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mmu_circCops4_641
Basic information of circular RNA
PanCircBase ID:
mmu_circCops4_641
mm39_Chr. Position ID:
chr5|100675839|100681528|+
Gene name:
Cops4
Transcript:
ENSMUST00000045993.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
2,3,4,5,6
Exon/intron offsets:
0,565,2073,5268,5538
Genomic length:
5689
Exon/intron sizes in nt:
8,01,52,10,41,54,151
Flanking exon/introns:
chr5:100666416-100675839|chr5:100681528-100685163
Splice length:
641
Other database IDs:
CIRCpedia: MMU_CIRCpedia_213761, circAtlas: mmu-Cops4_0009
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_159012
Human Ortholog IDs:
Mature spliced Sequence:
ATATCGTCAGATTCTGGAAAAAGCCATTCAGTTATCTGGGACAGAACAACTAGAAGCATTGAAAGCTTTTGTGGAAGCGATGGTGAATGAGAATGTCAGCCTCGTGATCTCACGGCAACTGCTAACAGATTTCTGCACACACCTCCCTAACCTGCCAGACAGCACAGCCAAGGAGGTCTACCATTTCACCTTGGAGAAGATCCAGCCTCGGGTCATTTCCTTTGAAGAGCAGGTTGCTTCCATAAGACAGCATCTGGCATCTATTTATGAGAAGGAGGAAGACTGGAGAAATGCAGCCCAAGTGTTGGTGGGGATTCCTCTGGAAACAGGACAAAAACAGTACAACGTAGATTATAAGCTGGAGACTTACCTGAAGATTGCAAGGCTATACCTGGAGGATGACGATCCCGTCCAGGCCGAGGCTTACATAAACCGAGCGTCCTTACTTCAGAACGAATCCACAAATGAACAGTTACAGATACACTATAAGGTTTGCTATGCGCGTGTCCTTGATTACAGAAGGAAATTCATTGAGGCCGCCCAGAGGTACAATGAGCTCTCTTACAAGACAATAGTCCATGAAAGTGAGAGACTAGAGGCCTTAAAGCATGCACTGCACTGCACCATCTTAGCATCGGCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGAGGCCTTAAAGCATGCACT
59.99
TTCTCATTCACCATCGCTTCCA
60.03
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ACTAGAGGCCTTAAAGCATGCA
59.76
TCATTCACCATCGCTTCCACA
60
140
PCR template sequence:
CAGAGGTACAATGAGCTCTCTTACAAGACAATAGTCCATGAAAGTGAGAGACTAGAGGCCTTAAAGCATGCACTGCACTGCACCATCTTAGCATCGGCAGATATCGTCAGATTCTGGAAAAAGCCATTCAGTTATCTGGGACAGAACAACTAGAAGCATTGAAAGCTTTTGTGGAAGCGATGGTGAATGAGAATGTCAGC
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
5
Interacting miRNAs (#binding sites)
mmu-miR-135a-5p(1), mmu-miR-152-3p(1), mmu-miR-148a-3p(1), mmu-miR-203-3p(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
TTAGCATCGGCAGATATCGTCAGATT
siRNA sets
AATCTGACGATATCTGCCG, ATCTGACGATATCTGCCGA, TGACGATATCTGCCGATGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCOPS4_641_ORF_1
1.0361
0.237963618
0.88742151
615
ORF sequence:
ATGGTGAATGAGAATGTCAGCCTCGTGATCTCACGGCAACTGCTAACAGATTTCTGCACACACCTCCCTAACCTGCCAGACAGCACAGCCAAGGAGGTCTACCATTTCACCTTGGAGAAGATCCAGCCTCGGGTCATTTCCTTTGAAGAGCAGGTTGCTTCCATAAGACAGCATCTGGCATCTATTTATGAGAAGGAGGAAGACTGGAGAAATGCAGCCCAAGTGTTGGTGGGGATTCCTCTGGAAACAGGACAAAAACAGTACAACGTAGATTATAAGCTGGAGACTTACCTGAAGATTGCAAGGCTATACCTGGAGGATGACGATCCCGTCCAGGCCGAGGCTTACATAAACCGAGCGTCCTTACTTCAGAACGAATCCACAAATGAACAGTTACAGATACACTATAAGGTTTGCTATGCGCGTGTCCTTGATTACAGAAGGAAATTCATTGAGGCCGCCCAGAGGTACAATGAGCTCTCTTACAAGACAATAGTCCATGAAAGTGAGAGACTAGAGGCCTTAAAGCATGCACTGCACTGCACCATCTTAGCATCGGCAGATATCGTCAGATTCTGGAAAAAGCCATTCAGTTATCTGGGACAGAACAACTAG
Peptide sequence:
MVNENVSLVISRQLLTDFCTHLPNLPDSTAKEVYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDWRNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTNEQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASADIVRFWKKPFSYLGQNN
IRESfinder result
IRESfinder score
0.614803666
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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