MmuALTD0012456-2/2 @ mm9
Alternative 5'ss
Gene
ENSMUSG00000023033 | Scn8a
Description
sodium channel, voltage-gated, type VIII, alpha [Source:MGI Symbol;Acc:MGI:103169]
Coordinates
chr15:100814120-100832597:+
Coord C1 exon
chr15:100814120-100814476
Coord A exon
chr15:100814477-100814506
Coord C2 exon
chr15:100832465-100832597
Length
30 bp
Sequences
Splice sites
5' ss Seq
AGTGTAAGG
5' ss Score
5.2
3' ss Seq
TGCTTTATTTTATTTCTCAGGCA
3' ss Score
9.26
Exon sequences
Seq C1 exon
TCGCTGCTCAGCATCCCAGGCTCGCCCTTCCTTTCCCGACACAACAGCAAAAGCAGCATCTTCAGCTTTCGGGGTCCTGGACGGTTCCGGGACCCCGGTTCGGAGAACGAGTTCGCAGACGACGAGCACAGCACAGTGGAGGAAAGTGAGGGCCGGCGCGACTCGCTCTTCATCCCGATCCGCGCCCGCGAGCGCCGCAGCAGCTACAGCGGCTACAGCGGCTACAGCCAGTGCAGCCGCTCGTCGCGCATCTTCCCCAGCCTGCGGCGCAGCGTGAAACGCAACAGCACCGTGGACTGCAATGGCGTGGTGTCGCTCATCGGGCCTGGCTCGCACATCGGGCGGCTCCTGCCTGAG
Seq A exon
GTGAAAATAGATAAGGCAGCTACAGACAGT
Seq C2 exon
GCAACAACTGAGGTGGAGATTAAGAAGAAAGGCCCTGGATCGCTCTTAGTCTCCATGGAACAACTCGCCTCCTACGGACGGAAGGACAGAATCAACAGTATAATGAGCGTTGTCACAAACACACTAGTGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000023033-12-11,13-11-2/2
Average complexity
Alt5
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.302 A=NA C2=0.016
Domain overlap (PFAM):
C1:
PF0310514=SPX=PD(27.7=44.5),PF119333=DUF3451=FE(52.0=100)
A:
NA
C2:
PF119333=DUF3451=PD(16.5=86.7)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AGCACCGTGGACTGCAATG
R:
TAAGAGCGATCCAGGGCCTTT
Band lengths:
120-150
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Pre-implantation embryo development
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types
Other AS DBs: