HsaINT0145771 @ hg19
Intron Retention
Gene
ENSG00000144285 | SCN1A
Description
sodium channel, voltage-gated, type I, alpha subunit [Source:HGNC Symbol;Acc:10585]
Coordinates
chr2:166898802-166900559:-
Coord C1 exon
chr2:166900179-166900559
Coord A exon
chr2:166898935-166900178
Coord C2 exon
chr2:166898802-166898934
Length
1244 bp
Sequences
Splice sites
5' ss Seq
AATGTAAGG
5' ss Score
6.17
3' ss Seq
ATTAGCATTTTTTTTTACAGGGA
3' ss Score
8.45
Exon sequences
Seq C1 exon
TCTTTGTTGAGCATCCGTGGCTCCCTATTTTCACCAAGGCGAAATAGCAGAACAAGCCTTTTCAGCTTTAGAGGGCGAGCAAAGGATGTGGGATCTGAGAACGACTTCGCAGATGATGAGCACAGCACCTTTGAGGATAACGAGAGCCGTAGAGATTCCTTGTTTGTGCCCCGACGACACGGAGAGAGACGCAACAGCAACCTGAGTCAGACCAGTAGGTCATCCCGGATGCTGGCAGTGTTTCCAGCGAATGGGAAGATGCACAGCACTGTGGATTGCAATGGTGTGGTTTCCTTGGTTGGTGGACCTTCAGTTCCTACATCGCCTGTTGGACAGCTTCTGCCAGAGGTGATAATAGATAAGCCAGCTACTGATGACAAT
Seq A exon
GTAAGGAAGTTTTAAATAGTTCAGGCATGGCTGGCTCACTATTGCTGCACCAGCCAGTGTTTCTACAGAACGGCAACCTTGAGAATGATTCCTGGTTGGTCACGCTGTGAATGCACCTGCATCTTGTAATATCTTTAATAGACTAACCAACTAAAACTTAAAACCTTAGCAGTCTCCTGCACAAACCTGAATGCATTTACTTATTAAAAGTGCTAAGGATTGATTAGACACAATAATTACTGCCTCCAGTTGGAGGATTTGCTATATACCCACACTGAATTTAGATAGCAGGACATTCTCCAAGGCTCTGGTATGAAAGTAAATGAATGATTCTATGTTTAAGTGTCAAGGGTATGTAATAAATCTTTCCAATGGATTCTTCAAGATCTCTGCTTTAGTTTAGATTTTCAAAAACACTGCTTAAGTAGATAGCTTCATTGTTACCTTAATACTCCTAGTACTCATATTTTTCTTACTAAAAAATGCTGATATAGGTCTTCTCAAAATTAAATGAAGAGACACAAATACATTATTAATACAGACAGATAAAATAATTGTCTGTGTACAAAGGTATGTTATGTGTTTGTGGATGTATACTCAGATGAGGAATTTCTAAACAGATGCTGCCTCTTCTTAGACTGTTTACTCACTTGGAAATATATCAGCATGAGGAGGCATGACTAAGTCAGAATTAGATGACTTATTGCTTTGGTACCCTGGATGAAACTGTTGTCCATGCAGCATGTGTGTGTTCTTTTTAACATAGAGTTTGTGTTGTCAATGACCATCTACATCTTGTGTCCAGAAAATAAGATGGCAGCTAAGTGTGTTGCAATCATTTATACTTCCTTAAAATTAAATAGCTACCTTCTCAAAAATCAAGTGCCTTGATCACTTGTAGGACTTTTAAGTTACTAGGCTTTTACTATTAGTTCAGAAATAAGGGTAATAACTGTTAAATATATCTCTTAAGAGTTTTATCAACTATATTAAAATTATTTTGTATTTTATAAAATTATGAAATCAGGAAGTTAACATCTTGGTTTTTGCTGTATGACTAAATGGTTAACAGTTTGAACATTCCAGGCTAATGATACAATAAGTCAGAAATATCTGCCATCACCAATTGAATATGAAAGTGCATGATGCATGTGTTTCATGAAATTCACTGTGTCACCATTTGGTTGTTTGCTTGTCATATTGCTCAAATTAATTGTTTAATGCATTAGCATTTTTTTTTACAG
Seq C2 exon
GGAACAACCACTGAAACTGAAATGAGAAAGAGAAGGTCAAGTTCTTTCCACGTTTCCATGGACTTTCTAGAAGATCCTTCCCAAAGGCAACGAGCAATGAGTATAGCCAGCATTCTAACAAATACAGTAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285-SCN1A:NM_001165963:11
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.641 A=NA C2=0.222
Domain overlap (PFAM):
C1:
PF0293211=Neur_chan_memb=PD(12.6=18.1),PF119333=DUF3451=FE(53.4=100)
A:
NA
C2:
PF119333=DUF3451=PD(15.7=82.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTTTGAGGATAACGAGAGCCG
R:
ATTGCTCGTTGCCTTTGGGAA
Band lengths:
352-1596
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)