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mmu_circStag1_379
Basic information of circular RNA
PanCircBase ID:
mmu_circStag1_379
mm39_Chr. Position ID:
chr9|100639742|100668749|+
Gene name:
Stag1
Transcript:
ENSMUST00000129269.8
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
5,6,7
Exon/intron offsets:
0,19066,28802
Genomic length:
29007
Exon/intron sizes in nt:
97,77,205
Flanking exon/introns:
chr9:100620195-100639742|chr9:100668749-100678756
Splice length:
379
Other database IDs:
CIRCpedia: MMU_CIRCpedia_290, circAtlas: mmu-Stag1_0020
circAtlas: hsa-STAG1_0026, CIRCpedia: HSA_CIRCpedia_148179
Human Ortholog IDs:
Mature spliced Sequence:
TCCGTGGTGGATGACTGGATTGAATTATATAAACAAGACAGGGACATCGCACTTCTGGATTTAATCAACTTTTTTATCCAGTGTTCAGGATGTCGAGGTACGGTCAGAATAGAGATGTTTCGAAATATGCAGAACGCAGAAATAATCAGAAAAATGACTGAAGAATTTGATGAGGACAGTGGTGACTACCCCCTTACAATGCCTGGTCCTCAGTGGAAAAAATTTCGTTCCAATTTTTGTGAATTTATTGGAGTCCTGATTCGACAGTGTCAATATAGCATAATTTATGATGAATATATGATGGACACCGTAATTTCCCTTTTGACTGGTTTGTCAGACTCCCAAGTCAGAGCTTTTAGGCATACAAGTACCCTTGCTG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
GACTGGTTTGTCAGACTCCCA
59.58
ACCTCGACATCCTGAACACTG
59.73
155
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
TGACTGGTTTGTCAGACTCCC
59.58
ACCTCGACATCCTGAACACTG
59.73
156
PCR template sequence:
ATAATTTATGATGAATATATGATGGACACCGTAATTTCCCTTTTGACTGGTTTGTCAGACTCCCAAGTCAGAGCTTTTAGGCATACAAGTACCCTTGCTGTCCGTGGTGGATGACTGGATTGAATTATATAAACAAGACAGGGACATCGCACTTCTGGATTTAATCAACTTTTTTATCCAGTGTTCAGGATGTCGAGGTA
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-200a-3p(1), mmu-miR-141-3p(1), mmu-miR-697(1)
siRNAs for circular RNA silencing
Junction sequence
AGTACCCTTGCTGTCCGTGGTGGATG
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCSTAG1_379_ORF_1
0.8117
-0.025735816
0.136668971
279
ORF sequence:
ATGTTTCGAAATATGCAGAACGCAGAAATAATCAGAAAAATGACTGAAGAATTTGATGAGGACAGTGGTGACTACCCCCTTACAATGCCTGGTCCTCAGTGGAAAAAATTTCGTTCCAATTTTTGTGAATTTATTGGAGTCCTGATTCGACAGTGTCAATATAGCATAATTTATGATGAATATATGATGGACACCGTAATTTCCCTTTTGACTGGTTTGTCAGACTCCCAAGTCAGAGCTTTTAGGCATACAAGTACCCTTGCTGTCCGTGGTGGATGA
Peptide sequence:
MFRNMQNAEIIRKMTEEFDEDSGDYPLTMPGPQWKKFRSNFCEFIGVLIRQCQYSIIYDEYMMDTVISLLTGLSDSQVRAFRHTSTLAVRGG
IRESfinder result
IRESfinder score
0.569656061
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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