HsaEX0060672 @ hg19
Exon Skipping
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:242011211-242021208:+
Coord C1 exon
chr2:242011211-242011293
Coord A exon
chr2:242012681-242012779
Coord C2 exon
chr2:242021092-242021208
Length
99 bp
Sequences
Splice sites
3' ss Seq
CACCGCCTGGCTTCTCCTAGAAC
3' ss Score
6.7
5' ss Seq
GAAGTGAGT
5' ss Score
7.97
Exon sequences
Seq C1 exon
GTTCTCGGAGCTTGTGGACGGCAGAGGAAGAGTGAGCGCCAGGTTCGGTGGCTCACCCAGCAAAGCAGCCACCGTGAGATCAC
Seq A exon
AACCCACAGCCTCGGCGCAGCTCGAGAACATGGAGGAAGCCCCCAAGCGGGTCAGCCTGGCCCTCCAGCTCCCTGAACACGGCAGCAAGGACATCGGAA
Seq C2 exon
ACGTCCCTGGCAACTGTTCAGAAAACCCCTGTCAGAACGGAGGCACTTGTGTGCCGGGCGCAGACGCCCACAGCTGTGACTGCGGGCCAGGGTTCAAAGGCAGACGCTGCGAGCTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804_CASSETTE6
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.971 A=0.918 C2=0.100
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
PF0000822=EGF=WD(100=77.5),PF055076=MAGP=PU(38.2=85.0)
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TTGTGGACGGCAGAGGAAGAG
R:
CGTCTGCCTTTGAACCCTGG
Band lengths:
178-277
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)