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mmu_circGapvd1_422
Basic information of circular RNA
PanCircBase ID:
mmu_circGapvd1_422
mm39_Chr. Position ID:
chr2|34583384|34590862|-
Gene name:
Gapvd1
Transcript:
ENSMUST00000102800.9
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
20,19,18,17
Exon/intron offsets:
0,2113,6453,7390
Genomic length:
7478
Exon/intron sizes in nt:
130,123,81,88
Flanking exon/introns:
chr2:34581227-34583384|chr2:34590862-34594177
Splice length:
422
Other database IDs:
circAtlas: mmu-Gapvd1_0030
circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_125694
Human Ortholog IDs:
Mature spliced Sequence:
ACTGAGGAACGCAAGGACAGTGACGATGAGAGGTCAGACAGGAGCAGGCCTTGGTGGAGGAAGCGCTTTGTTTCAGCTATGCCTAAAGCTCCTATACCATTTAGAAAGAAAGAAAAACAAGAAAAAGACAAAGATGATCTGGGTCCTGACAGATTCTCAACACTCACAGATGAGCCCAGCCCTAGGCTCAGTGCTCAAGCTCAGGTTGCTGAAGATATTCTGGACAAGTACCGGAATGCCATTAAACGGACCAGCCCCAGTGAAGGAGCAATGGCAAATGATGAGAGTGCAGAGGTCATGGGTGATGGTGAAAGTGCCCACGACTCTCCTCGTGAGGAAGCACTGCAGAACATCTCAGCCGACGACCTCCCGGACTCCGCCAGCCAGGCAGCCCACCCTCAGGACTCTGCTTTCTCTTACAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCAGAACATCTCAGCCGA
60.11
GCTGAAACAAAGCGCTTCCT
59.69
157
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CTGCAGAACATCTCAGCCGA
60.11
AGCTGAAACAAAGCGCTTCC
59.69
158
PCR template sequence:
ACTCTCCTCGTGAGGAAGCACTGCAGAACATCTCAGCCGACGACCTCCCGGACTCCGCCAGCCAGGCAGCCCACCCTCAGGACTCTGCTTTCTCTTACAGACTGAGGAACGCAAGGACAGTGACGATGAGAGGTCAGACAGGAGCAGGCCTTGGTGGAGGAAGCGCTTTGTTTCAGCTATGCCTAAAGCTCCTATACCAT
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
CTTTCTCTTACAGACTGAGGAACGCA
siRNA sets
NA
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCGAPVD1_422_ORF_1
0.9386
0.178811416
0.939013906
765
ORF sequence:
ATGCCTAAAGCTCCTATACCATTTAGAAAGAAAGAAAAACAAGAAAAAGACAAAGATGATCTGGGTCCTGACAGATTCTCAACACTCACAGATGAGCCCAGCCCTAGGCTCAGTGCTCAAGCTCAGGTTGCTGAAGATATTCTGGACAAGTACCGGAATGCCATTAAACGGACCAGCCCCAGTGAAGGAGCAATGGCAAATGATGAGAGTGCAGAGGTCATGGGTGATGGTGAAAGTGCCCACGACTCTCCTCGTGAGGAAGCACTGCAGAACATCTCAGCCGACGACCTCCCGGACTCCGCCAGCCAGGCAGCCCACCCTCAGGACTCTGCTTTCTCTTACAGACTGAGGAACGCAAGGACAGTGACGATGAGAGGTCAGACAGGAGCAGGCCTTGGTGGAGGAAGCGCTTTGTTTCAGCTATGCCTAAAGCTCCTATACCATTTAGAAAGAAAGAAAAACAAGAAAAAGACAAAGATGATCTGGGTCCTGACAGATTCTCAACACTCACAGATGAGCCCAGCCCTAGGCTCAGTGCTCAAGCTCAGGTTGCTGAAGATATTCTGGACAAGTACCGGAATGCCATTAAACGGACCAGCCCCAGTGAAGGAGCAATGGCAAATGATGAGAGTGCAGAGGTCATGGGTGATGGTGAAAGTGCCCACGACTCTCCTCGTGAGGAAGCACTGCAGAACATCTCAGCCGACGACCTCCCGGACTCCGCCAGCCAGGCAGCCCACCCTCAGGACTCTGCTTTCTCTTACA
Peptide sequence:
MPKAPIPFRKKEKQEKDKDDLGPDRFSTLTDEPSPRLSAQAQVAEDILDKYRNAIKRTSPSEGAMANDESAEVMGDGESAHDSPREEALQNISADDLPDSASQAAHPQDSAFSYRLRNARTVTMRGQTGAGLGGGSALFQLCLKLLYHLERKKNKKKTKMIWVLTDSQHSQMSPALGSVLKLRLLKIFWTSTGMPLNGPAPVKEQWQMMRVQRSWVMVKVPTTLLVRKHCRTSQPTTSRTPPARQPTLRTLLSLT
IRESfinder result
IRESfinder score
0.225088077
IRES/non IRES
non-IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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