HsaINT0155903 @ hg19
Intron Retention
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:242021092-242021779:+
Coord C1 exon
chr2:242021092-242021208
Coord A exon
chr2:242021209-242021691
Coord C2 exon
chr2:242021692-242021779
Length
483 bp
Sequences
Splice sites
5' ss Seq
TCGGTAAGT
5' ss Score
11.78
3' ss Seq
ACTGCCCTTCTTTGTCGCAGCCT
3' ss Score
8.5
Exon sequences
Seq C1 exon
ACGTCCCTGGCAACTGTTCAGAAAACCCCTGTCAGAACGGAGGCACTTGTGTGCCGGGCGCAGACGCCCACAGCTGTGACTGCGGGCCAGGGTTCAAAGGCAGACGCTGCGAGCTCG
Seq A exon
GTAAGTCGGGGCTTGGCCTCAGGGCGCCCCTTCCAACACAGCCTGTGCCTCAGCCTAGGACTGCTGGGCCACAGCTGGGTTTGCCACGGGAGCCTCCAAACGATGAGGTGCCAGACAGGGAGTCTGGTGCACGGGGCTGACCCCTGAGCCCCCAGGGGCTGCGCTGCTGCCCCAAGCACCAGGATGAGAGGTGCTGCCCATCACGGGGGTCAGAACAGCCACAGCATGCGAGGCACAGCTTCGGAGGGCTCCCTGACCCAGCCAGAGCGGTGTCAGGAGAAGGGACTCTCCACCCCCACAATACCAACCCACCCCGGCCTTAGAGGAAGCCAGCTGCAGACCCCCGGGCCCTCTCCCACCATCCCGCCTTGGAGGAAGCCAGCCTAAGGACCCCCGGGCCCTCTCCCTTGGGCAAGGCCTCTCAAGAGGGGCAGGAGGAGCCGTCAGGAGCACCTGGTGAGCCACTGCCCTTCTTTGTCGCAG
Seq C2 exon
CCTGTATAAAGGTGTCCCGCCCCTGCACAAGGCTGTTCTCCGAGACAAAGGCCTTTCCAGTCTGGGAGGGAGGCGTCTGTCACCACGT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804-SNED1:NM_001080437:28
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.100 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=77.5),PF055076=MAGP=PU(38.2=85.0)
A:
NA
C2:
PF055076=MAGP=FE(32.6=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTCCCTGGCAACTGTTCAGAA
R:
GGTGACAGACGCCTCCCT
Band lengths:
199-682
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)