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mmu_circCdc123_513
Basic information of circular RNA
PanCircBase ID:
mmu_circCdc123_513
mm39_Chr. Position ID:
chr2|5803171|5826193|-
Gene name:
Cdc123
Transcript:
ENSMUST00000043864.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
11,10,9,8,7,6
Exon/intron offsets:
0,5586,6550,9070,12435,22915
Genomic length:
23022
Exon/intron sizes in nt:
12,92,91,23,76,49,107
Flanking exon/introns:
chr2:5800497-5803171|chr2:5826193-5827912
Splice length:
513
Other database IDs:
circAtlas: mmu-Cdc123_0003
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_167172
Human Ortholog IDs:
Mature spliced Sequence:
GATGCGTACTGGATAGCGATGAACAGTTCCCTGAAGTGTAAAACTCTCAGTGATATCTTCCTGCTTTTCAAGAGTTCTGATTTCATCACCCATGACTTCACACAGCCGTTTATTCATTGCACTGATGACTCTCCAGACCCTTGTATAGAGTACGAGCTTGTTCTCCGAAAATGGTGTGAATTAATTCCTGGGGCTGAATTCCGATGTTTTGTCAAAGAAAATAAGCTTATTGGTATTTCTCAGAGGGATTACACACAATACTATGATCATATTTCTAAGCAAAAAGAAGAAATTTGCAGATGCATTCAAGACTTTTTCAAGGAACACCTACAGTATAAATTCTTAGATGAAGACTTTGTGTTCGATATATACAGGGACAGTAGGGGGAAGGTGTGGCTCATTGACTTTAATCCATTTGGGGAGGTCACAGACTCACTGTTGTTTACTTGGGAAGAGCTAACATCTGAGAACAACCTACGTGGTGAGGTCACTGAAGGAGATGCTCAGGAGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGGGAGGTCACAGACTCA
60.11
TCAGAACTCTTGAAAAGCAGGA
57.58
178
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TTGGGGAGGTCACAGACTCA
60.11
AGCAGGAAGATATCACTGAGAGT
58.45
163
PCR template sequence:
ATTTGGGGAGGTCACAGACTCACTGTTGTTTACTTGGGAAGAGCTAACATCTGAGAACAACCTACGTGGTGAGGTCACTGAAGGAGATGCTCAGGAGCAGGATGCGTACTGGATAGCGATGAACAGTTCCCTGAAGTGTAAAACTCTCAGTGATATCTTCCTGCTTTTCAAGAGTTCTGATTTCATCACCCATGACTTCA
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-30e-5p(1), mmu-miR-130a-3p(1), mmu-miR-152-3p(1), mmu-miR-381-3p(1), mmu-miR-433-5p(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
TGCTCAGGAGCAGGATGCGTACTGGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCDC123_513_ORF_1
0.8895
0.108684232
0.983785019
1008
ORF sequence:
ATGAACAGTTCCCTGAAGTGTAAAACTCTCAGTGATATCTTCCTGCTTTTCAAGAGTTCTGATTTCATCACCCATGACTTCACACAGCCGTTTATTCATTGCACTGATGACTCTCCAGACCCTTGTATAGAGTACGAGCTTGTTCTCCGAAAATGGTGTGAATTAATTCCTGGGGCTGAATTCCGATGTTTTGTCAAAGAAAATAAGCTTATTGGTATTTCTCAGAGGGATTACACACAATACTATGATCATATTTCTAAGCAAAAAGAAGAAATTTGCAGATGCATTCAAGACTTTTTCAAGGAACACCTACAGTATAAATTCTTAGATGAAGACTTTGTGTTCGATATATACAGGGACAGTAGGGGGAAGGTGTGGCTCATTGACTTTAATCCATTTGGGGAGGTCACAGACTCACTGTTGTTTACTTGGGAAGAGCTAACATCTGAGAACAACCTACGTGGTGAGGTCACTGAAGGAGATGCTCAGGAGCAGGATGCGTACTGGATAGCGATGAACAGTTCCCTGAAGTGTAAAACTCTCAGTGATATCTTCCTGCTTTTCAAGAGTTCTGATTTCATCACCCATGACTTCACACAGCCGTTTATTCATTGCACTGATGACTCTCCAGACCCTTGTATAGAGTACGAGCTTGTTCTCCGAAAATGGTGTGAATTAATTCCTGGGGCTGAATTCCGATGTTTTGTCAAAGAAAATAAGCTTATTGGTATTTCTCAGAGGGATTACACACAATACTATGATCATATTTCTAAGCAAAAAGAAGAAATTTGCAGATGCATTCAAGACTTTTTCAAGGAACACCTACAGTATAAATTCTTAGATGAAGACTTTGTGTTCGATATATACAGGGACAGTAGGGGGAAGGTGTGGCTCATTGACTTTAATCCATTTGGGGAGGTCACAGACTCACTGTTGTTTACTTGGGAAGAGCTAACATCTGAGAACAACCTACGTGGTGAGGTCACTGAAGGAGATGCTCAGGAGCAG
Peptide sequence:
MNSSLKCKTLSDIFLLFKSSDFITHDFTQPFIHCTDDSPDPCIEYELVLRKWCELIPGAEFRCFVKENKLIGISQRDYTQYYDHISKQKEEICRCIQDFFKEHLQYKFLDEDFVFDIYRDSRGKVWLIDFNPFGEVTDSLLFTWEELTSENNLRGEVTEGDAQEQDAYWIAMNSSLKCKTLSDIFLLFKSSDFITHDFTQPFIHCTDDSPDPCIEYELVLRKWCELIPGAEFRCFVKENKLIGISQRDYTQYYDHISKQKEEICRCIQDFFKEHLQYKFLDEDFVFDIYRDSRGKVWLIDFNPFGEVTDSLLFTWEELTSENNLRGEVTEGDAQEQ
IRESfinder result
IRESfinder score
0.741870035
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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