HsaEX6016407 @ hg19
Exon Skipping
Gene
ENSG00000144285 | SCN1A
Description
sodium channel, voltage-gated, type I, alpha subunit [Source:HGNC Symbol;Acc:10585]
Coordinates
chr2:166872117-166894642:-
Coord C1 exon
chr2:166894286-166894642
Coord A exon
chr2:166892558-166893040
Coord C2 exon
chr2:166872117-166872237
Length
483 bp
Sequences
Splice sites
3' ss Seq
ATGTTTTTGTTGTTTTTAAGGTC
3' ss Score
11.62
5' ss Seq
GAGGTAAGA
5' ss Score
10.06
Exon sequences
Seq C1 exon
CTGCGAGTTTTCAAGTTGGCAAAATCTTGGCCAACGTTAAATATGCTAATAAAGATCATCGGCAATTCCGTGGGGGCTCTGGGAAATTTAACCCTCGTCTTGGCCATCATCGTCTTCATTTTTGCCGTGGTCGGCATGCAGCTCTTTGGTAAAAGCTACAAAGATTGTGTCTGCAAGATCGCCAGTGATTGTCAACTCCCACGCTGGCACATGAATGACTTCTTCCACTCCTTCCTGATTGTGTTCCGCGTGCTGTGTGGGGAGTGGATAGAGACCATGTGGGACTGTATGGAGGTTGCTGGTCAAGCCATGTGCCTTACTGTCTTCATGATGGTCATGGTGATTGGAAACCTAGTG
Seq A exon
GTCCTGAATCTCTTTCTGGCCTTGCTTCTGAGCTCATTTAGTGCAGACAACCTTGCAGCCACTGATGATGATAATGAAATGAATAATCTCCAAATTGCTGTGGATAGGATGCACAAAGGAGTAGCTTATGTGAAAAGAAAAATATATGAATTTATTCAACAGTCCTTCATTAGGAAACAAAAGATTTTAGATGAAATTAAACCACTTGATGATCTAAACAACAAGAAAGACAGTTGTATGTCCAATCATACAGCAGAAATTGGGAAAGATCTTGACTATCTTAAAGATGTAAATGGAACTACAAGTGGTATAGGAACTGGCAGCAGTGTTGAAAAATACATTATTGATGAAAGTGATTACATGTCATTCATAAACAACCCCAGTCTTACTGTGACTGTACCAATTGCTGTAGGAGAATCTGACTTTGAAAATTTAAACACGGAAGACTTTAGTAGTGAATCGGATCTGGAAGAAAGCAAAGAG
Seq C2 exon
AAACTGAATGAAAGCAGTAGCTCATCAGAAGGTAGCACTGTGGACATCGGCGCACCTGTAGAAGAACAGCCCGTAGTGGAACCTGAAGAAACTCTTGAACCAGAAGCTTGTTTCACTGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285-'18-17,'18-16,19-17=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=0.099 C2=0.732
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=FE(62.1=100)
A:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(61.4=85.1)
C2:
PF065128=Na_trans_assoc=FE(17.9=100)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TAACCCTCGTCTTGGCCATCA
R:
ACGGGCTGTTCTTCTACAGGT
Band lengths:
343-826
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)