HsaEX6016402 @ hg19
Exon Skipping
Gene
ENSG00000144285 | SCN1A
Description
sodium channel, voltage-gated, type I, alpha subunit [Source:HGNC Symbol;Acc:10585]
Coordinates
chr2:166900179-166903486:-
Coord C1 exon
chr2:166903280-166903486
Coord A exon
chr2:166901553-166901837
Coord C2 exon
chr2:166900179-166900559
Length
285 bp
Sequences
Splice sites
3' ss Seq
ATCATTTCTCTTCAATATAGCAG
3' ss Score
5.9
5' ss Seq
CAGGTATGG
5' ss Score
9.99
Exon sequences
Seq C1 exon
ACATTACGTGCTGCTGGGAAAACGTACATGATATTTTTTGTATTGGTCATTTTCTTGGGCTCATTCTACCTAATAAATTTGATCCTGGCTGTGGTGGCCATGGCCTACGAGGAACAGAATCAGGCCACCTTGGAAGAAGCAGAACAGAAAGAGGCCGAATTTCAGCAGATGATTGAACAGCTTAAAAAGCAACAGGAGGCAGCTCAG
Seq A exon
CAGGCAGCAACGGCAACTGCCTCAGAACATTCCAGAGAGCCCAGTGCAGCAGGCAGGCTCTCAGACAGCTCATCTGAAGCCTCTAAGTTGAGTTCCAAGAGTGCTAAGGAAAGAAGAAATCGGAGGAAGAAAAGAAAACAGAAAGAGCAGTCTGGTGGGGAAGAGAAAGATGAGGATGAATTCCAAAAATCTGAATCTGAGGACAGCATCAGGAGGAAAGGTTTTCGCTTCTCCATTGAAGGGAACCGATTGACATATGAAAAGAGGTACTCCTCCCCACACCAG
Seq C2 exon
TCTTTGTTGAGCATCCGTGGCTCCCTATTTTCACCAAGGCGAAATAGCAGAACAAGCCTTTTCAGCTTTAGAGGGCGAGCAAAGGATGTGGGATCTGAGAACGACTTCGCAGATGATGAGCACAGCACCTTTGAGGATAACGAGAGCCGTAGAGATTCCTTGTTTGTGCCCCGACGACACGGAGAGAGACGCAACAGCAACCTGAGTCAGACCAGTAGGTCATCCCGGATGCTGGCAGTGTTTCCAGCGAATGGGAAGATGCACAGCACTGTGGATTGCAATGGTGTGGTTTCCTTGGTTGGTGGACCTTCAGTTCCTACATCGCCTGTTGGACAGCTTCTGCCAGAGGTGATAATAGATAAGCCAGCTACTGATGACAAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285-'10-11,'10-10,11-11=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.188 A=0.863 C2=0.641
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(11.6=44.9),PF0253517=Zip=FE(40.7=100),PF0293211=Neur_chan_memb=PU(33.2=89.9)
A:
PF0253517=Zip=PD(45.5=80.0),PF0293211=Neur_chan_memb=FE(50.3=100),PF119333=DUF3451=PU(29.7=73.7)
C2:
PF0293211=Neur_chan_memb=PD(12.6=18.1),PF119333=DUF3451=FE(53.4=100)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Primers PCR
Suggestions for RT-PCR validation
F:
AAAAAGCAACAGGAGGCAGCT
R:
CAGTGCTGTGCATCTTCCCAT
Band lengths:
295-580
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
Other AS DBs:
FasterDB (Includes CLIP-seq data)
AS-ALPS (AS-induced ALteration of Protein Structure, links to PINs)
APPRIS (Selection of principal isoform)
DEU primates (Only for human)