HsaINT0155896 @ hg19
Intron Retention
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF-like domains 1 [Source:HGNC Symbol;Acc:24696]
Coordinates
chr2:242004715-242007362:+
Coord C1 exon
chr2:242004715-242005011
Coord A exon
chr2:242005012-242007178
Coord C2 exon
chr2:242007179-242007362
Length
2167 bp
Sequences
Splice sites
5' ss Seq
CGCGTGAGT
5' ss Score
8.4
3' ss Seq
GAACAGTCCATTCCCCCTAGGAC
3' ss Score
6.66
Exon sequences
Seq C1 exon
AGCTCTTCCCACCGACGGCCCTCAAGATGGAGAGAGTGGAGGAGAGTGGGGTCTCTATCTCCTGGAACCCGCCCAATGGTCCAGCCGCCAGGCAGATGCTTGATGGCTACGCGGTCACCTACGTCTCCTCCGACGGCTCCTACCGCCGCACAGACTTTGTGGACAGGACCCGCTCCTCGCACCAGCTCCAGGCCCTGGCGGCCGGCAGGGCCTACAACATCTCCGTCTTCTCAGTGAAGCGAAACAGTAACAACAAGAATGACATCAGCAGGCCTGCCGTGCTGCTGGCCCGCACGC
Seq A exon
GTGAGTGTCCCCGAGCCTGGCCGTCCCTGCCCAGCCCCTGCCCCTCGAGGGCAGCGCTGGCCCCGGCACCTGCAGGGCGGCTGTCATGCCGTCCACCCTCCTAGTTCTTGCAGCAGCAAGACAGACAGCTGAGCTGGGGGTTGGAGGCACCGCCCTGCTGGAGACAGAGCTGTGTGGGAGTGGCCTTGGGTCCACAAGATACAGGCATGGGATTGGGGCGCATAGAATCGAGCCAAGAGTGGGAGCAGCACAACCCCCAGGCATGGAGCTAGGAAGTGGGACTGGGGAGGAATGGGGGCTTCCCAAAAGGGTCCCTAGAAGGAGCCAGTGTGGGAGACAGGGGCCGCGGGGGTGGGCTTGGGGGGGCTGGGACTCTGGGGTGCTCTGAAGGCCTGGGGAGAGTTTGAAAGAGGCACCTGCTCACAGGGATATGTAGGCGCTGAGGTGTGCTAAGGGGAGGCATCGGTGGCTCAATCGGGAAGAGCCGTGGGGCAGGCCCTAGATGGAATGACAGACCCAGAGCCTCCACCTGGAGCTGGCACTGAAAGCTGTGACCAGATGTGACCCCTGAAGAGGGGGTCCTAGGAGGAGCCTCCTCAGAGCCTGAGCCACCAAGATTGCAGGGGAGGCCCGGGTTGTGCACAGCCTGTGGGGTTGTTGCCGTGTCGGGGAGCAGAAGATGCTGAGCGCTCTAGGGAAGGCGTCAGGGCTTAGCGGGCTTGTGTGCTGCTGGGAGGGATTCTGGGAAGGAGAAAGGAGCCCTAGAACATGGCAGTGGACGGACAGGGGCAGGGCCGGAAGAAAGCAGAGGGCTGGCCTTCCACGGAGCCCGGCCGCATCAGCTAGAGCACAGGGGATCTCGGAACAGGCTGGGCAGGAACCAAGTGGGGTGCAGGGCCATGGGGCCATGGGACTCTCACCCAACATGCCTGTGGCCTCCAGACACAGGAGCAAGAATGGGGAAGGGGTGCTAGAGGCTCGAGGAAAGAGGAAAAGGTGCTGAGAGCACAGACTGCTGCGAAGTGGCGTGATGGATGGATGGGTGGGTGGGTGGCCAGGGCTTCAGGGAGGCCTAAGCATCCAGCAGGGCCCTGCGGGGCGGCCACGTGAGTTTGGTGAAACCTATGGGTAGCATGGCGGGTAGGTGGGGAGGAGCTCGGCGGTTCTCACAGGAGGAAAGCCTCCTGGCCACACCTGGGCCCTAGCTTGATGCCAATGCCAAGGGCATTGAGGGACAGGAGAAGGCATTCAAGGCAGCTTGAGCCCACCCAGAGGCCCACAAGGGCCTGTCCTGCAGGAGTTGACCACCAAGGGGCTGGAGTTCCCAACACAGCAAGGACACAGAGCACACCTCGGCCAGTGGAGAGCCTGGGCGCATGTGCGGGTGGCACTGAGCAGGTGTCAGCAGGAGCTGCCAGGGGCTGAGTAGGGGTGGCTCGCCTGGGCTGTTTTAGGAAGAAGCACCTGCAAGGCCGCCCCATGTGAGATCTGCCCTCGGAAGGTATCTGGAGTGAAGACAGAGCCCGCCCTGCCCGCTGCAGAGTTGGGGCTCCAGCCAGCCATGGTGGGTGGAAGGGACCGCTGTCCACAGACCGGGGTGCTGAGTTGCCGGGAGCTGAGCGCTGCCCTCTGGCTCTGCCTGGTGCATCAGCAGTGGCACTGGAGCTTCGGAGGAGACTGGCTGGGCGGGAAGCGGAGCTCACAAGTGGCCCCTTCCCTGCAGTTGCTGGGAGTTCTGTATGTCTGTCCTCCTAAGACAGCGTTGCCCAGACCAGGCCCGGATGTGTGCTCTTAGACCAAAATAGTCAACTGGCACAGAAAAGGGGAGGTCCGGGTTACTCATGTCCAGAGGGACTCCGGCCCATCCCCTGCCATGTCACTGCCACATCTAAATGGAGACTAAGACCCCTGCCTCTGGTAAGACGGGCTGGCCCACAGCGGGCTCTGCAGCCGTCATGCTCACAGCGGGTTCTGCAGCTGTCAGCCCTGGAGGCCAGAGCCTGGGCATCCCACTCAGCCCGAGTTCCCTGAGCAGTTGATGGGACACCCTCTCCAGTGCCTCTCTGTGGCCCCCAGCACCCTCCCAAGCCTGGTTTCATCTTGAGCCCCTGCACTCCCCCAGGAGCAAGGAGGGGCCGGCACCTGCTGAACAGTCCATTCCCCCTAG
Seq C2 exon
GACCCCGCCCTGTGGAAGGCTTCGAGGTCACCAATGTGACGGCTAGCACCATCTCAGTGCAGTGGGCCCTGCACAGGATCCGCCATGCCACCGTCAGTGGGGTCCGTGTGTCCATCCGCCACCCTGAGGCCCTCAGGGACCAGGCCACCGATGTGGACAGGAGTGTGGACAGGTTCACCTTTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804-SNED1:NM_001080437:21
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.180 A=NA C2=0.129
Domain overlap (PFAM):
C1:
PF0004116=fn3=WD(100=84.0)
A:
NA
C2:
PF0004116=fn3=PU(70.6=96.8)
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:
No suggested primer sequences
R:
No suggested primer sequences
Band lengths:
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)