HsaINT0145869 @ hg38
Intron Retention
Gene
ENSG00000007314 | SCN4A
Description
sodium voltage-gated channel alpha subunit 4 [Source:HGNC Symbol;Acc:HGNC:10591]
Coordinates
chr17:63948611-63949528:-
Coord C1 exon
chr17:63949393-63949528
Coord A exon
chr17:63948766-63949392
Coord C2 exon
chr17:63948611-63948765
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:ENST00000435607:15
Average complexity
IR
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
Other Skipping 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