HsaINT0155907 @ hg38
Intron Retention
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr2:241036790-241037353:+
Coord C1 exon
chr2:241036790-241036915
Coord A exon
chr2:241036916-241037239
Coord C2 exon
chr2:241037240-241037353
Length
324 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGT
5' ss Score
8.73
3' ss Seq
CAGCCTGCCCCATGTTTCAGACG
3' ss Score
6.41
Exon sequences
Seq C1 exon
CGTCCGTGTGCCTGGCCCTGCGCCCCTGCCTCAACGGCGGCAAGTGCATCGACGACTGCGTCACGGGCAACCCCTCCTACACCTGCTCCTGCCTCTCGGGCTTCACGGGGCGGAGGTGCCACCTGG
Seq A exon
GTGAGTGACTGGCCCAGGGCGGGACCACCCGCTGGCTGCGCTGGGCTCAGGAGGAGCACTGTAGGCTCCGCCAGTGGCCCTGGGCGCCCAGGGTCCCAGGTCAGGAGTCTCTGTCCCCAGGGTGTGGGTGACTTGCTTAGGGGACCACTGGGGACCAAAGGCCATGGCCCCCTGGAGTGAGCACCATGGGCGGGTGCAGTTGCTGCCCTCTCTGAGCCAATCTCGGGCTTGCTCCTCCTCCGTCCCCGGCCCAACCCGAGCCCTTAGAGAAAACTCCTCATCCGGGTTCCCGCCGCTGAGGCCTCAGCCTGCCCCATGTTTCAG
Seq C2 exon
ACGTGAACGAATGTGCCTCCCAGCCCTGTCAGAATGGTGGGACCTGTACTCACGGCATCAACAGTTTCCGCTGCCAGTGCCCGGCTGGCTTTGGGGGACCCACCTGTGAGACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804:ENST00000310397:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.001
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=83.7)
A:
NA
C2:
PF0000822=EGF=WD(100=79.5)
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTCAACGGCGGCAAGTG
R:
CTGTCTCACAGGTGGGTCCC
Band lengths:
212-536
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains