HsaINT0155895 @ hg19
Intron Retention
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:242004260-242005011:+
Coord C1 exon
chr2:242004260-242004373
Coord A exon
chr2:242004374-242004714
Coord C2 exon
chr2:242004715-242005011
Length
341 bp
Sequences
Splice sites
5' ss Seq
AAGGTGGGT
5' ss Score
8.23
3' ss Seq
TTTTGACCCAAACCCTGAAGAGC
3' ss Score
0.53
Exon sequences
Seq C1 exon
TGAGTGACCCCTGCTTCTCCAGCCCCTGTGGGGGCCGTGGCTATTGCCTGGCCAGCAACGGCTCCCACAGCTGCACCTGCAAAGTGGGCTACACGGGCGAGGACTGCGCCAAAG
Seq A exon
GTGGGTGGCGAGGGCGCCTCCAGTGAGGGAGCCACGAGGGGGTCCCCTCTCCCTAGAGGGCCCAACGGTCTCCAAGGGCAGAGCGTCTGGCCGCTGCTTGCCCAGGCCCCTTCCCTGAGGAACAGGGAGGGGATAAAATCCCCCGGTGGGCTTGAAACACGGTCACACATTCAAAAGTGTGACCCTCCTGGAGGTACGTGGCCAGGGACAAAGAAGGACTCTGCCAGCGATGGCTGTGTCAGGCCCAAGAGCCAGACCCGGCTGAGCCGCCGACGGGAGCCAGGCATGCATAGCTAACGGCTGACCAGTCCCCTCCCCTTGTTTTGACCCAAACCCTGAAG
Seq C2 exon
AGCTCTTCCCACCGACGGCCCTCAAGATGGAGAGAGTGGAGGAGAGTGGGGTCTCTATCTCCTGGAACCCGCCCAATGGTCCAGCCGCCAGGCAGATGCTTGATGGCTACGCGGTCACCTACGTCTCCTCCGACGGCTCCTACCGCCGCACAGACTTTGTGGACAGGACCCGCTCCTCGCACCAGCTCCAGGCCCTGGCGGCCGGCAGGGCCTACAACATCTCCGTCTTCTCAGTGAAGCGAAACAGTAACAACAAGAATGACATCAGCAGGCCTGCCGTGCTGCTGGCCCGCACGC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804-SNED1:NM_001080437:20
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.180
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=79.5)
A:
NA
C2:
PF0004116=fn3=WD(100=84.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGAGTGACCCCTGCTTCTCC
R:
AGACGGAGATGTTGTAGGCCC
Band lengths:
342-683
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)