HsaALTA1039996-3/4 @ hg38
Alternative 3'ss
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr2:241063587-241064125:+
Coord C1 exon
chr2:241063587-241063700
Coord A exon
chr2:241063968-241064033
Coord C2 exon
chr2:241064034-241064125
Length
66 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGG
5' ss Score
9.46
3' ss Seq
TCCTCTCCTCCCTCCCCCAGACT
3' ss Score
11.44
Exon sequences
Seq C1 exon
AGAGGGATGAGTGCCGAGCTCACCCGTGCAGAAATGGAGGGTCCTGCAGGAACCTCCCAGGGGCCTATGTCTGCCGGTGCCCTGCAGGCTTCGTTGGAGTCCACTGTGAGACAG
Seq A exon
ACTCCCCCCTTGCAGCTTGGGCCCACTCTCTGGGTGTTCTCCAGAGGTGGACGCCTGCGACTCCAG
Seq C2 exon
CCCCTGCCAGCATGGAGGCCGGTGTGAGAGCGGCGGCGGGGCCTACCTGTGCGTCTGCCCAGAGAGCTTCTTCGGCTACCACTGCGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804-54-60,54-59,54-58,54-57-3/4
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=79.5)
A:
NA
C2:
PF0000822=EGF=WD(100=79.5)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GTGCAGAAATGGAGGGTCCTG
R:
AGTGGTAGCCGAAGAAGCTCT
Band lengths:
172-238
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains