HsaINT0145874 @ hg38
Intron Retention
Gene
ENSG00000007314 | SCN4A
Description
sodium voltage-gated channel alpha subunit 4 [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr17:63972136-63972470:-
Coord C1 exon
chr17:63972352-63972470
Coord A exon
chr17:63972226-63972351
Coord C2 exon
chr17:63972136-63972225
Length
126 bp
Sequences
Splice sites
5' ss Seq
TGCATATCC
5' ss Score
-13.7
3' ss Seq
TTTCCTTGACCCTGCCCCACGCT
3' ss Score
-2.34
Exon sequences
Seq C1 exon
ACCTTCATCGTACTCAACAAGGGCAAGGCCATCTTCCGCTTCTCCGCCACACCTGCTCTCTACCTGCTGAGCCCCTTCAGCGTAGTCAGGCGCGGGGCCATCAAGGTGCTCATCCATGC
Seq A exon
ATATCCTGCCCAAGATGGGAGAGGCGGGAGGGGTTAGGGATGGGCGAGATGGGGTGCTGTGGCCCAGGAGACCCTCTATCACCTCCCATCCTAGCTGCTTCCTCACTTTCCTTGACCCTGCCCCAC
Seq C2 exon
GCTGTTCAGCATGTTCATCATGATCACCATCTTGACCAACTGCGTATTCATGACCATGAGTGACCCGCCTCCCTGGTCCAAGAATGTGGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000007314:ENST00000435607:2
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(0.7=6.5)
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:
TCGTACTCAACAAGGGCAAGG
R:
TCCACATTCTTGGACCAGGGA
Band lengths:
202-328
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