HsaINT0090839 @ hg19
Intron Retention
Gene
ENSG00000090661 | LASS4
Description
ceramide synthase 4 [Source:HGNC Symbol;Acc:23747]
Coordinates
chr19:8320491-8320763:+
Coord C1 exon
chr19:8320491-8320609
Coord A exon
chr19:8320610-8320705
Coord C2 exon
chr19:8320706-8320763
Length
96 bp
Sequences
Splice sites
5' ss Seq
CAGGTAAGC
5' ss Score
9.88
3' ss Seq
AGCTCCCTCCCCATCCACAGCTG
3' ss Score
8.11
Exon sequences
Seq C1 exon
CCCCAGCTGTCTCTCCTGGCCGCCCAGTGTGGCCTCACGCTGCAGCAGACCCAGCGATGGTTCCGGAGACGCCGGAACCAGGATCGACCCCAGCTGACCAAGAAGTTCTGTGAGGCCAG
Seq A exon
GTAAGCCCAGGATGGGGCTTCTGGGGTGCAGGGAAGCGGGCCGGGGTGGGGCGGGGCGGGTGTCTGCTATTTTCACAGCTCCCTCCCCATCCACAG
Seq C2 exon
CTGGAGGTTTCTCTTCTACCTGTCCTCCTTCGTGGGCGGCCTCTCGGTCCTGTACCAC
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000090661-LASS4:NM_024552:5
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(50.9=72.5),PF067288=PIG-U=FE(25.5=100),PF0379811=TRAM_LAG1_CLN8=PU(8.2=12.5)
A:
NA
C2:
PF067288=PIG-U=FE(12.4=100),PF0379811=TRAM_LAG1_CLN8=FE(31.1=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCCAGCTGTCTCTCCTGG
R:
GAGAGGCCGCCCACGAAG
Band lengths:
164-260
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
- Pre-implantation embryo development
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)