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mmu_circMed13_302
Basic information of circular RNA
PanCircBase ID:
mmu_circMed13_302
mm39_Chr. Position ID:
chr11|86169589|86170561|-
Gene name:
Med13
Transcript:
ENSMUST00000043624.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
25,24
Exon/intron offsets:
0,829
Genomic length:
972
Exon/intron sizes in nt:
1,59,143
Flanking exon/introns:
chr11:86169481-86169589|chr11:86170561-86174025
Splice length:
302
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GGCCCGTCGGAAAAAGGGTTCTGCTAGAAGATTTGGTCTACAGAAACTGTGGGAGTGGTGCTTGGGACTTGTTCAGATGAGCTCTTTACCATGGAGAGTTGTGATTGGTCGCCTGGGAAGGATTGGACATGGAGAGTTGAAAGATTGGAGTTGTTTGCTGAGTCGTCGAAACTTGCAATCTCTAAGCAAAAGGCTCAAAGACATGTGTAGGATGTGTGGCATATCTGCTGCAGACTCTCCAAGTATCCTTAGTGCTTGTTTGGTTGCAATGGAACCCCAAGGTTCTTTTGTTATCATGCCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCTGCAGACTCTCCAAGT
59.68
AGCACCACTCCCACAGTTTC
60.18
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCTGCAGACTCTCCAAGT
59.68
ACAAGTCCCAAGCACCACTC
60.18
150
PCR template sequence:
ATGTGTAGGATGTGTGGCATATCTGCTGCAGACTCTCCAAGTATCCTTAGTGCTTGTTTGGTTGCAATGGAACCCCAAGGTTCTTTTGTTATCATGCCAGGGCCCGTCGGAAAAAGGGTTCTGCTAGAAGATTTGGTCTACAGAAACTGTGGGAGTGGTGCTTGGGACTTGTTCAGATGAGCTCTTTACCATGGAGAGTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
3
Interacting miRNAs (#binding sites)
mmu-miR-29b-3p(1), mmu-miR-697(1), mmu-miR-7a-2-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTTATCATGCCAGGGCCCGTCGGAAA
siRNA sets
TTTCCGACGGGCCCTGGCA, TTCCGACGGGCCCTGGCAT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMED13_302_ORF_1
0.6925
-0.136162493
0.089646557
306
ORF sequence:
ATGAGCTCTTTACCATGGAGAGTTGTGATTGGTCGCCTGGGAAGGATTGGACATGGAGAGTTGAAAGATTGGAGTTGTTTGCTGAGTCGTCGAAACTTGCAATCTCTAAGCAAAAGGCTCAAAGACATGTGTAGGATGTGTGGCATATCTGCTGCAGACTCTCCAAGTATCCTTAGTGCTTGTTTGGTTGCAATGGAACCCCAAGGTTCTTTTGTTATCATGCCAGGGCCCGTCGGAAAAAGGGTTCTGCTAGAAGATTTGGTCTACAGAAACTGTGGGAGTGGTGCTTGGGACTTGTTCAGATGA
Peptide sequence:
MSSLPWRVVIGRLGRIGHGELKDWSCLLSRRNLQSLSKRLKDMCRMCGISAADSPSILSACLVAMEPQGSFVIMPGPVGKRVLLEDLVYRNCGSGAWDLFR
IRESfinder result
IRESfinder score
0.621135225
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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