HsaINT0155900 @ hg38
Intron Retention
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr2:241071576-241071878:+
Coord C1 exon
chr2:241071576-241071720
Coord A exon
chr2:241071721-241071795
Coord C2 exon
chr2:241071796-241071878
Length
75 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAT
5' ss Score
7.79
3' ss Seq
CCCTCCCACCCTCTCTGCAGGTT
3' ss Score
12.35
Exon sequences
Seq C1 exon
CCCCCAGGGATGGCGCTGACAGACGCTGGCACCAGGGAGGACACCACCCTCGGGTGCTCAAGAACAGACCGCCCCCGGCGCGCCTGCCGGAGCTGCGCCTGCTCAATGACCACAGCGCCCCCGAGACCCCCACCCAGCCCCCCAG
Seq A exon
GTACATGCCCCACCCATCGGCCCCATCGCCCGAGGCGGCGCTCGGACTGTGGTGACCCTCCCACCCTCTCTGCAG
Seq C2 exon
GTTCTCGGAGCTTGTGGACGGCAGAGGAAGAGTGAGCGCCAGGTTCGGTGGCTCACCCAGCAAAGCAGCCACCGTGAGATCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804:ENST00000310397:25
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.997 A=NA C2=0.970
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Cow
(bosTau6)
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:
CTCGGGTGCTCAAGAACAGAC
R:
GATCTCACGGTGGCTGCTTTG
Band lengths:
178-253
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains