HsaINT0145783 @ hg19
Intron Retention
Gene
ENSG00000144285 | SCN1A
Description
sodium channel, voltage-gated, type I, alpha subunit [Source:HGNC Symbol;Acc:10585]
Coordinates
chr2:166854548-166856286:-
Coord C1 exon
chr2:166856233-166856286
Coord A exon
chr2:166854686-166856232
Coord C2 exon
chr2:166854548-166854685
Length
1547 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGT
5' ss Score
8.62
3' ss Seq
AAAATATTCCCCTTTGGTAGGTG
3' ss Score
6.1
Exon sequences
Seq C1 exon
GCCACATTCAAAGGATGGATGGATATAATGTATGCAGCAGTTGATTCCAGAAAT
Seq A exon
GTAAGTATTCCTTGTATTCTAAGTCTTTTTACAATATTGATCAGGTGGTAAAATTAATCGAATAAAGCATAAACGACCAAATGAAATGATTCTATCTTGATTTAAAATATTTGGGAAAAAGTGTGACAGGTAAATATTCAAGCATAGCAATGTTTATCAGAAAGATCTTACTAAGATAATTCAACACATGAATTATTTTGAAAACCAAAGTAACAAATTCATGTATTTAGTAACTAACAAATATTTTCCTTTTAAATATTTTCTATTTTGTTTCCTATTTATCCACACATTATATAATTAGTAGTAATTTTAGTGTGCGGGACCAAATTTGAAGAAATATATGATTTCTATCATTAGTTGAAATGTATAGTCACCCTCCATATTAGACAGCATGAAAAGTTATGGATATTGTTCTGTCAGCCTTAGATTACTGTGATGATTTCTTTCAAATAATCCTATTTTAAACCATATAAAAGAATGTTTTTATATGATTTTTGCATTCATAAATTGACTGGAGCCTTTACTAATGTTGCAATCACTTCTGTGACCAACAGATTCCTTTAAGTGTATATCACCAAAATATAAACCTATTTTATTTGATTTCAGCCTCTTTCAGGCTCCAAGACCTAAACTGAAATTCATGCTCATTCCAACTTTGCTCTTCAAAACTTTGTAAGATGTAGTATTTTCTATCAACCTTCATCTTTCTATTCTCAAGTCCCATCTGTTTAGTTTATCATCATAAAGAATAACCTCTGTCCCTGCAGTCTTCAACCTGATAGAGTTTGATGTTATCTTTCTTGAAGTGCATTTCAAATAGCTTTAGTTTTATGTTGAATATCATTTTGATAACCTCCAGAGTTGTTTTATTTCACTTTGTCACTTATATTTTGTTTTGTGTGTTTAGTTGGTTTTTAACTTTGTTGCTTTTAGAAGGACATGAATCTGTTAAAAAACTATAGTGACCTTTCAGTCCATTACTAAATTATAAGTAATAGCCCATTTGTTTTAAGCACAATCTAGGAATTAAATAATCAACTGAGGATTTATAAAATGGACTGTCCATCTATGTCTACTTAATCTGAAAAATTCAATAACTGTTACTTTAGGGTAAAGTGCCAAACATCTGAATGAACAACTCATTTCTTATTTGCTACATTATTTCATGCATACATGAATGACTGTTTCTAAACCTAGCCTGTAGATATTTACAGTTTTAAATTTTTTATTAATAATTTTAAAATTACTAAAATTCAGTACCTTAAAAGCTTGCAAATTTAGCACATTACTGTTCAAATGGAAGAATATTATTTGTATTTATAGTTATAAAAATAGATTTTAGAATGTCATAATAGCCATATTTTTCACATGAAAACATCCCTAAAGGCCAATTTCAGGGATGTTTTTTAGAGGTAGTTGATTCAGAAAAAAAAAAAATGCTGACATATTAGTAAGAATAATTTTTTCTATTGTTATGAAAAAGCACCAGTGACATTTCCAGCACTAAAATGTATGGTAATATTTTACAAAATATTCCCCTTTGGTAG
Seq C2 exon
GTGGAACTCCAGCCTAAGTATGAAGAAAGTCTGTACATGTATCTTTACTTTGTTATTTTCATCATCTTTGGGTCCTTCTTCACCTTGAACCTGTTTATTGGTGTCATCATAGATAATTTCAACCAGCAGAAAAAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285-SCN1A:NM_001165963:22
Average complexity
IR-S
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(7.4=100)
A:
NA
C2:
PF0052026=Ion_trans=PD(15.3=76.1)
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:
AAGGATGGATGGATATAATGTATGCA
R:
CTTCTTTTTCTGCTGGTTGAAATTAT
Band lengths:
182-1729
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)