HsaINT0145780 @ hg19
Intron Retention
Gene
ENSG00000144285 | SCN1A
Description
sodium channel, voltage-gated, type I, alpha subunit [Source:HGNC Symbol;Acc:10585]
Coordinates
chr2:166912921-166915198:-
Coord C1 exon
chr2:166915078-166915198
Coord A exon
chr2:166913009-166915077
Coord C2 exon
chr2:166912921-166913008
Length
2069 bp
Sequences
Splice sites
5' ss Seq
CATATCCTT
5' ss Score
-20.06
3' ss Seq
TCCTTAACAATAACCTACATTAT
3' ss Score
-5.01
Exon sequences
Seq C1 exon
ACTTTTATAGTATTGAATAAAGGGAAGGCCATCTTCCGGTTCAGTGCCACCTCTGCCCTGTACATTTTAACTCCCTTCAATCCTCTTAGGAAAATAGCTATTAAGATTTTGGTACATTCAT
Seq A exon
ATCCTTTTTCAAGTGATTAATATTAACTATTTGTACATGATCTGTAAGCACTTTATAGCTAAATATCAAATTAAGTTGGGAAATGTCCATATTATATAGTTTTCATCACTCTCATTTTGCATCTTTGTCATATTAGCCTCATTCTTAAAGTTCATTAATCACATAGACATTACTGAAACATGTACTCTTTAACATTTTATATATTATATATAAACATGTATTTATGTACTTTTGTTATCTTTCTAAAAACACTTATATGTATTGAATCCTACAAATCTAAAGTAAGATAACCATGTTTACCTCTACCATCTTTATACAAAGTTTGTGATGGTGTAGAATTTTCAGTGAGCAATGATATGATAACAGAAAAATCTACTTCCAGACTCAAGTTTATCCATAGTTATGATATAAAACACTTCAGTGTATCTTAGAATAAACCTTTAAGTATATTTTCTGTCAGAGAATGTCAGGAGTCTTTGGCCAGTACTTAGTTAATTCTTGAAATTTCCTGATGATTTTTGTGAAGGAAGTACTGGAATATTGGCTGAATTTCAAATTCAAGTCATGAGTTATGATGCTGCCATGCAAAACTGTTTGCTTAGTAAAGACTCCGGAAGTTAATGAGAGAAGTTGGCATATATTTCCAAATGGTCTTAAGGGATTTGGTTTCATGATTCCCATTGGTGTTAAAAAGGACTCCACGACTAAATTCATTTGTTAATCAATTTAGGAAAACAATTCACTTCTGATTGTATCTTGTTTGATAGCTTTGACAATAATAGATATTAAAATACCATTATAATTATCATAAGCTCATACTTTTTTTTAAAGGATTCTAAAATTTGAACGGCCATTCTAATTTTAATATGACAGCAAGAAATTTCTTTAGTGGTATAAATATGCTATTACTAAAATTAAAAGATTTGAAACATAAAAATCATATGATAGGGTTTTTATACTTAGGGAAGTTTCCTTGTCCCAGTTTGTATTCCTAGCGCCATCATGTGGTCATTTGATGAAAACTTTCTTTTTCAATTATGGAAAATTTTTGTTTTGGCAGTAAACTATAGTGGAAAGAATATTGGATCTTAATGTAGGAAACTTATATTCTAGTCCTGGACCCTTTATCTGATTCCTCTAGAGCTTAGTAAGGCCTTATTTCCCTGATTTTTAAAATATAGTGATAAACTAATTTTTAGGGTCCCTTTCAGTTTTATAATTCTGTTATGTCTGTTCATTTGTTTTAGCTACCACTTAGAGTATATTTACTTACGTACCGTGACTGTTCCAAGCATTTCCAATACATTAACTCATTTAATCTGCATGTAGAAATGGTTACATTACAAAATGAGTACATTATTAGCTCCATTGTAGAGAAGTAGGAAGAGATACAAGGCAATGGCACAGAGAGGTTGAGTCTCTTGGCCAACATCACTTTGCTATGTTGAATTTTAATTACATTCCCATCATGTTAAGTGTCAACCTTCAAGAATATTCACTTTTAATGTTATCGAATCCTGCTGCACTTGTATAAACTCAGTCAAAATAGAGCAACCCAACAATTAGCATCGTGCTGTACTTTGACTACAAATTGTTTTCATGCGTTGAACTGTGTTGGATAAGATGTGTTTAAGAAATTACAATATTGCAGATAAGTGGCCTTCCTCAACAATTTACTAGTTTATTCACCTGAATGAGCTCAAGTCAATACTTTCTGCTGAAAAACTGTGCAACTCCAGGTAGCACAAAAATAGTCTTCCCACTGAAGTTCTCTGGGAGGTGAATATATTGATTTAATAATAGTTGTAAAAACAACACCTTATACTGATATAATGCTTTCATATACATTACCTCATTTAATCTATACAAATACTCAGTGAAGGTGATATTATTACCCACATTTTACACATGAAGAAATTGAAATGTAAGGAGATTAGAAGACTTGCCCACAATGCATTTATCCCTGAATTTTGGCTAAGCTGCAGTTTGGGCTTTTCAATGTTAGCTTTTTGTAATATAACACTTGGATTTTGATTTTCTTTTGTGTGTTCCTTAACAATAACCTACAT
Seq C2 exon
TATTCAGCATGCTAATTATGTGCACTATTTTGACAAACTGTGTGTTTATGACAATGAGTAACCCTCCTGATTGGACAAAGAATGTAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000144285-SCN1A:NM_001165963:2
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:
NO
A:
NA
C2:
PF0052026=Ion_trans=PU(0.7=6.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
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)