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mmu_circH13_541
Basic information of circular RNA
PanCircBase ID:
mmu_circH13_541
mm39_Chr. Position ID:
chr2|152519461|152531821|+
Gene name:
H13
Transcript:
ENSMUST00000125366.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
6
Exon/intron indexes:
2,3,4,5,6,7
Exon/intron offsets:
0,3509,8556,11121,11295,12302
Genomic length:
12360
Exon/intron sizes in nt:
99,83,89,86,126,58
Flanking exon/introns:
chr2:152511684-152519461|chr2:152531821-152533712
Splice length:
541
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
AGCTCTTCGGACATGCCAGAAACCATCACCAGTCGAGATGCCGCCCGCTTCCCCATCATCGCCAGCTGCACACTCCTGGGGCTCTACCTCTTTTTCAAAATATTCTCCCAGGAGTACATCAACCTCTTGCTGTCCATGTATTTCTTCGTGCTGGGGATCCTGGCCCTGTCACACACCATCAGCCCCTTCATGAATAAGTTTTTTCCAGCCAACTTCCCAAACCGCCAGTATCAGCTGCTCTTCACACAGGGCTCTGGGGAAAACAAAGAAGAGATCATCAACTATGAGTTTGACACTAAGGACCTGGTGTGCCTGGGCCTAAGCAGCGTCGTTGGTGTCTGGTACCTTCTGAGGAAGCACTGGATTGCCAACAACCTGTTTGGCCTGGCCTTCTCCCTTAATGGGGTAGAGCTCCTGCACCTGAACAACGTGAGCACTGGCTGTATCCTGCTCGGAGGACTCTTCATCTATGACATCTTCTGGGTATTCGGCACCAACGTGATGGTGACAGTGGCCAAGTCCTTTGAGGCACCAATAAAAT
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGGGTATTCGGCACCAAC
60.04
AAGAGGTAGAGCCCCAGGAG
60.03
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTTCTGGGTATTCGGCACCA
59.75
AAGAGGTAGAGCCCCAGGAG
60.03
157
PCR template sequence:
TGTATCCTGCTCGGAGGACTCTTCATCTATGACATCTTCTGGGTATTCGGCACCAACGTGATGGTGACAGTGGCCAAGTCCTTTGAGGCACCAATAAAATAGCTCTTCGGACATGCCAGAAACCATCACCAGTCGAGATGCCGCCCGCTTCCCCATCATCGCCAGCTGCACACTCCTGGGGCTCTACCTCTTTTTCAAAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
4
Interacting miRNAs (#binding sites)
mmu-miR-122-5p(1), mmu-miR-138-5p(1), mmu-miR-434-5p(1), mmu-miR-3105-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCACCAATAAAATAGCTCTTCGGACA
siRNA sets
AAGAGCTATTTTATTGGTG, CGAAGAGCTATTTTATTGG, AGAGCTATTTTATTGGTGC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCH13_541_ORF_1
1.1803
0.389323605
0.912948605
531
ORF sequence:
ATGCCAGAAACCATCACCAGTCGAGATGCCGCCCGCTTCCCCATCATCGCCAGCTGCACACTCCTGGGGCTCTACCTCTTTTTCAAAATATTCTCCCAGGAGTACATCAACCTCTTGCTGTCCATGTATTTCTTCGTGCTGGGGATCCTGGCCCTGTCACACACCATCAGCCCCTTCATGAATAAGTTTTTTCCAGCCAACTTCCCAAACCGCCAGTATCAGCTGCTCTTCACACAGGGCTCTGGGGAAAACAAAGAAGAGATCATCAACTATGAGTTTGACACTAAGGACCTGGTGTGCCTGGGCCTAAGCAGCGTCGTTGGTGTCTGGTACCTTCTGAGGAAGCACTGGATTGCCAACAACCTGTTTGGCCTGGCCTTCTCCCTTAATGGGGTAGAGCTCCTGCACCTGAACAACGTGAGCACTGGCTGTATCCTGCTCGGAGGACTCTTCATCTATGACATCTTCTGGGTATTCGGCACCAACGTGATGGTGACAGTGGCCAAGTCCTTTGAGGCACCAATAAAATAG
Peptide sequence:
MPETITSRDAARFPIIASCTLLGLYLFFKIFSQEYINLLLSMYFFVLGILALSHTISPFMNKFFPANFPNRQYQLLFTQGSGENKEEIINYEFDTKDLVCLGLSSVVGVWYLLRKHWIANNLFGLAFSLNGVELLHLNNVSTGCILLGGLFIYDIFWVFGTNVMVTVAKSFEAPIK
IRESfinder result
IRESfinder score
0.563939975
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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