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mmu_circSmarcc1_248
Basic information of circular RNA
PanCircBase ID:
mmu_circSmarcc1_248
mm39_Chr. Position ID:
chr9|109996672|110000135|+
Gene name:
Smarcc1
Transcript:
ENSMUST00000088716.12
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
2
Exon/intron indexes:
9,10
Exon/intron offsets:
0,3341
Genomic length:
3463
Exon/intron sizes in nt:
1,26,122
Flanking exon/introns:
chr9:109993945-109996672|chr9:110000135-110002948
Splice length:
248
Other database IDs:
CIRCpedia: MMU_CIRCpedia_2795, circAtlas: mmu-Smarcc1_0023
circBase: hsa_circ_0123965, circAtlas: hsa-SMARCC1_0031, CIRCpedia: HSA_CIRCpedia_104454
Human Ortholog IDs:
Mature spliced Sequence:
GTTCATGTAAAATGGATTTTGGACACTGACGTTTTCAATGAATGGATGAATGAAGAGGATTATGAAGTGGATGAGAACAGAAAGCCAGTGAGCTTTCGTCAACGAATTTCAACAAAGAATGAAGAGCCAGTCAGAAGTCCAGAAAGGAGAGACAGAAAAGCCTCTGCCAACTCTAGGAAGAGGAAACCTTCCCCTTCTCCTCCTCCTCCCACAGCCACAGAGTCCCGCAAGAAGAGCGGGAAGAAAGG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TTCTCCTCCTCCTCCCACAG
59.96
AGCTCACTGGCTTTCTGTTCT
59.58
148
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTTCTCCTCCTCCTCCCACA
59.96
AGCTCACTGGCTTTCTGTTCT
59.58
149
PCR template sequence:
GAGACAGAAAAGCCTCTGCCAACTCTAGGAAGAGGAAACCTTCCCCTTCTCCTCCTCCTCCCACAGCCACAGAGTCCCGCAAGAAGAGCGGGAAGAAAGGGTTCATGTAAAATGGATTTTGGACACTGACGTTTTCAATGAATGGATGAATGAAGAGGATTATGAAGTGGATGAGAACAGAAAGCCAGTGAGCTTTCGTC
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-135a-5p(1), mmu-miR-298-5p(1), mmu-miR-705(1), mmu-miR-296-3p(1)
siRNAs for circular RNA silencing
Junction sequence
GCGGGAAGAAAGGGTTCATGTAAAAT
siRNA sets
ATTTTACATGAACCCTTTC, TACATGAACCCTTTCTTCC, TTTTACATGAACCCTTTCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSMARCC1_248_ORF_1
0.844
0.195306713
0.205937601
213
ORF sequence:
ATGAATGAAGAGGATTATGAAGTGGATGAGAACAGAAAGCCAGTGAGCTTTCGTCAACGAATTTCAACAAAGAATGAAGAGCCAGTCAGAAGTCCAGAAAGGAGAGACAGAAAAGCCTCTGCCAACTCTAGGAAGAGGAAACCTTCCCCTTCTCCTCCTCCTCCCACAGCCACAGAGTCCCGCAAGAAGAGCGGGAAGAAAGGGTTCATGTAA
Peptide sequence:
MNEEDYEVDENRKPVSFRQRISTKNEEPVRSPERRDRKASANSRKRKPSPSPPPPTATESRKKSGKKGFM
IRESfinder result
IRESfinder score
0.475306814
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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