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mmu_circCacna2d1_353
Basic information of circular RNA
PanCircBase ID:
mmu_circCacna2d1_353
mm39_Chr. Position ID:
chr5|16451663|16472473|+
Gene name:
Cacna2d1
Transcript:
ENSMUST00000167946.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
7,8,9,10
Exon/intron offsets:
0,17592,20021,20710
Genomic length:
20810
Exon/intron sizes in nt:
1,32,70,51,100
Flanking exon/introns:
chr5:16418003-16451663|chr5:16472473-16504926
Splice length:
353
Other database IDs:
CIRCpedia: MMU_CIRCpedia_223182, circAtlas: mmu-Cac2d1_0002
circBase: hsa_circ_0134825, circAtlas: hsa-CAC2D1_0002, CIRCpedia: HSA_CIRCpedia_59111
Human Ortholog IDs:
Mature spliced Sequence:
CAACCATAGTGTTAAACGAACTCAACTGGACAAGTGCCTTAGATGAAGTATTCAAAAGAAATCGAGACGAAGACCCTACACTGCTGTGGCAAGTGTTTGGCAGCGCCACTGGCCTGGCCCGATATTATCCAGCTTCTCCATGGGTGGATAATAGTAGAACTCCAAACAAGATTGATCTATATGATGTACGCAGAAGACCATGGTACATCCAGGGAGCTGCATCCCCCAAGGACATGCTCATTCTGGTGGACGTGAGTGGAAGTGTGAGCGGATTGACTCTGAAACTCATCCGAACATCTGTCTCCGAGATGTTAGAAACCCTCTCTGATGATGATTTCGTGAATGTAGCTTCA
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGTGAGCGGATTGACTCTG
60.07
CAGCAGTGTAGGGTCTTCGT
59.4
179
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
AGTGTGAGCGGATTGACTCTG
60.07
ACAGCAGTGTAGGGTCTTCG
59.4
180
PCR template sequence:
GAGTGGAAGTGTGAGCGGATTGACTCTGAAACTCATCCGAACATCTGTCTCCGAGATGTTAGAAACCCTCTCTGATGATGATTTCGTGAATGTAGCTTCACAACCATAGTGTTAAACGAACTCAACTGGACAAGTGCCTTAGATGAAGTATTCAAAAGAAATCGAGACGAAGACCCTACACTGCTGTGGCAAGTGTTTGG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
2
Interacting miRNAs (#binding sites)
mmu-miR-382-3p(1), mmu-miR-5101(1)
siRNAs for circular RNA silencing
Junction sequence
GAATGTAGCTTCACAACCATAGTGTT
siRNA sets
AACACTATGGTTGTGAAGC,ACACTATGGTTGTGAAGCT
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCACNA2D1_353_ORF_5
0.9968
0.22284341
0.17308546
129
ORF sequence:
ATGCTCATTCTGGTGGACGTGAGTGGAAGTGTGAGCGGATTGACTCTGAAACTCATCCGAACATCTGTCTCCGAGATGTTAGAAACCCTCTCTGATGATGATTTCGTGAATGTAGCTTCACAACCATAG
Peptide sequence:
MLILVDVSGSVSGLTLKLIRTSVSEMLETLSDDDFVNVASQP
IRESfinder result
IRESfinder score
0.565833992
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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