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mmu_circSnrnp200_421
Basic information of circular RNA
PanCircBase ID:
mmu_circSnrnp200_421
mm39_Chr. Position ID:
chr2|127052613|127054324|+
Gene name:
Snrnp200
Transcript:
ENSMUST00000142327.2
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
3,4,5
Exon/intron offsets:
0,906,1655
Genomic length:
1711
Exon/intron sizes in nt:
172,193,56
Flanking exon/introns:
chr2:127051057-127052613|chr2:127054324-127056726
Splice length:
421
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GAGGAGAAAACGTGATGAGGACCGGCATGACATGAACAAGATGAAAGGCTACACGCTGCTGTCTGAGGGCATTGATGAGATGGTGGGCATCATCTACAAGCCTAAGACGAAGGAGACCCGAGAGACCTACGAGGTGCTGCTCAGCTTCATCCAGGCTGCGCTGGGAGATCAGCCTCGAGATATTCTTTGTGGAGCAGCTGATGAAGTCCTGGCTGTGCTGAAGAATGAAAAGCTTCGAGACAAGGAGAGAAGACGGGAGATTGACCTGCTGCTGGGTCAGACAGATGATACCAGATACCATGTGCTGGTAAACCTGGGCAAGAAGATCACAGACTACGGTGGCGACAAGGAGATACAGAATATGGATGACAACATTGATGAGACTTATGGTGTGAACGTGCAGTTTGAGTCTGATGAGGAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GATCACAGACTACGGTGGCG
60.53
TCAATGCCCTCAGACAGCAG
60.04
172
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CGGTGGCGACAAGGAGATAC
60.53
TCAATGCCCTCAGACAGCAG
60.04
160
PCR template sequence:
GAAGATCACAGACTACGGTGGCGACAAGGAGATACAGAATATGGATGACAACATTGATGAGACTTATGGTGTGAACGTGCAGTTTGAGTCTGATGAGGAGGAGGAGAAAACGTGATGAGGACCGGCATGACATGAACAAGATGAAAGGCTACACGCTGCTGTCTGAGGGCATTGATGAGATGGTGGGCATCATCTACAAG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-322-5p(2), mmu-miR-16-5p(1), mmu-miR-15a-5p(1), mmu-miR-15b-5p(1), mmu-miR-127-5p(1), mmu-miR-335-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GTCTGATGAGGAGGAGGAGAAAACGT
siRNA sets
TTTCTCCTCCTCCTCATCA, TTCTCCTCCTCCTCATCAG, ACGTTTTCTCCTCCTCCTC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSNRNP200_421_ORF_1
1.2483
0.642850757
0.941735572
429
ORF sequence:
ATGAGGAGGAGGAGAAAACGTGATGAGGACCGGCATGACATGAACAAGATGAAAGGCTACACGCTGCTGTCTGAGGGCATTGATGAGATGGTGGGCATCATCTACAAGCCTAAGACGAAGGAGACCCGAGAGACCTACGAGGTGCTGCTCAGCTTCATCCAGGCTGCGCTGGGAGATCAGCCTCGAGATATTCTTTGTGGAGCAGCTGATGAAGTCCTGGCTGTGCTGAAGAATGAAAAGCTTCGAGACAAGGAGAGAAGACGGGAGATTGACCTGCTGCTGGGTCAGACAGATGATACCAGATACCATGTGCTGGTAAACCTGGGCAAGAAGATCACAGACTACGGTGGCGACAAGGAGATACAGAATATGGATGACAACATTGATGAGACTTATGGTGTGAACGTGCAGTTTGAGTCTGATGAGGAG
Peptide sequence:
MRRRRKRDEDRHDMNKMKGYTLLSEGIDEMVGIIYKPKTKETRETYEVLLSFIQAALGDQPRDILCGAADEVLAVLKNEKLRDKERRREIDLLLGQTDDTRYHVLVNLGKKITDYGGDKEIQNMDDNIDETYGVNVQFESDEE
IRESfinder result
IRESfinder score
0.200646038
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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