HsaINT0145944 @ hg38
Intron Retention
Gene
ENSG00000196876 | SCN8A
Description
sodium voltage-gated channel alpha subunit 8 [Source:HGNC Symbol;Acc:HGNC:10596]
Coordinates
chr12:51705417-51706715:+
Coord C1 exon
chr12:51705417-51705623
Coord A exon
chr12:51705624-51706421
Coord C2 exon
chr12:51706422-51706715
Length
798 bp
Sequences
Splice sites
5' ss Seq
CAGGTTGGT
5' ss Score
8.08
3' ss Seq
TGCTGTGGCTTCTTTCCTAGGCT
3' ss Score
8.65
Exon sequences
Seq C1 exon
ACTTTACGAGCAGCCGGGAAAACATACATGATCTTCTTCGTCTTGGTCATCTTTGTGGGTTCTTTCTATCTGGTGAACTTGATCTTGGCTGTGGTGGCCATGGCTTATGAAGAACAGAATCAGGCAACACTGGAGGAGGCAGAACAAAAAGAGGCTGAATTTAAAGCAATGTTGGAGCAACTTAAGAAGCAACAGGAAGAGGCACAG
Seq A exon
GTTGGTGATGAATTCTTTGCAATAGACCTTCCTGCCAGATCATGGTGACTAAGACCCCATCTGATTTTCACTGCAGTTGATCTTTTCTAGGCATATTTTCAAATAGAGGCCATTGGTCTGATGAAAATAACCCAAGTAACAACTGCAGATGGTTGCTCCAATTATTCCATTTGTCTTAACAGCCAAATTGTTTGTTCATATCATCTTTTGTTGAATTGCTCAACTGTTCAGTGTGCAACCGCCATGATGACTGGGAAGAAAAAAGTGACCAGGGCAGTTTATATAGTGTTTCACATAAGCATATTCTTTTTCTTGGGAGAAATGTTAAGATTCCTGTGGTCATAAAAAGTATTATTTCTAATTAAAAAGAAGATACAGGCAAAATATTAAAGTAAAACTTGAAAGACATTTGTGATCTCATCACCTTAACACTTAACTTTCTCATCCTTATCTAAATGTACATGTATTTATACATTTTTAGGACCCATAATATATAATGTTACTTAGCATTCATTTCCAGACTTGCTCAGAAGGGATCCTCTGGTACCAAGGCAGCAGTCAAGTTCTTGTCTGAAATGCTCAAGAGAATAACTCCCAAAGTTCTCACCACTGGGTTCTGCTCTGTTCACTTAGGGCTGTGTGCCAGAATACACAGAAACCCTCTAACAGTCTAGGTTTCCTGCCTCCTTTTTTCCTCCTTTCCCTTCAGTAGGGAAATGTTCTGTACTAACTGGTTGGCTTTGGGTGGCTCCAGTTAATTGCCCTGGTCTGGCTTCCCTGCTGTGGCTTCTTTCCTAG
Seq C2 exon
GCTGCTGCGATGGCCACTTCAGCAGGAACTGTCTCAGAAGATGCCATAGAGGAAGAAGGTGAAGAAGGAGGGGGCTCCCCTCGGAGCTCTTCTGAAATCTCTAAACTCAGCTCAAAGAGTGCAAAGGAAAGACGTAACAGGAGAAAGAAGAGGAAGCAAAAGGAACTCTCTGAAGGAGAGGAGAAAGGGGATCCCGAGAAGGTGTTTAAGTCAGAGTCAGAAGATGGCATGAGAAGGAAGGCCTTTCGGCTGCCAGACAACAGAATAGGGAGGAAATTTTCCATCATGAATCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196876:ENST00000354534:10
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.116 A=NA C2=0.898
Domain overlap (PFAM):
C1:
PF0052026=Ion_trans=PD(12.4=44.9),PF0310514=SPX=PU(19.3=58.0)
A:
NA
C2:
PF0310514=SPX=FE(46.9=100),PF119333=DUF3451=PU(31.3=68.4)
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:
CAACACTGGAGGAGGCAGAAC
R:
TATTCTGTTGTCTGGCAGCCG
Band lengths:
350-1148
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