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mmu_circStx18_347
Basic information of circular RNA
PanCircBase ID:
mmu_circStx18_347
mm39_Chr. Position ID:
chr5|38263907|38278643|+
Gene name:
Stx18
Transcript:
ENSMUST00000114126.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
4,5,6,7
Exon/intron offsets:
0,262,9521,14647
Genomic length:
14736
Exon/intron sizes in nt:
78,67,113,89
Flanking exon/introns:
chr5:38262337-38263907|chr5:38278643-38284275
Splice length:
347
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
CCCACAAGGAGATACATTCCCAGCAAGTGAAGGAACACAGGACTGCCGTTTTGGATTTCGTTGACGATTACTTAAAAAGAGTGTGTAAGCTTTACTCTGAACAAAGAGCCATCCGAGTGAAGCGCGTGGTGGACAAGAAAAGACTATCTAAGCTGGAACCTGAGCCACATACCAAGAGGAAAGACTCCACATCTGAGAAAGCCCCTCAGAACGCTTCCCAGGACTCTGAAGGAAAGCCTGCTGCTGAGGAGCTGCCAGAAAAGCCTTTGGCTGAATCACAGCCCGAACTGGGAACCTGGGGCGATGGCAAGGGTGAAGATGAGCTGTCTCCAGAAGAGATACAGATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGCCAGAAAAGCCTTTGG
60.32
GGCAGTCCTGTGTTCCTTCA
59.89
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCTGCCAGAAAAGCCTTTGG
60.32
ATCCAAAACGGCAGTCCTGT
59.89
153
PCR template sequence:
GGAGCTGCCAGAAAAGCCTTTGGCTGAATCACAGCCCGAACTGGGAACCTGGGGCGATGGCAAGGGTGAAGATGAGCTGTCTCCAGAAGAGATACAGATGCCCACAAGGAGATACATTCCCAGCAAGTGAAGGAACACAGGACTGCCGTTTTGGATTTCGTTGACGATTACTTAAAAAGAGTGTGTAAGCTTTACTCTGA
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-135a-5p(1), mmu-miR-24-3p(1), mmu-miR-191-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGAGATACAGATGCCCACAAGGAGAT
siRNA sets
ATCTCCTTGTGGGCATCTG, TTGTGGGCATCTGTATCTC, TCTCCTTGTGGGCATCTGT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSTX18_347_ORF_1
0.7241
-0.076518229
0.03088027
108
ORF sequence:
ATGGCAAGGGTGAAGATGAGCTGTCTCCAGAAGAGATACAGATGCCCACAAGGAGATACATTCCCAGCAAGTGAAGGAACACAGGACTGCCGTTTTGGATTTCGTTGA
Peptide sequence:
MARVKMSCLQKRYRCPQGDTFPASEGTQDCRFGFR
IRESfinder result
IRESfinder score
0.318113543
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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