HsaINT0145895 @ hg19
Intron Retention
Gene
ENSG00000183873 | SCN5A
Description
sodium channel, voltage-gated, type V, alpha subunit [Source:HGNC Symbol;Acc:10593]
Coordinates
chr3:38645203-38646399:-
Coord C1 exon
chr3:38646220-38646399
Coord A exon
chr3:38645575-38646219
Coord C2 exon
chr3:38645203-38645574
Length
645 bp
Sequences
Splice sites
5' ss Seq
ATGGTAATC
5' ss Score
4.14
3' ss Seq
CCCTCTCCTCATGCCCTTAGAAT
3' ss Score
9.59
Exon sequences
Seq C1 exon
GCCCTCACCATCAGGGGTGTGGATACCGTGTCCCGTAGCTCCTTGGAGATGTCCCCTTTGGCCCCAGTAAACAGCCATGAGAGAAGAAGCAAGAGGAGAAAACGGATGTCTTCAGGAACTGAGGAGTGTGGGGAGGACAGGCTCCCCAAGTCTGACTCAGAAGATGGTCCCAGAGCAATG
Seq A exon
GTAATCCCAGCTGTGGTTCTAGCTTTTCCAGGGTGGGTCTGGCATGAAAATCCCATCATGCTAGGCCCCTGTACAGTCACAGCCCCCATGGTTGCTCATCTCTGCGCTTCCTGTTTCCCATGGCCTTCCTTAGAGTAGGGGAGCTCTGGGCAGAGGGACAGGGTAGTTTTGGGTGTTGTGATATCCCCAACCTGAGGCCAGTATCCCGGCACTGGAGCCGGGGCTGGGGGACGAGACCCCATGGTATGGGTTGGTAGGAGTTCAAGGACATGCCCATAAGAGTGAGGGTCCATTCCGAGTGCCCCAGGTCCTCCTCAGGCCGGGCCTGTCTGCAACACCAGGAGCCTTCCTGCCTCCTTCTCCCTTGCCCAGCCTGAGCTCTAACTCCAAGCCCAGTTAAGTTTCAGGCTCCCAGCTCCAGAGACATAGATTTGAGGGGAGTAGACATCCCAGAAGATACAGGATTATCTCTAACCCCACATCCCCTCTTCCAAATACCCCCGGCCCAACCCACCTGGTTCCTGTGTGGCCAAAAAAGCCCTCAATGCTCTGAGAAGTTTAGCTGAGGCCAGTGGCACAAAAGACAGGCTGGGAGCACATGAAGAGCACATGTCATGGTCGTGTCCCCTCTCCTCATGCCCTTAG
Seq C2 exon
AATCATCTCAGCCTCACCCGTGGCCTCAGCAGGACTTCTATGAAGCCACGTTCCAGCCGCGGGAGCATTTTCACCTTTCGCAGGCGAGACCTGGGTTCTGAAGCAGATTTTGCAGATGATGAAAACAGCACAGCGGGGGAGAGCGAGAGCCACCACACATCACTGCTGGTGCCCTGGCCCCTGCGCCGGACCAGTGCCCAGGGACAGCCCAGTCCCGGAACCTCGGCTCCTGGCCACGCCCTCCATGGCAAAAAGAACAGCACTGTGGACTGCAATGGGGTGGTCTCATTACTGGGGGCAGGCGACCCAGAGGCCACATCCCCAGGAAGCCACCTCCTCCGCCCTGTGATGCTAGAGCACCCGCCAGACACG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000183873-SCN5A:NM_001160161:11
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.733 A=NA C2=0.968
Domain overlap (PFAM):
C1:
PF083255=WLM=FE(46.5=100),PF119333=DUF3451=PU(21.6=75.0)
A:
NA
C2:
PF083255=WLM=PD(34.6=35.5),PF119333=DUF3451=FE(59.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAACTGAGGAGTGTGGGGAGG
R:
AATGAGACCACCCCATTGCAG
Band lengths:
355-1000
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
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)