HsaEX0060669 @ hg19
Exon Skipping
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:241992570-242003117:+
Coord C1 exon
chr2:241992570-241992743
Coord A exon
chr2:242002208-242002321
Coord C2 exon
chr2:242003004-242003117
Length
114 bp
Sequences
Splice sites
3' ss Seq
CTTGGGCTCTCTCCTCTCAGAAA
3' ss Score
9.77
5' ss Seq
TGGGTAAGA
5' ss Score
8.91
Exon sequences
Seq C1 exon
AGGTGGACTGCGGCCCCCCGGAGGAGGTGAAGCACGCCACACTGCGCTTCAACGGCACGCGGCTGGGCGCGGTGGCCCTGTATGCATGTGACCGTGGCTACAGCCTGAGCGCCCCCAGCCGCATCCGGGTCTGCCAGCCACACGGTGTCTGGAGTGAGCCTCCCCAGTGCCTTG
Seq A exon
AAATCGATGAGTGCCGGTCTCAGCCGTGCCTGCATGGGGGCTCTTGTCAGGACCGCGTTGCTGGGTACCTGTGCCTCTGCAGCACAGGCTATGAGGGCGCCCACTGTGAGCTGG
Seq C2 exon
AGAGGGATGAGTGCCGAGCTCACCCGTGCAGAAATGGAGGGTCCTGCAGGAACCTCCCAGGGGCCTATGTCTGCCGGTGCCCTGCAGGCTTCGTTGGAGTCCACTGTGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804_CASSETTE3
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
Alternative protein isoforms (Ref)
Show structural model
Features
Disorder rate (Iupred):
C1=0.000 A=0.000 C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
PF0000822=EGF=WD(100=79.5)
C2:
PF0000822=EGF=WD(100=79.5)
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCACACTGCGCTTCAACGG
R:
TCTCACAGTGGACTCCAACGA
Band lengths:
249-363
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)