HsaINT0145986 @ hg19
Intron Retention
Gene
ENSG00000169432 | SCN9A
Description
sodium channel, voltage-gated, type IX, alpha subunit [Source:HGNC Symbol;Acc:10597]
Coordinates
chr2:167060465-167060974:-
Coord C1 exon
chr2:167060870-167060974
Coord A exon
chr2:167060736-167060869
Coord C2 exon
chr2:167060465-167060735
Length
134 bp
Sequences
Splice sites
5' ss Seq
GGGGTAAAA
5' ss Score
2.56
3' ss Seq
TTATTCTTATTTCTTTGCAGAAC
3' ss Score
11.5
Exon sequences
Seq C1 exon
CTTGGAGGTCAAGACATCTTTATGACAGAAGAACAGAAGAAATACTATAATGCAATGAAAAAGCTGGGGTCCAAGAAGCCACAAAAGCCAATTCCTCGACCAGGG
Seq A exon
GTAAAAAAATATATATATCTTTAGCATATAGATTTTCAAATTATTTCTAATTCATTTTTAATGCACATCTTTAATTTCTGGATAATACTTGAAAAGTTTACTCTGCATTCGATATTATTCTTATTTCTTTGCAG
Seq C2 exon
AACAAAATCCAAGGATGTATATTTGACCTAGTGACAAATCAAGCCTTTGATATTAGTATCATGGTTCTTATCTGTCTCAACATGGTAACCATGATGGTAGAAAAGGAGGGTCAAAGTCAACATATGACTGAAGTTTTATATTGGATAAATGTGGTTTTTATAATCCTTTTCACTGGAGAATGTGTGCTAAAACTGATCTCCCTCAGACACTACTACTTCACTGTAGGATGGAATATTTTTGATTTTGTGGTTGTGATTATCTCCATTGTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000169432-SCN9A:NM_002977:25
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(20.4=47.3)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGGTCCAAGAAGCCACAAAA
R:
AGTGTCTGAGGGAGATCAGTT
Band lengths:
251-385
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
- Pre-implantation embryo development
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)