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mmu_circMsrb3_216
Basic information of circular RNA
PanCircBase ID:
mmu_circMsrb3_216
mm39_Chr. Position ID:
chr10|120661012|120687997|-
Gene name:
Msrb3
Transcript:
ENSMUST00000092143.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,4,3
Exon/intron offsets:
0,24868,26876
Genomic length:
26985
Exon/intron sizes in nt:
29,78,109
Flanking exon/introns:
chr10:120627404-120661012|chr10:120687997-120706939
Splice length:
216
Other database IDs:
circBase: mmu_circ_0002009, CIRCpedia: MMU_CIRCpedia_5235, circAtlas: mmu-Msrb3_0004
circAtlas: hsa-MSRB3_0001, CIRCpedia: HSA_CIRCpedia_9349
Human Ortholog IDs:
Mature spliced Sequence:
GGTCATGTAGGGATAAAAAGAACTGTAAGGTGGTCTTTTCCCAGCAGGAACTGAGGAAGCGGCTGACACCCCTACAGTACCATGTCACTCAGGAGAAAGGAACTGAAAGTGCCTTTGAAGGAGAGTACACACATCACAAAGATCCTGGAATATATAAATGTGTTGTCTGTGGAACTCCGTTGTTCAAGTCAGAAACCAAATTTGACTCTGGTTCAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGTCTGTGGAACTCCGTTGT
59.17
GTGACATGGTACTGTAGGGGTG
60.09
141
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGTTGTCTGTGGAACTCCGT
59.17
GTGACATGGTACTGTAGGGGTG
60.09
144
PCR template sequence:
GAAGGAGAGTACACACATCACAAAGATCCTGGAATATATAAATGTGTTGTCTGTGGAACTCCGTTGTTCAAGTCAGAAACCAAATTTGACTCTGGTTCAGGGTCATGTAGGGATAAAAAGAACTGTAAGGTGGTCTTTTCCCAGCAGGAACTGAGGAAGCGGCTGACACCCCTACAGTACCATGTCACTCAGGAGAAAGG
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-370-3p(1), mmu-miR-466a-5p(1), mmu-miR-466p-5p(1)
siRNAs for circular RNA silencing
Junction sequence
GACTCTGGTTCAGGGTCATGTAGGGA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCMSRB3_216_ORF_1
0.9167
-0.185765038
0.050016182
189
ORF sequence:
ATGTCACTCAGGAGAAAGGAACTGAAAGTGCCTTTGAAGGAGAGTACACACATCACAAAGATCCTGGAATATATAAATGTGTTGTCTGTGGAACTCCGTTGTTCAAGTCAGAAACCAAATTTGACTCTGGTTCAGGGTCATGTAGGGATAAAAAGAACTGTAAGGTGGTCTTTTCCCAGCAGGAACTGA
Peptide sequence:
MSLRRKELKVPLKESTHITKILEYINVLSVELRCSSQKPNLTLVQGHVGIKRTVRWSFPSRN
IRESfinder result
IRESfinder score
0.668620043
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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