HsaEX0062042 @ hg19
Exon Skipping
Gene
ENSG00000136840 | ST6GALNAC4
Description
ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4 [Source:HGNC Symbol;Acc:17846]
Coordinates
chr9:130676935-130679305:-
Coord C1 exon
chr9:130679105-130679305
Coord A exon
chr9:130678687-130678773
Coord C2 exon
chr9:130676935-130677120
Length
87 bp
Sequences
Splice sites
3' ss Seq
GAGTTTCTGGGTCTTGGCAGGTG
3' ss Score
7.33
5' ss Seq
CCGGTAAGT
5' ss Score
10.91
Exon sequences
Seq C1 exon
GCGCGGATCAGCTTCCAGCCCAGTCGGCCCGGCCCGGGGGCCATGGAGCTCCGAGCGGCGGATCGCGAGCCTCCTGCGAACCCCAGCCTGCACGCCCGGTTAGCATTCGGCCGGGAGATGCGGCAGTGGAATCTGGAAGGGCGGTGAAAAACCTACGTCCTGCCCTCGCCCGGCCTCTCCATTCGTCCCCCGGGTAGAGAG
Seq A exon
GTGCCCGGCTCCCACCCCTTCCCAGCCCCAGCCCTGGAGACAGCAGCCCCTAGACTACTGAGGGACAGCGACAGCATGAAGGCTCCG
Seq C2 exon
GGTCGGCTCGTGCTCATCATCCTGTGCTCCGTGGTCTTCTCTGCCGTCTACATCCTCCTGTGCTGCTGGGCCGGCCTGCCCCTCTGCCTGGCCACCTGCCTGGACCACCACTTCCCCACAGGCTCCAGGCCCACTGTGCCGGGACCCCTGCACTTCAGTGGATATAGCAGTGTGCCAGATGGGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000136840_MULTIEX1-1/2=C1-2
Average complexity
S*
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref, Alt. ATG (>10 exons))
Show structural model
Features
Disorder rate (Iupred):
C1=NA A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
NA
A:
NO
C2:
PF0077713=Glyco_transf_29=PU(5.3=21.0)
Main Skipping Isoform:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTAGCATTCGGCCGGGAGAT
R:
AGCAGCACAGGAGGATGTAGA
Band lengths:
169-256
Functional annotations
There are 1 annotated functions for this event
PMID: 32249828
This event
[CRISPR screen]. This alternative exon is implicated in cell fitness by a CRISPR-based exon deletion phenotypic screen in RPE-1 cells.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- 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)