MmuALTA1026434-1/2 @ mm10
Alternative 3'ss
Gene
ENSMUSG00000034533 | Scn10a
Description
sodium channel, voltage-gated, type X, alpha [Source:MGI Symbol;Acc:MGI:108029]
Coordinates
chr9:119633741-119635895:-
Coord C1 exon
chr9:119635443-119635895
Coord A exon
NA
Coord C2 exon
chr9:119633741-119633878
Length
0 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGA
5' ss Score
9.22
3' ss Seq
GGGCCCTCTCTCATCAGCAGGAG
3' ss Score
5.39
Exon sequences
Seq C1 exon
GTGCTCAACCTATTCATCGCTTTACTGCTGAACTCCTTCAGTGCGGACAACCTCACAGCCCCAGAGGATGACGGGGAGGTGAACAACTTGCAGGTAGCACTGGCCCGGATTCAGGTATTTGGCCATCGGGCCAGTCGGGCCATTACCAGTTACATCAGAAGCCACTGCCGGCTCCGCTGGCCCAAGGTGGAGACCCAGCTGGGGATGAAACCCCCACTCACCAGCTGCAAAGCTGAGAACCACATTGCTACTGATGCTGTCAATGCTGCAGTGGGGAACCTGGCAAAGCCAGCTCTTGGTGGCCCCAAGGAGAACCACGGGGACTTCATCACTGATCCTAACGTGTGGGTCTCTGTGCCCATTGCTGAGGGGGAGTCCGACCTTGATGAGCTCGAGGAAGATGTGGAGCATGCTTCTCAGAGCTCCTGGCAGGAAGAGAGCCCCAAAGGGCAG
Seq A exon
NA
Seq C2 exon
GAGCTGCTGCAGCAAGTCCAAAAGTGTGAAGATCACCAGGCAGCCCGAAGCCCACCCTCCGGGATGTCCTCTGAGGACCTGGCTCCATACCTGGGGGAGAGATGGCAGAGGGAGGAGAGCCCTCGGGTCCCTGCCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSMUSG00000034533-21-21,21-20-1/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.374 A=NA C2=1.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.3),PF065128=Na_trans_assoc=PU(48.7=84.1)
A:
NA
C2:
PF065128=Na_trans_assoc=FE(17.3=100)
Other Inclusion Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGCTCGAGGAAGATGTGGA
R:
CACTTTTGGACTTGCTGCAGC
Band lengths:
93-96
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