MmuALTA1000432-2/2 @ mm10
Alternative 3'ss
Gene
ENSMUSG00000001027 | Scn4a
Description
sodium channel, voltage-gated, type IV, alpha [Source:MGI Symbol;Acc:MGI:98250]
Coordinates
chr11:106324447-106326253:-
Coord C1 exon
chr11:106326131-106326253
Coord A exon
chr11:106324643-106324725
Coord C2 exon
chr11:106324447-106324642
Length
83 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGT
5' ss Score
9.25
3' ss Seq
ACCACCACCCTGGCCCCTAGGTG
3' ss Score
8.34
Exon sequences
Seq C1 exon
GTCTCCATCATCAGTCTGGTGGCTAACTGGCTGGGCTACTCTGAGCTGGGGCCCATCAAATCCCTGCGCACGCTCCGGGCCCTGCGACCTCTGAGGGCACTGTCCCGATTTGAAGGCATGAGG
Seq A exon
GTGGTGGTGAACGCCCTTCTGGGAGCCATCCCTTCCATCATGAACGTGCTCCTTGTCTGCCTCATCTTCTGGCTCATCTTCAG
Seq C2 exon
CATCATGGGGGTCAACTTGTTTGCTGGAAAGTTCTACTACTGCATCAACACAACCACCTCCGAGAGATTCGACATCTCTGTGGTCAACAACAAGTCCGAGTGTGAGAGCCTCATGTACACCGGCCAGGTCCGCTGGATGAACGTCAAGGTCAACTATGACAACGTGGGTCTCGGCTACCTCTCTCTTCTTCAGGTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000001027-22-24,22-23-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(17.5=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(40.4=100)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCCATCATCAGTCTGGTGGCT
R:
GGAGGTGGTTGTGTTGATGCA
Band lengths:
181-264
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Ribosome-engaged transcriptomes of neuronal types
- Neural differentiation time course
- Muscular differentiation time course
- Spermatogenesis cell types
- Reprogramming of fibroblasts to iPSCs
- Hematopoietic precursors and cell types