HsaINT0145863 @ hg38
Intron Retention
Gene
ENSG00000007314 | SCN4A
Description
sodium voltage-gated channel alpha subunit 4 [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr17:63972352-63972918:-
Coord C1 exon
chr17:63972569-63972918
Coord A exon
chr17:63972471-63972568
Coord C2 exon
chr17:63972352-63972470
Length
98 bp
Sequences
Splice sites
5' ss Seq
AAGGTCTGG
5' ss Score
3.93
3' ss Seq
CAGCCTCTCTCCCACCTTAGACC
3' ss Score
8.35
Exon sequences
Seq C1 exon
CCAGCACCCCGGGGCTGCGCACTGCAGCTCCCCAGGCCACCCACCACCCTTCTGGTCTCTGAGCCCAGGATGCGAGGATGGCCAGACCATCTCTGTGCACCCTGGTGCCTCTGGGCCCTGAGTGCTTGCGCCCCTTCACCCGGGAGTCACTGGCAGCCATAGAACAGCGGGCGGTGGAGGAGGAGGCCCGGCTGCAGCGGAATAAGCAGATGGAGATTGAGGAGCCCGAACGGAAGCCACGAAGTGACTTGGAGGCTGGCAAGAACCTACCCATGATCTACGGAGACCCCCCGCCGGAGGTCATCGGCATCCCCCTGGAGGACCTGGATCCCTACTACAGCAATAAGAAG
Seq A exon
GTCTGGGCCTGGGAAGGCTTCCTCTGTCTGTCTGCCATCCATCCATCTGTCTGCCTGTCTGTCTGTCCCTGGGTCTCACAGCCTCTCTCCCACCTTAG
Seq C2 exon
ACCTTCATCGTACTCAACAAGGGCAAGGCCATCTTCCGCTTCTCCGCCACACCTGCTCTCTACCTGCTGAGCCCCTTCAGCGTAGTCAGGCGCGGGGCCATCAAGGTGCTCATCCATGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007314:ENST00000435607:1
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.220 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
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:
GCTGGCAAGAACCTACCCATG
R:
CTCAGCAGGTAGAGAGCAGGT
Band lengths:
167-265
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