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mmu_ciGramd1b_253
Basic information of circular RNA
PanCircBase ID:
mmu_ciGramd1b_253
mm39_Chr. Position ID:
chr9|40219335|40219588|-
Gene name:
Gramd1b
Transcript:
ENSMUST00000137454.8
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
2
Exon/intron offsets:
0
Genomic length:
253
Exon/intron sizes in nt:
253
Flanking exon/introns:
chr9:40219295-40219588
Splice length:
253
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTGAGCCCCTGAATTCAGGTCTGGAGAACCCCCTTCACCTCTCCGTTTTGCAACATGTCTCGAGTCAAAAATCCAAGTTCTGGATCTCAGTGTGTTCCCCATACCAAGCAGCTAAGGTCTCAGAGAAGAGAAGTGATGCAGGCAAAAGTATTAACAGTGAGCCATGAGCCCAGCCACCCTTCCCTTAGTGGTAGCAGCCACGTCAGACTCAGAGATATCGGTGTCTCAGGGTGTCACCACAGCCTCCAGTCTC
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CAGCCACGTCAGACTCAGAG
60.11
GGGGAACACACTGAGATCCA
59.02
159
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGCCACGTCAGACTCAGAGA
60.25
GGGGAACACACTGAGATCCA
59.02
158
PCR template sequence:
ACAGTGAGCCATGAGCCCAGCCACCCTTCCCTTAGTGGTAGCAGCCACGTCAGACTCAGAGATATCGGTGTCTCAGGGTGTCACCACAGCCTCCAGTCTCGTGAGCCCCTGAATTCAGGTCTGGAGAACCCCCTTCACCTCTCCGTTTTGCAACATGTCTCGAGTCAAAAATCCAAGTTCTGGATCTCAGTGTGTTCCCC
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-125b-5p(1), mmu-miR-351-5p(1), mmu-miR-125a-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AGCCTCCAGTCTCGTGAGCCCCTGAA
siRNA sets
TTCAGGGGCTCACGAGACT, AGGGGCTCACGAGACTGGA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIGRAMD1B_253_ORF_1
0.6282
0.00780778
0.195659696
366
ORF sequence:
ATGTCTCGAGTCAAAAATCCAAGTTCTGGATCTCAGTGTGTTCCCCATACCAAGCAGCTAAGGTCTCAGAGAAGAGAAGTGATGCAGGCAAAAGTATTAACAGTGAGCCATGAGCCCAGCCACCCTTCCCTTAGTGGTAGCAGCCACGTCAGACTCAGAGATATCGGTGTCTCAGGGTGTCACCACAGCCTCCAGTCTCGTGAGCCCCTGAATTCAGGTCTGGAGAACCCCCTTCACCTCTCCGTTTTGCAACATGTCTCGAGTCAAAAATCCAAGTTCTGGATCTCAGTGTGTTCCCCATACCAAGCAGCTAAGGTCTCAGAGAAGAGAAGTGATGCAGGCAAAAGTATTAACAGTGAGCCATGA
Peptide sequence:
MSRVKNPSSGSQCVPHTKQLRSQRREVMQAKVLTVSHEPSHPSLSGSSHVRLRDIGVSGCHHSLQSREPLNSGLENPLHLSVLQHVSSQKSKFWISVCSPYQAAKVSEKRSDAGKSINSEP
IRESfinder result
IRESfinder score
0.592032947
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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