HsaEX0060661 @ hg19
Exon Skipping
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:241979717-241987857:+
Coord C1 exon
chr2:241979717-241979830
Coord A exon
chr2:241983837-241983947
Coord C2 exon
chr2:241987732-241987857
Length
111 bp
Sequences
Splice sites
3' ss Seq
CTCTCCCCCACTGAATACAGCTA
3' ss Score
4.15
5' ss Seq
GTGGTGAGT
5' ss Score
8.95
Exon sequences
Seq C1 exon
ATGTGGACGACTGCAGCCCTGACCCCTGCCTGAATGGAGGCTCTTGTGTTGACCTAGTGGGGAATTACACCTGCTTGTGTGCCGAGCCCTTCAAGGGACTTCGCTGTGAGACAG
Seq A exon
CTACAATCCTGGACAGAATGCATGGAGTAGCTGTCAGAGGACTCTGAAAAGTAAATAGTAGCAGGTGGATTGGGGAAGAAGACCAAGCTTCGAAGTACCACCAAACCAGTG
Seq C2 exon
GAGACCATCCAGTGCCAGACGCCTGCCTCTCGGCCCCTTGCCACAATGGGGGCACCTGTGTGGATGCGGACCAGGGCTACGTGTGCGAGTGCCCCGAAGGCTTCATGGGCCTGGACTGCAGGGAGA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804-'14-20,'14-18,16-20
Average complexity
S*
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion
Show structural model
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=79.5)
A:
NO
C2:
PF0000822=EGF=WD(100=72.1)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
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:
ATGTGGACGACTGCAGCCC
R:
TGCAGTCCAGGCCCATGAAG
Band lengths:
234-345
Functional annotations
There are 0 annotated functions for this event
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)