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mmu_circSgsm1_796
Basic information of circular RNA
PanCircBase ID:
mmu_circSgsm1_796
mm39_Chr. Position ID:
chr5|113406656|113411702|-
Gene name:
Sgsm1
Transcript:
ENSMUST00000048112.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
21,20,19
Exon/intron offsets:
0,1258,4458
Genomic length:
5046
Exon/intron sizes in nt:
8,31,25,588
Flanking exon/introns:
chr5:113403227-113406656|chr5:113411702-113413744
Splice length:
796
Other database IDs:
circBase: hsa_circ_0116297, circAtlas: hsa-SGSM1_0015, CIRCpedia: HSA_CIRCpedia_168437
Human Ortholog IDs:
Mature spliced Sequence:
GTATTTGAGTCTGTGGATGAGGTGGAGCAGACAGAGGCAGAAGGCAGGTCAGAAGAAAAACATCCCAAAATCCCCAATGGGAACCCAGCCAACGGCACTTGCTCCCCAGACTCCGGACACCCTTCCTCCCACAACTTCTCCTCTGGTCTCTCCGAGCACTCTGAGCCCAGTCTTAGCACTGAAGACAGCGTCTTGGATGCCCAACGCAGCCTTCCAGCTGTGTTTCGGCCTGGGGACAGCAGCGTGGAAGATGGGCAGAGCAGCGAAGCCACCACATCCCGGGACGAGGCCCCTCGGGAGGAGCTGGCCGTGCAAGATAGCCTTGAGAGTGACCTCCTTGCCAACGAGAGCTTGGAGGAGTTCATGTCTATCCCTGGCAGCCTGGACGTGGCCCTACCTGAGAAGGATGGCGCGGTGATGGACGGCTGGCCCGGTGAGGCGGACAAGCCCAGTCGGGCTGACAGTGAGGACAACCTCTCAGAAGAGCCTGAGATGGAGAGCCTGTTCCCTGCCCTGGCTTCTCTGGCTGTGACCTCCTCTGCCAATAACGAGGCATCCCCTGTGTCCTCCAGTGGAGTCACCTATTCTCCAGAACTACTGGACCTGTACACCGTGAACCTGCACCGCATTGAGAAAGATGTGCAGAGGTGTGACCGCAGCTACTGGTACTTCACAGCAGCCAACCTGGAGAAGCTGAGGAACATCATGTGCAGCTATATCTGGCAGCACATCGAGATCGGCTACGTCCAGGGCATGTGTGACCTCCTGGCCCCGTTGCTGGTCATCCTGGATGATG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCAGCTATATCTGGCAGCA
59.24
TCTTCTGACCTGCCTTCTGC
59.68
144
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TCTGGCAGCACATCGAGATC
59.9
TTGGCTGGGTTCCCATTGG
60.23
170
PCR template sequence:
AGGAACATCATGTGCAGCTATATCTGGCAGCACATCGAGATCGGCTACGTCCAGGGCATGTGTGACCTCCTGGCCCCGTTGCTGGTCATCCTGGATGATGGTATTTGAGTCTGTGGATGAGGTGGAGCAGACAGAGGCAGAAGGCAGGTCAGAAGAAAAACATCCCAAAATCCCCAATGGGAACCCAGCCAACGGCACTT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
7
Interacting miRNAs (#binding sites)
mmu-miR-298-5p(1), mmu-miR-199b-3p(1), mmu-miR-182-5p(1), mmu-miR-199a-3p(1), mmu-miR-705(1), mmu-miR-690(1), mmu-miR-207(1)
siRNAs for circular RNA silencing
Junction sequence
ATCCTGGATGATGGTATTTGAGTCTG
siRNA sets
CAAATACCATCATCCAGGA, TCAAATACCATCATCCAGG, GACTCAAATACCATCATCC
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSGSM1_796_ORF_1
1.1221
0.51527842
0.990927605
801
ORF sequence:
ATGATGGTATTTGAGTCTGTGGATGAGGTGGAGCAGACAGAGGCAGAAGGCAGGTCAGAAGAAAAACATCCCAAAATCCCCAATGGGAACCCAGCCAACGGCACTTGCTCCCCAGACTCCGGACACCCTTCCTCCCACAACTTCTCCTCTGGTCTCTCCGAGCACTCTGAGCCCAGTCTTAGCACTGAAGACAGCGTCTTGGATGCCCAACGCAGCCTTCCAGCTGTGTTTCGGCCTGGGGACAGCAGCGTGGAAGATGGGCAGAGCAGCGAAGCCACCACATCCCGGGACGAGGCCCCTCGGGAGGAGCTGGCCGTGCAAGATAGCCTTGAGAGTGACCTCCTTGCCAACGAGAGCTTGGAGGAGTTCATGTCTATCCCTGGCAGCCTGGACGTGGCCCTACCTGAGAAGGATGGCGCGGTGATGGACGGCTGGCCCGGTGAGGCGGACAAGCCCAGTCGGGCTGACAGTGAGGACAACCTCTCAGAAGAGCCTGAGATGGAGAGCCTGTTCCCTGCCCTGGCTTCTCTGGCTGTGACCTCCTCTGCCAATAACGAGGCATCCCCTGTGTCCTCCAGTGGAGTCACCTATTCTCCAGAACTACTGGACCTGTACACCGTGAACCTGCACCGCATTGAGAAAGATGTGCAGAGGTGTGACCGCAGCTACTGGTACTTCACAGCAGCCAACCTGGAGAAGCTGAGGAACATCATGTGCAGCTATATCTGGCAGCACATCGAGATCGGCTACGTCCAGGGCATGTGTGACCTCCTGGCCCCGTTGCTGGTCATCCTGGATGAT
Peptide sequence:
MMVFESVDEVEQTEAEGRSEEKHPKIPNGNPANGTCSPDSGHPSSHNFSSGLSEHSEPSLSTEDSVLDAQRSLPAVFRPGDSSVEDGQSSEATTSRDEAPREELAVQDSLESDLLANESLEEFMSIPGSLDVALPEKDGAVMDGWPGEADKPSRADSEDNLSEEPEMESLFPALASLAVTSSANNEASPVSSSGVTYSPELLDLYTVNLHRIEKDVQRCDRSYWYFTAANLEKLRNIMCSYIWQHIEIGYVQGMCDLLAPLLVILDD
IRESfinder result
IRESfinder score
0.389942658
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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