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mmu_ciGnpda1_998
Basic information of circular RNA
PanCircBase ID:
mmu_ciGnpda1_998
mm39_Chr. Position ID:
chr18|38465208|38466206|-
Gene name:
Gnpda1
Transcript:
ENSMUST00000237487.2
CircRNA type:
Circular intronic (ci)RNA
Exon/Intron count:
1
Exon/intron indexes:
4
Exon/intron offsets:
0
Genomic length:
998
Exon/intron sizes in nt:
998
Flanking exon/introns:
chr18:38462026-38466206
Splice length:
998
Other database IDs:
Human Ortholog IDs:
Mature spliced Sequence:
GTAAGCATGGCACGTTCCACGGTGTGTATCCGGGCCCATGCCTGGAGTGACTGCAGTACGTGGGCAGGAGAACATGCCACGCCTTCTTCACTTGGTCCCTTAGTGCTAACACAGCAGAGTCATCCATCACTATGCGGGACAGGAAAGGCATAGAGTGGGAGCCCTGGATCCTGCCTCAGCCCTTCTGCTCTGGAGCTGTGTGACCAAGATAGCTTCTTCATGCACTCAGTGCCTTGCAGAGGTTTGGATTTGGATCCTGATGTCCTCAAGACTACCTGACCAGACATCCATGTAACTCAGCTAAACATTTAAAGTCCTAGACTCCAGTTTCAAAACACAACGTGCAGTCCTTGTGTGCGGTTTATCAGTTGAACCCCAGGGAAGCATGGAGAGAAGGTGGGAACCTGGGTGTCTGCTTCTTGGGTGCTGACAGTGTCGATGTGCTGTCATGTTGGGAGTCACCTTGGGTTTAAACCTGGATGGTATCTTACTCCTTAACCTAACCCTCATAAGAGAAGAAGGAGGGCTGGACATTGTGGCAACATCTTTAATCCCAGCACTTGGAAGGTGGAGGCAGGTGGATCTCTGAGCTCCAGCACTGCCAGGGCTATATAATAGACTCTGCCCTTATTTAAAAGAAGGAAATAAAGAAAATAGTAAGGAGGAGTGAGGAGCTTGCAGGTCCTGAGGCTGAGGTTTGTTTGCTGGGTTCCACCTCTGGGGAGGAGGGGAGAAGGTGTACTGCCCCACAGTGTGGGGTGAGAGGGACGCGACCTTTCACAGTTCTGCGCTGTCTGAGGGTGCAAGCAAGTCACCAGAGCCTTGTGTGTGGCTCAAGTCTCAGAGATGGGGAGGGAGGTCACGTGCTTGAGGAAGATCTGACCTAGTGTCCAATGAGAAGAAATGCGGTTTTCAAGGACCCTTTTCCAAGCAGAGGACACGATCTGTTGTTGAAGGTTTTGGTCCCTGTAACTCACAGAGCTACTCTGCCGTCTGCG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGCGGTTTTCAAGGACCCTT
60.11
CGTACTGCAGTCACTCCAGG
60.11
154
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
ATGCGGTTTTCAAGGACCCT
59.89
CGTACTGCAGTCACTCCAGG
60.11
155
PCR template sequence:
AAGAAATGCGGTTTTCAAGGACCCTTTTCCAAGCAGAGGACACGATCTGTTGTTGAAGGTTTTGGTCCCTGTAACTCACAGAGCTACTCTGCCGTCTGCGGTAAGCATGGCACGTTCCACGGTGTGTATCCGGGCCCATGCCTGGAGTGACTGCAGTACGTGGGCAGGAGAACATGCCACGCCTTCTTCACTTGGTCCCT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
9
Interacting miRNAs (#binding sites)
mmu-miR-124-3p(1), mmu-miR-34c-5p(1), mmu-miR-34a-5p(1), mmu-miR-196a-5p(1), mmu-miR-709(1), mmu-miR-541-5p(1), mmu-miR-207(1), mmu-miR-296-3p(1), mmu-miR-7a-1-3p(1)
siRNAs for circular RNA silencing
Junction sequence
TCTGCCGTCTGCGGTAAGCATGGCAC
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIGNPDA1_998_ORF_1
0.6793
-0.07469839
0.077979782
258
ORF sequence:
ATGAGAAGAAATGCGGTTTTCAAGGACCCTTTTCCAAGCAGAGGACACGATCTGTTGTTGAAGGTTTTGGTCCCTGTAACTCACAGAGCTACTCTGCCGTCTGCGGTAAGCATGGCACGTTCCACGGTGTGTATCCGGGCCCATGCCTGGAGTGACTGCAGTACGTGGGCAGGAGAACATGCCACGCCTTCTTCACTTGGTCCCTTAGTGCTAACACAGCAGAGTCATCCATCACTATGCGGGACAGGAAAGGCATAG
Peptide sequence:
MRRNAVFKDPFPSRGHDLLLKVLVPVTHRATLPSAVSMARSTVCIRAHAWSDCSTWAGEHATPSSLGPLVLTQQSHPSLCGTGKA
IRESfinder result
IRESfinder score
0.577834276
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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