HsaINT0155909 @ hg19
Intron Retention
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:241979492-241979830:+
Coord C1 exon
chr2:241979492-241979605
Coord A exon
chr2:241979606-241979716
Coord C2 exon
chr2:241979717-241979830
Length
111 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
GCACCTCTGCTGCCCCTCAGATG
3' ss Score
7.92
Exon sequences
Seq C1 exon
CCCAATCCCCCTGTGACACCAAAGAGTGTCAACATGGTGGCCAGTGCCAGGTGGAGAATGGCTCTGCGGTGTGTGTGTGCCAGGCCGGATACACCGGAGCAGCCTGCGAGATGG
Seq A exon
GTGAGTGGCCTGGCTTCGGATTGGAGAGGGGCTCCTGCCCGTGGCCAGGTGCTGGGCACAGGGTGGTTGTGGCCTGGCTCAAGCCAAGCCCGCACCTCTGCTGCCCCTCAG
Seq C2 exon
ATGTGGACGACTGCAGCCCTGACCCCTGCCTGAATGGAGGCTCTTGTGTTGACCTAGTGGGGAATTACACCTGCTTGTGTGCCGAGCCCTTCAAGGGACTTCGCTGTGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804-SNED1:NM_001080437:7
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=76.9)
A:
NA
C2:
PF0000822=EGF=WD(100=79.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CAATCCCCCTGTGACACCAAA
R:
CTGTCTCACAGCGAAGTCCCT
Band lengths:
226-337
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains
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)