HsaINT0145869 @ hg19
Intron Retention
Gene
ENSG00000007314 | SCN4A
Description
sodium channel, voltage-gated, type IV, alpha subunit [Source:HGNC Symbol;Acc:10591]
Coordinates
chr17:62025971-62026888:-
Coord C1 exon
chr17:62026753-62026888
Coord A exon
chr17:62026126-62026752
Coord C2 exon
chr17:62025971-62026125
Length
627 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGG
5' ss Score
7.13
3' ss Seq
GTCCCCCCTCACCCCATCAGCCT
3' ss Score
4.29
Exon sequences
Seq C1 exon
AAGCCGCCGCAGCCTCTCTATGATGGGAACTCGTCCGTCTGCAGCACAGCTGACTACAAGCCCCCCGAGGAGGACCCTGAGGAGCAGGCAGAGGAGAACCCCGAGGGGGAGCAGCCTGAGGAGTGCTTCACTGAGG
Seq A exon
GTGAGGGCACCCCTCACCTCATCTGGGTGTCTCCCCCAGGCCTGCAGCCCCTGCAAGGGGCAGGCTACACCAGGACCAAAAGCACACGGACCTGGGGCTGCCTGGCCATCCCCGTGCCTCACGTGTCTAGGGGTGGTGGCAGTGCATGCCCAGAACTGTGGTGCAAGATCCATGCAGAGCCCTTGGTGCAGACCTAGCTTGGAGCCAACGTGCAGGAGTGTGGGTGTCAGCTCCTGAGATCCTCCCCTCCATCTTCAGGGAGCAAGGCCTTCAGGACATGGCACTGGAGAAATGTCCTTGTCCATAGAGCTTGCTGGGCTGTGCAGGATGGAGACCGCCTGGGCGAGGTGGGGGGTGGGGCAGCACTGGGGCTGGGGGCCAGGAGGCCTTTCCTCTGCATGCCCATCCCCAGCAGCCATTGACGCATGTTGGATCCAGCTGTGAAGGGAGGTCCTGAGTCCCCCATGTGAGCCAGATGGAGCTGGGTGAGGGAGGAGGTGGGGGCCCTGGGTCTGGGAGCTGGAGAGGGGCATCCTGGGATGCCATGGGAGGGCGCTGACTGTGCACCCCAAGGCAACCCCAGGCCCATGATGTGGTGCCTGTCCCTGTCCCCCCTCACCCCATCAG
Seq C2 exon
CCTGCGTGCAGCGCTGGCCCTGCCTCTACGTGGACATCTCCCAGGGCCGTGGGAAGAAGTGGTGGACTCTGCGCAGGGCCTGCTTCAAGATTGTCGAGCACAACTGGTTCGAGACCTTCATTGTCTTCATGATCCTGCTCAGCAGTGGGGCTCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007314-SCN4A:NM_000334:15
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.870 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF065128=Na_trans_assoc=FE(19.9=100)
A:
NA
C2:
PF065128=Na_trans_assoc=PD(19.5=84.6)
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:
GCCGCAGCCTCTCTATGATG
R:
CAGAGCCCCACTGCTGAGC
Band lengths:
286-913
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)