HsaINT0145876 @ hg19
Intron Retention
Gene
ENSG00000007314 | SCN4A
Description
sodium channel, voltage-gated, type IV, alpha subunit [Source:HGNC Symbol;Acc:10591]
Coordinates
chr17:62021106-62022170:-
Coord C1 exon
chr17:62022033-62022170
Coord A exon
chr17:62021211-62022032
Coord C2 exon
chr17:62021106-62021210
Length
822 bp
Sequences
Splice sites
5' ss Seq
AAGATGAGT
5' ss Score
2.29
3' ss Seq
CAAGCCCTATCCCACTATACTTA
3' ss Score
-4.58
Exon sequences
Seq C1 exon
AAGGAGGAGCAGCCGCAGTACGAGGTGAACCTCTACATGTACCTCTACTTTGTCATCTTCATCATCTTTGGCTCCTTCTTCACCCTCAACCTCTTCATTGGCGTCATCATTGACAACTTCAACCAGCAGAAGAAGAAG
Seq A exon
ATGAGTATCAGCCCAGCCCCTCGGGCCCTCCCGGTGCTGGGCCTCCCTCCTGCCTCCTTTGTCCACTCTCCATTGCACAAACCCACAAACGCTGCCTGAGCACCTACCAGGTTGTTGGTTCAGGCAGCTAGCTTGGGTCCCAGTCCCACCAGGCCACCTTGAACAAGTGGCTTGGCCTCCATGAACCTCGGTGTCCTTATCTGTAAAATGAGACTGCTGGGCCAGGCACGGTGGCTCATGCTTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACAAGGTCAGGAGTTCGAGACCACCCTGGCTAACGTGGTAAAACCCTGTCTATACTAAAAATACAAAAAAAATTAAAAAAAGAAATTAGCCAGGCGTGGTGGCAGGCATCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTAAACCCAGGAGATGGAGGTTGCAGTGGGCCAAGATCGCGCCACTGCACTCCAGCCTGGTGACAGAGCGAGACTCCATCTCAACAACAAAAAAAAAGACGAGGCTGCTACAACCTGCCTTGTGGGTTACTCTAGGGCTCAGCGAGATGTTGATGAAAAGTAGCCAGAAACAGGCTGCAAGACAGCATTGATCCCCACTCCCCTTCCCTCCCTTCTCCTCGGTCCCGCATTCTCCCCTTGTCCCTCCATCTCTGACCCTCCCGCTTCCTCCAGGCTGATCAACAGGGGCGGGGGCTGCCTTAAAGGTGAGGTGCCCCACTGAGGTGGGGGTGGTCCTGGAGGCAGGAAGGGGAACTGCACCTCAACCTGACAAGCCCTATCCCACTATAC
Seq C2 exon
TTAGGGGGGAAAGACATCTTTATGACGGAGGAACAGAAGAAATACTATAACGCCATGAAGAAGCTTGGCTCCAAGAAGCCTCAGAAGCCAATTCCCCGGCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007314-SCN4A:NM_000334:21
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=0.029
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(15.4=76.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGGAGCAGCCGCAGTA
R:
CTGGGGCCGGGGAATTGG
Band lengths:
241-1063
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)