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mmu_circMed13_708
Basic information of circular RNA
PanCircBase ID:
mmu_circMed13_708
mm39_Chr. Position ID:
chr11|86219993|86236854|-
Gene name:
Med13
Transcript:
ENSMUST00000043624.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,5,4,3
Exon/intron offsets:
0,1820,2715,16692
Genomic length:
16861
Exon/intron sizes in nt:
1,95,19,81,46,169
Flanking exon/introns:
chr11:86219435-86219993|chr11:86236854-86246099
Splice length:
708
Other database IDs:
circAtlas: mmu-Med13_0049
circBase: hsa_circ_0045098, CIRCpedia: HSA_CIRCpedia_179391
Human Ortholog IDs:
Mature spliced Sequence:
AAGAGGAAGATGGAGTATGGGAGAATGGCCTTTCCTATGAATGCCGTACTTTGCTTTTCAAAGCAGTTCACAATCTGTTGGAGCGATGTTTGATGAACCGAAACTTTGTACGAATTGGCAAGTGGTTTGTGAAGCCATATGAGAAAGATGAAAAACCTATAAATAAAAGTGAACACTTGTCCTGCTCTTTCACCTTTTTCTTGCATGGAGACAGCAATGTTTGTACCAGTGTGGAAATTAACCAACATCAACCTGTATACCTTCTCAGTGAAGAGCATGTCACCCTTGCTCAACAGTCTAATAGCCCATTTCAAGTTATCTTAAGTCCATTTGGACTAAATGGCACTCTCACGGGACAGGCTTTCAAGATGTCTGATTCAGCTACGAAAAAATTAATTGGTGAATGGAAACAGTTCTATCCTATTTCATGTGGTTTGAAGGAGATGTCTGAGGAGAAACAGGACGATATGGATTGGGAAGACGATTCTTTGGCTGCGGTGGAAGTTCTTGTTGCGGGTGTCCGAATGATCTACCCAGCATGCTTTGTGCTAGTCCCTCAGTCAGACATTCCTGCTCCTAGCTCTGTGGGAGCTTCTCACTGTTCAGCTTCTTGCTTGGGTATCCATCAAGTGCCTGCTTCCACAAGAGATCCTGCTATGTCTTCAGTTACTCTCACTCCACCTACATCTCCTGAGGAAGTCCAAACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GTGCCTGCTTCCACAAGAGA
60.25
CGGTTCATCAAACATCGCTCC
59.94
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGCCTGCTTCCACAAGAG
60.25
CGGTTCATCAAACATCGCTCC
59.94
180
PCR template sequence:
TCTTGCTTGGGTATCCATCAAGTGCCTGCTTCCACAAGAGATCCTGCTATGTCTTCAGTTACTCTCACTCCACCTACATCTCCTGAGGAAGTCCAAACAGAAGAGGAAGATGGAGTATGGGAGAATGGCCTTTCCTATGAATGCCGTACTTTGCTTTTCAAAGCAGTTCACAATCTGTTGGAGCGATGTTTGATGAACCG
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-382-3p(1), mmu-miR-300-3p(1), mmu-miR-335-3p(1), mmu-miR-350-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GAAGTCCAAACAGAAGAGGAAGATGG
siRNA sets
ATCTTCCTCTTCTGTTTGG, CATCTTCCTCTTCTGTTTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMED13_708_ORF_1
0.9228
0.064147177
0.998072001
1323
ORF sequence:
ATGAACCGAAACTTTGTACGAATTGGCAAGTGGTTTGTGAAGCCATATGAGAAAGATGAAAAACCTATAAATAAAAGTGAACACTTGTCCTGCTCTTTCACCTTTTTCTTGCATGGAGACAGCAATGTTTGTACCAGTGTGGAAATTAACCAACATCAACCTGTATACCTTCTCAGTGAAGAGCATGTCACCCTTGCTCAACAGTCTAATAGCCCATTTCAAGTTATCTTAAGTCCATTTGGACTAAATGGCACTCTCACGGGACAGGCTTTCAAGATGTCTGATTCAGCTACGAAAAAATTAATTGGTGAATGGAAACAGTTCTATCCTATTTCATGTGGTTTGAAGGAGATGTCTGAGGAGAAACAGGACGATATGGATTGGGAAGACGATTCTTTGGCTGCGGTGGAAGTTCTTGTTGCGGGTGTCCGAATGATCTACCCAGCATGCTTTGTGCTAGTCCCTCAGTCAGACATTCCTGCTCCTAGCTCTGTGGGAGCTTCTCACTGTTCAGCTTCTTGCTTGGGTATCCATCAAGTGCCTGCTTCCACAAGAGATCCTGCTATGTCTTCAGTTACTCTCACTCCACCTACATCTCCTGAGGAAGTCCAAACAGAAGAGGAAGATGGAGTATGGGAGAATGGCCTTTCCTATGAATGCCGTACTTTGCTTTTCAAAGCAGTTCACAATCTGTTGGAGCGATGTTTGATGAACCGAAACTTTGTACGAATTGGCAAGTGGTTTGTGAAGCCATATGAGAAAGATGAAAAACCTATAAATAAAAGTGAACACTTGTCCTGCTCTTTCACCTTTTTCTTGCATGGAGACAGCAATGTTTGTACCAGTGTGGAAATTAACCAACATCAACCTGTATACCTTCTCAGTGAAGAGCATGTCACCCTTGCTCAACAGTCTAATAGCCCATTTCAAGTTATCTTAAGTCCATTTGGACTAAATGGCACTCTCACGGGACAGGCTTTCAAGATGTCTGATTCAGCTACGAAAAAATTAATTGGTGAATGGAAACAGTTCTATCCTATTTCATGTGGTTTGAAGGAGATGTCTGAGGAGAAACAGGACGATATGGATTGGGAAGACGATTCTTTGGCTGCGGTGGAAGTTCTTGTTGCGGGTGTCCGAATGATCTACCCAGCATGCTTTGTGCTAGTCCCTCAGTCAGACATTCCTGCTCCTAGCTCTGTGGGAGCTTCTCACTGTTCAGCTTCTTGCTTGGGTATCCATCAAGTGCCTGCTTCCACAAGAGATCCTGCTATGTCTTCAGTTACTCTCACTCCACCTACATCTCCTGAGGAAGTCCAAACA
Peptide sequence:
MNRNFVRIGKWFVKPYEKDEKPINKSEHLSCSFTFFLHGDSNVCTSVEINQHQPVYLLSEEHVTLAQQSNSPFQVILSPFGLNGTLTGQAFKMSDSATKKLIGEWKQFYPISCGLKEMSEEKQDDMDWEDDSLAAVEVLVAGVRMIYPACFVLVPQSDIPAPSSVGASHCSASCLGIHQVPASTRDPAMSSVTLTPPTSPEEVQTEEEDGVWENGLSYECRTLLFKAVHNLLERCLMNRNFVRIGKWFVKPYEKDEKPINKSEHLSCSFTFFLHGDSNVCTSVEINQHQPVYLLSEEHVTLAQQSNSPFQVILSPFGLNGTLTGQAFKMSDSATKKLIGEWKQFYPISCGLKEMSEEKQDDMDWEDDSLAAVEVLVAGVRMIYPACFVLVPQSDIPAPSSVGASHCSASCLGIHQVPASTRDPAMSSVTLTPPTSPEEVQT
IRESfinder result
IRESfinder score
0.670582418
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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