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mmu_circCdc123_355
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc123_355
mm39_Chr. Position ID:
chr2|5809721|5826193|-
Gene name:
Cdc123
Transcript:
ENSMUST00000043864.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
9,8,7,6
Exon/intron offsets:
0,2520,5885,16365
Genomic length:
16472
Exon/intron sizes in nt:
1,23,76,49,107
Flanking exon/introns:
chr2:5808786-5809721|chr2:5826193-5827912
Splice length:
355
Other database IDs:
circAtlas: hsa-SCAF8_0001
Human Ortholog IDs:
Mature spliced Sequence:
GATGCGTACTGGATAGCGATGAACAGTTCCCTGAAGTGTAAAACTCTCAGTGATATCTTCCTGCTTTTCAAGAGTTCTGATTTCATCACCCATGACTTCACACAGCCGTTTATTCATTGCACTGATGACTCTCCAGACCCTTGTATAGAGTACGAGCTTGTTCTCCGAAAATGGTGTGAATTAATTCCTGGGGCTGAATTCCGATGTTTTGTCAAAGAAAATAAGCTTATTGGTATTTCTCAGAGGGATTACACACAATACTATGATCATATTTCTAAGCAAAAAGAAGAAATTTGCAGATGCATTCAAGACTTTTTCAAGGAACACCTACAGTATAAATTCTTAGATGAAGACT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGATGCATTCAAGACTTTTTCA
58.78
TCAGAACTCTTGAAAAGCAGGA
57.58
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAGATGCATTCAAGACTTTTTCA
58.78
TCAGAACTCTTGAAAAGCAGGAA
58.22
140
PCR template sequence:
CAATACTATGATCATATTTCTAAGCAAAAAGAAGAAATTTGCAGATGCATTCAAGACTTTTTCAAGGAACACCTACAGTATAAATTCTTAGATGAAGACTGATGCGTACTGGATAGCGATGAACAGTTCCCTGAAGTGTAAAACTCTCAGTGATATCTTCCTGCTTTTCAAGAGTTCTGATTTCATCACCCATGACTTCA
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-130a-3p(1), mmu-miR-152-3p(1), mmu-miR-381-3p(1), mmu-miR-130b-3p(1), mmu-miR-301b-3p(1), mmu-miR-721(1), mmu-miR-301a-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TTAGATGAAGACTGATGCGTACTGGA
siRNA sets
GTACGCATCAGTCTTCATC, TACGCATCAGTCTTCATCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC123_355_ORF_1
0.813
0.091480592
0.319888316
363
ORF sequence:
ATGAAGACTGATGCGTACTGGATAGCGATGAACAGTTCCCTGAAGTGTAAAACTCTCAGTGATATCTTCCTGCTTTTCAAGAGTTCTGATTTCATCACCCATGACTTCACACAGCCGTTTATTCATTGCACTGATGACTCTCCAGACCCTTGTATAGAGTACGAGCTTGTTCTCCGAAAATGGTGTGAATTAATTCCTGGGGCTGAATTCCGATGTTTTGTCAAAGAAAATAAGCTTATTGGTATTTCTCAGAGGGATTACACACAATACTATGATCATATTTCTAAGCAAAAAGAAGAAATTTGCAGATGCATTCAAGACTTTTTCAAGGAACACCTACAGTATAAATTCTTAGATGAAGAC
Peptide sequence:
MKTDAYWIAMNSSLKCKTLSDIFLLFKSSDFITHDFTQPFIHCTDDSPDPCIEYELVLRKWCELIPGAEFRCFVKENKLIGISQRDYTQYYDHISKQKEEICRCIQDFFKEHLQYKFLDED
IRESfinder result
IRESfinder score
0.74742779
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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