HsaINT0145880 @ hg19
Intron Retention
Gene
ENSG00000007314 | SCN4A
Description
sodium channel, voltage-gated, type IV, alpha subunit [Source:HGNC Symbol;Acc:10591]
Coordinates
chr17:62048522-62049210:-
Coord C1 exon
chr17:62049082-62049210
Coord A exon
chr17:62048614-62049081
Coord C2 exon
chr17:62048522-62048613
Length
468 bp
Sequences
Splice sites
5' ss Seq
GGCGTGAGC
5' ss Score
2.44
3' ss Seq
CCCCTCCACCCCCTACCCAGGTA
3' ss Score
8.1
Exon sequences
Seq C1 exon
GTACACCTTCACAGGGATCTACACCTTTGAGTCCCTCATCAAGATACTGGCCCGAGGCTTCTGTGTCGACGACTTCACATTCCTCCGGGACCCCTGGAACTGGCTGGACTTCAGTGTCATCATGATGGC
Seq A exon
GTGAGCAGGGGCCCCAGGACATCCTGAGGCTGGGGTGGGTGAGGGGAGGGGGCCAGGCCTTAAAGAGGGAAGCTGCCTGGGCTGAGGGCTGCAGGGGACATCGGTCAGTTGTGCAGATGGGGAGCTGCACAATTCTAGAAGCTGCCATTCTCAGGGTCTGGCTCAGCACTCTCCTGATGGACTCCTGATAATCACATGAGGCAGCCCTGACCCACAGACCCATGGGTCCTCACCTGCTGGGTGAGCCGGGCTATCTTTGCCATCCCCACTCCCCCAGAGCTCCTGCACTGTCCTTCCCAACCCTTGGGCTCCCAGAGGAGCTTTGGGGGTGTCTGCCCTGCCCCCCAGACCCTGTGGTACCCCCAATTTCTTGGGAATCCTCATCCCAGGCCTGGAGGAGCCCTGATTTCTGTCCTACCACCCACCCCAGGCTCTGACAGTCCCCACCCCCCTCCACCCCCTACCCAG
Seq C2 exon
GTACCTGACAGAGTTTGTGGACTTGGGCAACATCTCAGCCCTGAGGACCTTCCGGGTGCTGCGGGCCCTCAAAACCATCACGGTCATCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007314-SCN4A:NM_000334:4
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:
PF0052026=Ion_trans=FE(14.9=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(10.8=100)
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:
ACCTTCACAGGGATCTACACCT
R:
CTGGGATGACCGTGATGG
Band lengths:
217-685
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)