HsaINT0145873 @ hg38
Intron Retention
Gene
ENSG00000007314 | SCN4A
Description
sodium voltage-gated channel alpha subunit 4 [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr17:63945007-63945638:-
Coord C1 exon
chr17:63945360-63945638
Coord A exon
chr17:63945061-63945359
Coord C2 exon
chr17:63945007-63945060
Length
299 bp
Sequences
Splice sites
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
3' ss Seq
CCCCAACCACACTCTCTCAGGCC
3' ss Score
4.71
Exon sequences
Seq C1 exon
GTGGTGGTGAACGCCCTCCTAGGCGCCATCCCCTCCATCATGAATGTGCTGCTTGTCTGCCTCATCTTCTGGCTGATCTTCAGCATCATGGGTGTCAACCTGTTTGCCGGCAAGTTCTACTACTGCATCAACACCACCACCTCTGAGAGGTTCGACATCTCCGAGGTCAACAACAAGTCTGAGTGCGAGAGCCTCATGCACACAGGCCAGGTCCGCTGGCTCAATGTCAAGGTCAACTACGACAACGTGGGTCTGGGCTACCTCTCCCTCCTGCAGGTG
Seq A exon
GTGAGTGTGACCCACCACCCCTGCCGGGAACCTGGATGGAGGTGCCCCCCACCCCGGTCCTCTCGTTGTACCCAACCCCAGTGTCACTCCTGGTTAGGGGACCGCCCACCCTGCTTCCAATGCTGTGGGATCCCCAGGCAGTGTCTAGACCTCTCTGGTCTTTATTTGATGCTAGCCCAGTGGGGCTCTGGCAGGCGGCCTCTGGCAGGGGAGGACCAGGTTGGGTGGGGGAGGGAAACTCATGGATGATGAAAGCAGGGAGCAGCCCCCCGGCTCACTCCCCAACCACACTCTCTCAG
Seq C2 exon
GCCACCTTCAAGGGTTGGATGGACATCATGTATGCAGCCGTGGACTCCCGGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007314:ENST00000435607:19
Average complexity
IR
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(40.4=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(7.5=100)
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:
TCCCCTCCATCATGAATGTGC
R:
CCACGGCTGCATACATGATGT
Band lengths:
294-593
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