HsaINT0145959 @ hg19
Intron Retention
Gene
ENSG00000196876 | SCN8A
Description
sodium channel, voltage gated, type VIII, alpha subunit [Source:HGNC Symbol;Acc:10596]
Coordinates
chr12:52183065-52184286:+
Coord C1 exon
chr12:52183065-52183202
Coord A exon
chr12:52183203-52184181
Coord C2 exon
chr12:52184182-52184286
Length
979 bp
Sequences
Splice sites
5' ss Seq
AAGATAGGT
5' ss Score
2.1
3' ss Seq
TTTCTTCTTCCCTCCTTTACTTC
3' ss Score
2.8
Exon sequences
Seq C1 exon
CCTGATGAGCAGCCTAAGTATGAGGACAATATCTACATGTACATCTATTTTGTCATCTTCATCATCTTCGGCTCCTTCTTCACCCTGAACCTGTTCATTGGTGTCATCATTGATAACTTCAATCAACAAAAGAAAAAG
Seq A exon
ATAGGTCTCCTCCCCTCATTGCCAGTGGTTGGAAGTCAGCCCAGATAAGAGGCACCTTTGTCCCTATCTCTAGAAAGAAAATGTCCCTCTTTCTTTCTCTAAAATCTATATTGTTAGCTCACTGTGACCCTGGCCCCCATACGTTAGCCCCAACCCACTCTTTCTGTTCGGGGCTGGATTTTGCAGCATGTAGTTTACCACACTTACTAGCAGTCTTTTATTCTTGAGGCCTATTACTGGTCTTGGTCTCCCACCAGAAGCAGGTAGGTCAGAGAGTGCAGTCGAGCAACAGAGATGAAAAGGAAAGAAACAGATGAATAGCTATCGCAAGAAGTAGAAACTGTCTAGACTTGTGATTATCTAGTCAATCTCTGAGCACAAGCAAATTGGGATTTGAGAGACCCACCTTTGGAAAGTTTACTTCCTTACTTGTTCTAGATGGTTAACAAGTTTTACAAAGCAAATTGAAAAAATTGCTCGTTGCTCATTTTGTAAGTCAAGTCTATCCCAGCATACTCCAAGACACCCTCCAAATTGCTTTCTTGCACCAGAATTTCCAAATTTTGGGTATCATCTAAAATAAATTGGCTATCAGCCAGGACACAAAGATCTTTTTATTCTAAAATGTGTTTTCTAGAATGTATCAGGAAAGCTGGCCCCCAGAAAATGAGACTCTGAGATATGACTGCCTTCAGAGTCACTGCTCTCAAGTTTACCCTTTCTGAGGGTCTATAATTGGATAGTCCATTTCCTTTCTACCTTGGGACTGGAAGATCTTAGAAATCCTGAGCTAAAAACAAAGGCAGGTATCTCTTTAGAGCTGAATGATTATCGCGGGTCTACCCCACTCTGGGACAGCTATTAGCTACAAAGGAAAGGGATAGGTCTCCCCTCAGTTCTCAGTATTGAACCTTAGGTCCAAACCCATAGCATGTTGAGAGCCAGTTGTAATTGTCTGTTTTCTTCTTCCCTCCTTTAC
Seq C2 exon
TTCGGAGGTCAGGACATCTTCATGACCGAAGAACAGAAGAAGTACTACAATGCCATGAAAAAGCTGGGCTCAAAGAAGCCACAGAAACCTATTCCCCGCCCCTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000196876-SCN8A:NM_014191:24
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=PD(23.2=76.1)
A:
NA
C2:
NO
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:
CCTGATGAGCAGCCTAAGTATGA
R:
GGCGGGGAATAGGTTTCTGTG
Band lengths:
238-1217
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)