HsaEX0060665 @ hg19
Exon Skipping
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:242012681-242021208:+
Coord C1 exon
chr2:242012681-242012779
Coord A exon
chr2:242013728-242013813
Coord C2 exon
chr2:242021092-242021208
Length
86 bp
Sequences
Splice sites
3' ss Seq
CCCCGCCCTCACCATACAAGGTC
3' ss Score
5.57
5' ss Seq
CAGGTGTGG
5' ss Score
6.34
Exon sequences
Seq C1 exon
AACCCACAGCCTCGGCGCAGCTCGAGAACATGGAGGAAGCCCCCAAGCGGGTCAGCCTGGCCCTCCAGCTCCCTGAACACGGCAGCAAGGACATCGGAA
Seq A exon
GTCTGGACTTGCTGCTAGCCCCTGTGAGCACCAGGAGGACTGGTTTGTGCATCCGACGCAGAGAGTGAAGGATTCTCTTAATTCAG
Seq C2 exon
ACGTCCCTGGCAACTGTTCAGAAAACCCCTGTCAGAACGGAGGCACTTGTGTGCCGGGCGCAGACGCCCACAGCTGTGACTGCGGGCCAGGGTTCAAAGGCAGACGCTGCGAGCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804-'41-47,'41-46,43-47
Average complexity
C1
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.918 A=0.455 C2=0.100
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
PF0000822=EGF=WD(100=77.5),PF055076=MAGP=PU(38.2=85.0)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
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:
GCTCGAGAACATGGAGGAAGC
R:
CTGCCTTTGAACCCTGGCC
Band lengths:
183-269
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)