HsaINT0145853 @ hg19
Intron Retention
Gene
ENSG00000153253 | SCN3A
Description
sodium channel, voltage-gated, type III, alpha subunit [Source:HGNC Symbol;Acc:10590]
Coordinates
chr2:166020128-166021030:-
Coord C1 exon
chr2:166020902-166021030
Coord A exon
chr2:166020220-166020901
Coord C2 exon
chr2:166020128-166020219
Length
682 bp
Sequences
Splice sites
5' ss Seq
GGCGTGAGT
5' ss Score
7
3' ss Seq
TGTGAACTCCCCTATTACAGATA
3' ss Score
7.61
Exon sequences
Seq C1 exon
GTACACATTCACTGGAATCTATACCTTTGAGTCACTTATAAAAATCTTGGCAAGAGGGTTTTGCTTAGAAGATTTTACGTTTCTTCGTGATCCATGGAACTGGCTGGATTTCAGTGTCATTGTGATGGC
Seq A exon
GTGAGTAACTTTGAAAATTTGATAAGCGCAAAGGAGTGAAAATAGTCATAGTACAAACAAGGTCTTTGTGTCATATATTAAATGTAGAGCTTTCTTGTTAGTCAAGTTAACTATATGGATTGTGTATTTTAAGAATACATATTAGAATACATATTGCAATGTAAATATATCCAGTAAATGATCAATAAATGGGGTTATCTTCATGTCATATAGTCTTTCTCTTCATCAAAATGAAGTTATTCATTGACTACAATTTAATAGCAACAACTGTACTTGGATTAGTTTTGCAAACAAATGTGTTCATATTAGTGAAAATTACATTGAAATAAAGCAACACGATTTTGTTTCTTAAAAGCAACCTTTAGCATATGGCAGCCTGAGGTCTATAGCAATTCCATTTGTTAAACTCACAGGGCTCTATGTGCCAAACCCAGCATTAAGTCCTTATTTAGTATAAACTTTGCCAAAACTATCAGTAACTCTGATTTAATTCTGCAGGTATGTAACAGAATTTGTAAGCCTAGGCAATGTTTCAGCCCTTCGAACTTTCAGAGTCTTGAGAGCTCTGAAAACTATTTCTGTAATTCCAGGTAAGAAGAAACTGGTGTAAGGTAGTAGGCCCCTTATATCTCCAACTTTTCTTGTGTGTTATTGTGTTTGTGTGTGAACTCCCCTATTACAG
Seq C2 exon
ATATGTGACAGAGTTTGTGGACCTGGGCAATGTCTCAGCGTTGAGAACATTCAGAGTTCTCCGAGCACTGAAAACAATTTCAGTCATTCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153253-SCN3A:NM_006922:6
Average complexity
IR-C
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(16.0=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(11.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTACACATTCACTGGAATCTATACCT
R:
TTGTTTTCAGTGCTCGGAGAACT
Band lengths:
206-888
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)