAtlas: mmu-Cdc23_0006
circAtlas: hsa-CDC23_0006, CIRCpedia: HSA_CIRCpedia_363369
Human Ortholog IDs:
Mature spliced Sequence:
TCTGGAGAGAAGAAGAAGGATGACGAAACAGTTGATAGCCTAGGACCCCTAGAGAAGGGACAAGTCAAAAACGAGGCTCTCAGAGAACTGAGAGTGGAACTCAGCCGGAAGCACCAGGCTCGGGGACTTGATGGATTCGGCCTTTACCTGTATGGGGTGGTGCTTCGGAAACTGGACTTAGTGAAAGAGGCCATTGATGTGTTTGTGGAGGCTACTCATGTTTTGCCTTTGCACTGGGGAGCCTGGTTAGAGCTGTGTAACCTGATCACAGACAAAGAGATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGGGGAGCCTGGTTAGAG
60.62
CAGTTCTCTGAGAGCCTCGT
58.83
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTGGGGAGCCTGGTTAGAG
60.62
TCAGTTCTCTGAGAGCCTCGT
60.27
141
PCR template sequence:
GAAAGAGGCCATTGATGTGTTTGTGGAGGCTACTCATGTTTTGCCTTTGCACTGGGGAGCCTGGTTAGAGCTGTGTAACCTGATCACAGACAAAGAGATGTCTGGAGAGAAGAAGAAGGATGACGAAACAGTTGATAGCCTAGGACCCCTAGAGAAGGGACAAGTCAAAAACGAGGCTCTCAGAGAACTGAGAGTGGAAC
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-135a-5p(1), mmu-miR-19b-3p(1), mmu-miR-29b-3p(1), mmu-miR-29a-3p(1), mmu-miR-29c-3p(1), mmu-miR-130a-3p(1), mmu-miR-19a-3p(1), mmu-miR-152-3p(1), mmu-miR-148b-3p(1), mmu-miR-148a-3p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1)
siRNAs for circular RNA silencing
Junction sequence
AGACAAAGAGATGTCTGGAGAGAAGA
siRNA sets
TCTTCTCTCCAGACATCTC, CTTCTCTCCAGACATCTCT, TTCTCTCCAGACATCTCTT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC23_282_ORF_1
1.1486
0.329361544
0.570271129
285
ORF sequence:
ATGTCTGGAGAGAAGAAGAAGGATGACGAAACAGTTGATAGCCTAGGACCCCTAGAGAAGGGACAAGTCAAAAACGAGGCTCTCAGAGAACTGAGAGTGGAACTCAGCCGGAAGCACCAGGCTCGGGGACTTGATGGATTCGGCCTTTACCTGTATGGGGTGGTGCTTCGGAAACTGGACTTAGTGAAAGAGGCCATTGATGTGTTTGTGGAGGCTACTCATGTTTTGCCTTTGCACTGGGGAGCCTGGTTAGAGCTGTGTAACCTGATCACAGACAAAGAGATG
Peptide sequence:
MSGEKKKDDETVDSLGPLEKGQVKNEALRELRVELSRKHQARGLDGFGLYLYGVVLRKLDLVKEAIDVFVEATHVLPLHWGAWLELCNLITDKEM
IRESfinder result
IRESfinder score
0.411119473
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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