HsaINT0145964 @ hg19
Intron Retention
Gene
ENSG00000196876 | SCN8A
Description
sodium channel, voltage gated, type VIII, alpha subunit [Source:HGNC Symbol;Acc:10596]
Coordinates
chr12:52080875-52082633:+
Coord C1 exon
chr12:52080875-52081003
Coord A exon
chr12:52081004-52082541
Coord C2 exon
chr12:52082542-52082633
Length
1538 bp
Sequences
Splice sites
5' ss Seq
GGCGTAAGT
5' ss Score
9.39
3' ss Seq
ACTTTGGTTTGATTCTGCAGGTA
3' ss Score
9.14
Exon sequences
Seq C1 exon
GTACACGTTCACAGGGATTTATACATTTGAATCACTAGTGAAAATCATTGCAAGAGGTTTCTGCATAGATGGCTTTACCTTTTTACGGGACCCATGGAACTGGTTAGATTTCAGTGTCATCATGATGGC
Seq A exon
GTAAGTTCTCCCCTTACTTTATTGGTGTTCTGGGTGTGATTCTGTGTGTGGAGTTGTACTCCTGGGTCTGTTTGTAGGTGTGCATTTGTGGACACAGCTGTATGAGGAATTAATGGATAACCATGTAAGGCCCTGTGGGCTTATGTCTATGATTCTTGCTTGTGAGGGCCTCTTGTGGTTCAGGCGATGATAATGTGATTATGTGGGAGAAGGCAAGCAGAGGCTTTACAGCTGGGAGAGAAAGGAGGAGGTGATTTCCCATTGGCACTCTCTCGTATTTTATTCCTCCTTGTAACGATCACGGTTTGCACACCTATCATTACAAGGCCTCTGTGAAGACTTGAAATTTTTTAGTTGTAAACTTTCAGCTGAAAATTAGTTTCCTGGGTATGTCTTACCGTATGTAATTTAATAAGGCTGGCCAGGAGTTGCAGACTTCAGAGCACATTTTAGAGTCAAAACATGAGCCAAGGTACCCACACTGGCACTTCCTGAAGAGTTACTAACCAGAATTTCGAACTATTGCTCAAGATCAGTGTAACTCCACATTGGTATGTTACTGCTCTTGCTCATTTGTGTTGTTTTAGCAATAAAAATGTATCTTTGGGAAACTTAGCTGATGATAGAAGAGTTATAGCAGGCTTTAATATTTTTATTTCCAGGTTGGGAAAGCGTTTTGTGGTTTGAGAGTGTAGTGGGGGTGGTGTATAGGTTTTGCATGTATGCATGATGTGTAAGAAAGAGTGCATTTAAATATGTATTGATCTGAGCATCTGGTGGAAAGATGTATTTCAACTGTAAAATGTGAATAAATGATATGCATCGAATACTTGAAACTGAAACTGACTTTCTGTTATATAAAGGCAATGTCTTACTTTCTAGCATTATGAATACACATTAGTGTTCATTTAAAATTTTTAAGTGTCCTTGCTAGGCACAGAGCTTGTAATTAAAATGAGCACTTAACACAATATTTGCTCTGATCCCATGATTTGGATTTTCCTGAGCCCTGCTTTTGTATGTCACAGGCCAAAACTTCGTTTATAGACATGACTACAATCATATGATTACAACTCCTGATTAAGTCATATATACAGACATTTAGTCAATTTTGCCATTGTCAACTAGGGAGTTACTTTAATGTAGATTTGTTTTTGTGGGGCTCCTGCTGCAGAAATTTGTCTCCCTCTCTTAAGAAATTGTTCGCAAAACCTGGGAACATAAGTCTTTGATACCTCCTGGCCTTCCTTTTTACTAAAAAATGTGAATGGGCTGACAGTAAAGCCATTCTGATTGGGATCAGCACATTACTATGCTGATTAAAGGAGTAAATCCCAAAAACCTCCTTTCTAATATACTTTTGAATTCTTCTTGTCCAATTAAAAACAAATGTTCCTTAAATGTTTGTATTTTGAAGCTTTTCTTTTTCAAGGAAAAAAAATGAAACCATAGCTTGTATATAAGACCCTTTCTTCCCCCCATTCTCAAACCCTCGCCCAGTGGTACCATTACAAGTTAACTTTGGTTTGATTCTGCAG
Seq C2 exon
GTATATAACAGAGTTTGTAAACCTAGGCAATGTTTCAGCTCTACGCACTTTCAGGGTACTGAGGGCTTTGAAAACTATTTCGGTAATCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196876-SCN8A:NM_014191:5
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(17.1=100)
A:
NA
C2:
PF0052026=Ion_trans=FE(12.4=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTACACGTTCACAGGGATTTATACA
R:
TACCGAAATAGTTTTCAAAGCCCTCA
Band lengths:
214-1752
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)