HsaINT0145778 @ hg19
Intron Retention
Gene
ENSG00000144285 | SCN1A
Description
sodium channel, voltage-gated, type I, alpha subunit [Source:HGNC Symbol;Acc:10585]
Coordinates
chr2:166868619-166870408:-
Coord C1 exon
chr2:166870254-166870408
Coord A exon
chr2:166868793-166870253
Coord C2 exon
chr2:166868619-166868792
Length
1461 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
GTGTAACATTTTCTTTATAGGCA
3' ss Score
8.16
Exon sequences
Seq C1 exon
GCTGTGTACAAAGATTCAAGTGTTGTCAAATCAATGTGGAAGAAGGCAGAGGAAAACAATGGTGGAACCTGAGAAGGACGTGTTTCCGAATAGTTGAACATAACTGGTTTGAGACCTTCATTGTTTTCATGATTCTCCTTAGTAGTGGTGCTCTG
Seq A exon
GTGAGTGAGATTAAGAAAAGGTGATACAGCACTAATTTTTAGAACACTCTAATACTGATGACTTATTAATCCTTTGTTTCATTGTCTTAGTATCCAATGCATTTTTAATTATCCCACCTTGTATCTTCTATAGATTTACTCTATAACTCTATATTTCTGGATTAACTTTTACTATGTATGTAAATATAATTTTAAGAAGCTAATCATTAATTTTTGCTTACTATTAAATAGCCCAGAAAGTGTAGCCCTTCAGCTTATTCATTAACACCAAAGGATGTGAATATTCAATTACTCATTGTTTAATTAAAAAAAGTTATTGGAAGCCCTGGGATGGGAATATATATTCTCTGAGTTCTGACGAATTTTGTTTCTAAATGGTATTTATTATTATTATCTCTTGATGGACAGTAGTAAGTCCTTAGGGACCACTTCTCTGTCTTTTTCCAATTGTGTGCTCACTATTTTTGTGCTACTTAAGAAATAATGAAAGTTGGTAACAATAAATATTGGGCAGCATGCCCAAGAGATTCATTTAAGGATGGGTTTATCTTTATAACAAGGTGTTCACTTCATCAGAATCAATTTATTTTTATAGGAAAATTATTTATAAAACTATAAATAAAACATACAGATAGCATTTTAGGGAAACACTAACACAAAGGAAATACCATAGATAGAAAAAGAGAAAGAAAGAGAGAGAAACAGAGTTTGCCTGATTGAAATGCAAGTGTGTTACAAGTTTAACTTTTTATAATTCTAACACAGACATATATTTACCTGTAATTTTTCTGAAGAAAGAAATATTTTCTACACGCTACTTTAGAAGTCTTTCACCGTTGAAAGGAATGCATACTTAGAAGTGAAACATCGAGAGGTTCATAATAGAAGAATATATATTAGAATCTAAATGAAAAGTAATTTCATTTAATCATTGTCACACTGTATGTCTGTTGAGAAACATAAATTATTAAAAAAATAACAAACAACAACAAAAAAGAAGCAGATGAACCCAACTATTTAGTCAAATTGGAGACTGCGAAGATCAATCACAATTTCTGCTTTACAAAAGCACAAGCTTTCATTATTTCTTCAACCTCCTTTCTATAGCAAAAAAAAAAAAAAAAAAAAAAAGCCAATAGAAGGAAGCAAAATAAATGAAACAAAAGGAATACATAACTTCAAGTTGGGATGGCCACATCAGGATACAACATCAAGAACTATTTCCTGACTAAGTCAAATTAATTCATTGGAATCATACTTTTCTTTTTCTTCCACCAATAGTCTTTCCCCTGATTAAATAAGTAAAAGACCTTTGCGAGGAAAAAAAAAAAGTAACAGTAACTACTGTTTCTCTGCCCTCCTATTCCAATGAAATGTCATATGCATATGATTAATTTTTTAAATAGCTTATGGAGTATAATTATTTTTGAAAGCTAATAATGTGTAACATTTTCTTTATAG
Seq C2 exon
GCATTTGAAGATATATATATTGATCAGCGAAAGACGATTAAGACGATGTTGGAATATGCTGACAAGGTTTTCACTTACATTTTCATTCTGGAAATGCTTCTAAAATGGGTGGCATATGGCTATCAAACATATTTCACCAATGCCTGGTGTTGGCTGGACTTCTTAATTGTTGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285-SCN1A:NM_001165963:18
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:
PF065128=Na_trans_assoc=PD(19.7=84.6)
A:
NA
C2:
PF0052026=Ion_trans=PU(17.0=67.2)
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:
GCTGTGTACAAAGATTCAAGTGTTGT
R:
TCAACAATTAAGAAGTCCAGCCA
Band lengths:
328-1789
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)