HsaINT0155911 @ hg38
Intron Retention
Gene
ENSG00000162804 | SNED1
Description
sushi, nidogen and EGF like domains 1 [Source:HGNC Symbol;Acc:HGNC:24696]
Coordinates
chr2:241048315-241048766:+
Coord C1 exon
chr2:241048315-241048440
Coord A exon
chr2:241048441-241048661
Coord C2 exon
chr2:241048662-241048766
Length
221 bp
Sequences
Splice sites
5' ss Seq
AGAGTGCGT
5' ss Score
3.85
3' ss Seq
CCTCCCTCTCTTCGTGGCAGGAG
3' ss Score
9.09
Exon sequences
Seq C1 exon
GAGACCATCCAGTGCCAGACGCCTGCCTCTCGGCCCCTTGCCACAATGGGGGCACCTGTGTGGATGCGGACCAGGGCTACGTGTGCGAGTGCCCCGAAGGCTTCATGGGCCTGGACTGCAGGGAGA
Seq A exon
GTGCGTCTGGGCTGCAAGGGCTGCCGTTTTAGGGCTGGGGCAGGAGACCCAGGGAGGGCCTTCCTGTGGGTGCATGCAGGAAACGCCCCGAAAAGAAACGTGTGAGTGCGCGTCCACTGCAATTTGTATGGGAAGTTGGCCAGGAGCAGGGCAGGGTCTGGAGCGAGGGTGCCATCTTTCTGCGCCCCCACATGGGAGGCTCCTCCCTCTCTTCGTGGCAG
Seq C2 exon
GAGTCCCCGATGACTGTGAGTGCCGCAACGGAGGCAGATGCCTGGGCGCCAACACCACCCTCTGCCAGTGCCCCCTGGGATTCTTTGGGCTTCTCTGTGAATTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000162804:ENST00000310397:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.004 A=NA C2=0.041
Domain overlap (PFAM):
C1:
PF0000822=EGF=WD(100=72.1)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGACCATCCAGTGCCAGACG
R:
ATTCACAGAGAAGCCCAAAGA
Band lengths:
228-449
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains