HsaINT0145773 @ hg19
Intron Retention
Gene
ENSG00000144285 | SCN1A
Description
sodium channel, voltage-gated, type I, alpha subunit [Source:HGNC Symbol;Acc:10585]
Coordinates
chr2:166895933-166897979:-
Coord C1 exon
chr2:166897741-166897979
Coord A exon
chr2:166896107-166897740
Coord C2 exon
chr2:166895933-166896106
Length
1634 bp
Sequences
Splice sites
5' ss Seq
TTGGTAAGC
5' ss Score
8.72
3' ss Seq
TAATTTTGTTTTGATCTTAGGTT
3' ss Score
7.51
Exon sequences
Seq C1 exon
AACTTGAAGAATCCAGGCAGAAATGCCCACCCTGTTGGTATAAATTTTCCAACATATTCTTAATCTGGGACTGTTCTCCATATTGGTTAAAAGTGAAACATGTTGTCAACCTGGTTGTGATGGACCCATTTGTTGACCTGGCCATCACCATCTGTATTGTCTTAAATACTCTTTTCATGGCCATGGAGCACTATCCAATGACGGACCATTTCAATAATGTGCTTACAGTAGGAAACTTG
Seq A exon
GTAAGCATATTGGAAGGTAAATGTGTTTAGTCTTCAAATTTTCTGCTTGAAAAACTGTTTACATTTAATTGTGTATAGCAGTCTTTCAACCATCCTTCATGCTTCCTGGCCCCTGCAAAATCGCAATTATATTTAGCTGGCTATACTCTACTTTTTTGCCAAAAATAATCACCCTTAATGTGCTCACAAAAACTGAGAAAGGCATAGGCCTACAGCACTACTTGAAAAGTCAACAGCAATATTTATAATTTTTCAGGATCCAGAAGTAGCTCATAGATTAAGAACATACTTTTTGAGATATTATTACAATTTCCCTTACTGTAGAAGATTAAAATAAAATTGTGGATCTCTTTTATCCTTCTTAGTCATCATCACTGCAAGAAATAATTTAACAACTCAAAAATGTCTCCAGCTTTTCCTCTTCCAGGATCTAAGTAGTACATGTATTGTTTATCCATCTATTCTATATCAAAACCATGAACTATTGAAAACTTCCAGTACATTTTGTGTGTTATATGATTACAAAGGTCATTTTTGGTGAAGATTGCCACTTAATTTTTCCTTTTTGTGCTTCAAAAACATAAATTATTAAAGTGTTTGCCAGTCAACTCAACTTAGGAATACTAGCTTTTATTTGCTGAAGGAAAGAGCTATCTAAAGTAATTTATGCATTTCCTGTAATATTTGGTTTGAAGTTTAGGATTTTTGATGGTAGAAAACAAAAGCATCATGCATAACAACCTGCATTTTATTAGTTATATTTTTGAAGTTCTACTATTTATACTACAGAAGTAAATTTATTTTTTTCATGTGCATAACAAAGAATGACAATAGTAATGCACCTAGTATAATAGATAAGAATGTATAACTCTGATTGAGGGAAATAGGAATAAGCTTATAGATAAATAAAAGTGCTCATGGGCAAAATGTTGTCAGTACTTGTGGTATATAAAGTCTGGACAAAAAGGTAGTTTGGTATAATGGAAAGAGCACTGTTAAAAATAGATGACTTGGGCTGGGCGCAGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGACGGATCACGAGGTCAGGAGATCGAGACCATCCTGCCTAACATGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGGCGGGCGTGGTGGCGGGCGCCTGTAGTCCCAGCTACTCGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCAGGAGCTTGCAGTGAGCCAAGATGGCACCACTACACTCCAGCCTGGGCGACAGACTGACACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGATGACTTGTACTCAAATCCTAGTTTTGCCATTTTCTTGCTGTATGATATCAAGCAAGCCATTTCACCCATCTGAAGACCTCAGTTTCCTTATCTGTAAAGTAATAATTGTATATTATCTACTTCGCGTTTCCACAAGGATAAAATTAAATAATGTATATGAAAGTCTTTCATCAACTACAAATTGCCATACAAATTTAAGTTAGTAATAGAATCATTGTGGGAAAATAGCATAAGCATTATGTTCTAAGAGCAAATCTTATGTCATGTATGTTATTATCTGGTGGAATTAGATTAATTTTGTTTTGATCTTAG
Seq C2 exon
GTTTTCACTGGGATCTTTACAGCAGAAATGTTTCTGAAAATTATTGCCATGGATCCTTACTATTATTTCCAAGAAGGCTGGAATATCTTTGACGGTTTTATTGTGACGCTTAGCCTGGTAGAACTTGGACTCGCCAATGTGGAAGGATTATCTGTTCTCCGTTCATTTCGATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285-SCN1A:NM_001165963:13
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=PU(1.6=3.8)
A:
NA
C2:
PF0052026=Ion_trans=FE(30.0=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:
CAGAAATGCCCACCCTGTTGG
R:
TGGCGAGTCCAAGTTCTACCA
Band lengths:
358-1992
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)