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mmu_circArfgef1_345
Basic information of circular RNA
PanCircBase ID:
mmu_circArfgef1_345
mm39_Chr. Position ID:
chr1|10217627|10223749|-
Gene name:
Arfgef1
Transcript:
ENSMUST00000088615.11
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
3
Exon/intron indexes:
33,32,31
Exon/intron offsets:
0,4398,5983
Genomic length:
6122
Exon/intron sizes in nt:
1,33,73,139
Flanking exon/introns:
chr1:10215082-10217627|chr1:10223749-10223831
Splice length:
345
Other database IDs:
circAtlas: hsa-ARFGEF1_0092, CIRCpedia: HSA_CIRCpedia_149542
Human Ortholog IDs:
Mature spliced Sequence:
ACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTGGTTATTCTGAATGGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAAGATCTTCAGATAACAGACAGCAAGCACCACTGGTTTCTGTTTCTACTGTGAGTGAAGAAGTTAGCAAAGTGAAATCCACAGCAA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AACAGACAGCAAGCACCACT
60.11
TTTTCACCATTCAGAATAACCACGT
59.47
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GCAAGCACCACTGGTTTCTG
59.97
ACACGTTTTATCCCAGATTTCA
56
163
PCR template sequence:
GATTCTATTCAACCAAGATCTTCAGATAACAGACAGCAAGCACCACTGGTTTCTGTTTCTACTGTGAGTGAAGAAGTTAGCAAAGTGAAATCCACAGCAAACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTGGTTATTCTGAATGGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAA
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-135a-5p(1), mmu-miR-297a-5p(1), mmu-miR-673-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAATCCACAGCAAACAATGAGCAGTT
siRNA sets
AACTGCTCATTGTTTGCTG,CTGCTCATTGTTTGCTGTG,TGCTCATTGTTTGCTGTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
NA
NA
NA
NA
NA
ORF sequence:
NA
Peptide sequence:
NA
IRESfinder result
IRESfinder score
0.758962513
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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