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mmu_circCops4_732
Basic information of circular RNA
PanCircBase ID:
mmu_circCops4_732
mm39_Chr. Position ID:
chr5|100676404|100685334|+
Gene name:
Cops4
Transcript:
ENSMUST00000045993.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
5
Exon/intron indexes:
3,4,5,6,7
Exon/intron offsets:
0,1508,4703,4973,8759
Genomic length:
8930
Exon/intron sizes in nt:
15,21,04,15,41,51,171
Flanking exon/introns:
chr5:100675919-100676404|chr5:100685334-100689402
Splice length:
732
Other database IDs:
CIRCpedia: MMU_CIRCpedia_185, circAtlas: mmu-Cops4_0008
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_68845
Human Ortholog IDs:
Mature spliced Sequence:
TGGTGAATGAGAATGTCAGCCTCGTGATCTCACGGCAACTGCTAACAGATTTCTGCACACACCTCCCTAACCTGCCAGACAGCACAGCCAAGGAGGTCTACCATTTCACCTTGGAGAAGATCCAGCCTCGGGTCATTTCCTTTGAAGAGCAGGTTGCTTCCATAAGACAGCATCTGGCATCTATTTATGAGAAGGAGGAAGACTGGAGAAATGCAGCCCAAGTGTTGGTGGGGATTCCTCTGGAAACAGGACAAAAACAGTACAACGTAGATTATAAGCTGGAGACTTACCTGAAGATTGCAAGGCTATACCTGGAGGATGACGATCCCGTCCAGGCCGAGGCTTACATAAACCGAGCGTCCTTACTTCAGAACGAATCCACAAATGAACAGTTACAGATACACTATAAGGTTTGCTATGCGCGTGTCCTTGATTACAGAAGGAAATTCATTGAGGCCGCCCAGAGGTACAATGAGCTCTCTTACAAGACAATAGTCCATGAAAGTGAGAGACTAGAGGCCTTAAAGCATGCACTGCACTGCACCATCTTAGCATCGGCAGGACAGCAGCGCTCTCGGATGCTGGCTACTCTTTTTAAGGATGAAAGGTGCCAGCAACTAGCTGCATATGGGATCCTAGAGAAGATGTACCTAGACAGAATCATCAGAGGGAACCAGCTTCAAGAATTTGCTGCTATGCTGATGCCACACCAAAAAGCAACGACAGCTGATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTGCTGCTATGCTGATGCCA
60.39
TAGACCTCCTTGGCTGTGCT
60.55
145
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCTATGCTGATGCCACAC
59.34
TAGACCTCCTTGGCTGTGCT
60.55
142
PCR template sequence:
ATCCTAGAGAAGATGTACCTAGACAGAATCATCAGAGGGAACCAGCTTCAAGAATTTGCTGCTATGCTGATGCCACACCAAAAAGCAACGACAGCTGATGTGGTGAATGAGAATGTCAGCCTCGTGATCTCACGGCAACTGCTAACAGATTTCTGCACACACCTCCCTAACCTGCCAGACAGCACAGCCAAGGAGGTCTA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
8
Interacting miRNAs (#binding sites)
mmu-miR-322-5p(1), mmu-miR-15b-5p(1), mmu-miR-152-3p(1), mmu-miR-148a-3p(1), mmu-miR-203-3p(1), mmu-miR-29b-1-5p(1), mmu-miR-207(1), mmu-miR-338-3p(1)
siRNAs for circular RNA silencing
Junction sequence
ACGACAGCTGATGTGGTGAATGAGAA
siRNA sets
TTCTCATTCACCACATCAG, TCTCATTCACCACATCAGC, CTCATTCACCACATCAGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCOPS4_732_ORF_1
1.1164
0.244049472
0.984977134
885
ORF sequence:
ATGCTGGCTACTCTTTTTAAGGATGAAAGGTGCCAGCAACTAGCTGCATATGGGATCCTAGAGAAGATGTACCTAGACAGAATCATCAGAGGGAACCAGCTTCAAGAATTTGCTGCTATGCTGATGCCACACCAAAAAGCAACGACAGCTGATGTGGTGAATGAGAATGTCAGCCTCGTGATCTCACGGCAACTGCTAACAGATTTCTGCACACACCTCCCTAACCTGCCAGACAGCACAGCCAAGGAGGTCTACCATTTCACCTTGGAGAAGATCCAGCCTCGGGTCATTTCCTTTGAAGAGCAGGTTGCTTCCATAAGACAGCATCTGGCATCTATTTATGAGAAGGAGGAAGACTGGAGAAATGCAGCCCAAGTGTTGGTGGGGATTCCTCTGGAAACAGGACAAAAACAGTACAACGTAGATTATAAGCTGGAGACTTACCTGAAGATTGCAAGGCTATACCTGGAGGATGACGATCCCGTCCAGGCCGAGGCTTACATAAACCGAGCGTCCTTACTTCAGAACGAATCCACAAATGAACAGTTACAGATACACTATAAGGTTTGCTATGCGCGTGTCCTTGATTACAGAAGGAAATTCATTGAGGCCGCCCAGAGGTACAATGAGCTCTCTTACAAGACAATAGTCCATGAAAGTGAGAGACTAGAGGCCTTAAAGCATGCACTGCACTGCACCATCTTAGCATCGGCAGGACAGCAGCGCTCTCGGATGCTGGCTACTCTTTTTAAGGATGAAAGGTGCCAGCAACTAGCTGCATATGGGATCCTAGAGAAGATGTACCTAGACAGAATCATCAGAGGGAACCAGCTTCAAGAATTTGCTGCTATGCTGATGCCACACCAAAAAGCAACGACAGCTGAT
Peptide sequence:
MLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTADVVNENVSLVISRQLLTDFCTHLPNLPDSTAKEVYHFTLEKIQPRVISFEEQVASIRQHLASIYEKEEDWRNAAQVLVGIPLETGQKQYNVDYKLETYLKIARLYLEDDDPVQAEAYINRASLLQNESTNEQLQIHYKVCYARVLDYRRKFIEAAQRYNELSYKTIVHESERLEALKHALHCTILASAGQQRSRMLATLFKDERCQQLAAYGILEKMYLDRIIRGNQLQEFAAMLMPHQKATTAD
IRESfinder result
IRESfinder score
0.493845286
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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