HsaEX0060671 @ hg19
Exon Skipping
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:242009335-242011293:+
Coord C1 exon
chr2:242009335-242009616
Coord A exon
chr2:242010991-242011135
Coord C2 exon
chr2:242011211-242011293
Length
145 bp
Sequences
Splice sites
3' ss Seq
TCCTCCTGCCTGCTCTGCAGCCC
3' ss Score
8.41
5' ss Seq
CAGGTACAT
5' ss Score
7.79
Exon sequences
Seq C1 exon
GGCCCCTGCCTCCAGCAAACCTGACCGCCGCCCGAGTCACTGCCACCTCTGCCCACGTGGTCTGGGATGCCCCGACTCCAGGCAGCTTGCTGGAGGCTTATGTCATCAATGTGACCACCAGCCAGAGCACCAAGAGCCGCTATGTCCCCAACGGGAAGCTGGCGTCCTACACGGTGCGCGACCTGCTGCCGGGACGGCGGTACCAGCTCTCTGTGATAGCAGTGCAGAGCACGGAGCTCGGGCCGCAGCACAGCGAGCCCGCCCACCTCTACATCATCACCT
Seq A exon
CCCCCAGGGATGGCGCTGACAGACGCTGGCACCAGGGAGGACACCACCCTCGGGTGCTCAAGAACAGACCGCCCCCGGCGCGCCTGCCGGAGCTGCGCCTGCTCAATGACCACAGCGCCCCCGAGACCCCCACCCAGCCCCCCAG
Seq C2 exon
GTTCTCGGAGCTTGTGGACGGCAGAGGAAGAGTGAGCGCCAGGTTCGGTGGCTCACCCAGCAAAGCAGCCACCGTGAGATCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804_CASSETTE5
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence exclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.326 A=0.997 C2=0.971
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=86.3)
A:
NO
C2:
NO
Main Skipping Isoform:
NA
Other Inclusion Isoforms:
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAATGTGACCACCAGCCAGAG
R:
GATCTCACGGTGGCTGCTTTG
Band lengths:
257-402
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)