HsaEX6016408 @ hg19
Exon Skipping
Gene
ENSG00000144285 | SCN1A
Description
sodium channel, voltage-gated, type I, alpha subunit [Source:HGNC Symbol;Acc:10585]
Coordinates
chr2:166870254-166893040:-
Coord C1 exon
chr2:166892558-166893040
Coord A exon
chr2:166872117-166872237
Coord C2 exon
chr2:166870254-166870408
Length
121 bp
Sequences
Splice sites
3' ss Seq
TATGTCCATCTCACTTACAGAAA
3' ss Score
9.63
5' ss Seq
AAGGTAAAG
5' ss Score
9.06
Exon sequences
Seq C1 exon
GTCCTGAATCTCTTTCTGGCCTTGCTTCTGAGCTCATTTAGTGCAGACAACCTTGCAGCCACTGATGATGATAATGAAATGAATAATCTCCAAATTGCTGTGGATAGGATGCACAAAGGAGTAGCTTATGTGAAAAGAAAAATATATGAATTTATTCAACAGTCCTTCATTAGGAAACAAAAGATTTTAGATGAAATTAAACCACTTGATGATCTAAACAACAAGAAAGACAGTTGTATGTCCAATCATACAGCAGAAATTGGGAAAGATCTTGACTATCTTAAAGATGTAAATGGAACTACAAGTGGTATAGGAACTGGCAGCAGTGTTGAAAAATACATTATTGATGAAAGTGATTACATGTCATTCATAAACAACCCCAGTCTTACTGTGACTGTACCAATTGCTGTAGGAGAATCTGACTTTGAAAATTTAAACACGGAAGACTTTAGTAGTGAATCGGATCTGGAAGAAAGCAAAGAG
Seq A exon
AAACTGAATGAAAGCAGTAGCTCATCAGAAGGTAGCACTGTGGACATCGGCGCACCTGTAGAAGAACAGCCCGTAGTGGAACCTGAAGAAACTCTTGAACCAGAAGCTTGTTTCACTGAAG
Seq C2 exon
GCTGTGTACAAAGATTCAAGTGTTGTCAAATCAATGTGGAAGAAGGCAGAGGAAAACAATGGTGGAACCTGAGAAGGACGTGTTTCCGAATAGTTGAACATAACTGGTTTGAGACCTTCATTGTTTTCATGATTCTCCTTAGTAGTGGTGCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285-'19-18,'19-17,20-18=AN
Average complexity
A_S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence exclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.099 A=0.732 C2=0.000
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(4.2=5.0),PF065128=Na_trans_assoc=PU(61.4=85.1)
A:
PF065128=Na_trans_assoc=FE(17.9=100)
C2:
PF065128=Na_trans_assoc=PD(19.7=84.6)
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:
GGAACTGGCAGCAGTGTTGAA
R:
ACACGTCCTTCTCAGGTTCCA
Band lengths:
254-375
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)