HsaINT0090814 @ hg19
Intron Retention
Gene
ENSG00000143418 | LASS2
Description
ceramide synthase 2 [Source:HGNC Symbol;Acc:14076]
Coordinates
chr1:150940559-150940988:-
Coord C1 exon
chr1:150940871-150940988
Coord A exon
chr1:150940678-150940870
Coord C2 exon
chr1:150940559-150940677
Length
193 bp
Sequences
Splice sites
5' ss Seq
CAGGTATGA
5' ss Score
9.46
3' ss Seq
GGCTTCTTCACTGTGCCCAGGTG
3' ss Score
6.75
Exon sequences
Seq C1 exon
GTACGTGGCTACACCACTGGCTGCCCTCTTGAACATAAAGGAGAAAACTCGGCTGCGGGCACCTCCCAACGCCACCTTGGAACATTTCTACCTGACCAGTGGCAAGCAGCCCAAGCAG
Seq A exon
GTATGAGCCGCATGCTGCTCTGGCTCTGGGAATCACTGAGTTTGGTGGTGGGGGGACAGGGTTTGAATGTTAGCTCTGGCAGGTGAAGAGATGGGGAAGCAGTGGTGCTGACTGAGGTTGTTACTGGGAGAGGCTGGGGATGCTGCTGAGTTCCGAAGGTAAACATAACAATGGGCTTCTTCACTGTGCCCAG
Seq C2 exon
GTGGAAGTAGAGCTTTTGTCCCGGCAGAGCGGGCTCTCTGGCCGCCAGGTAGAGCGTTGGTTCCGTCGCCGCCGCAACCAGGACCGGCCCAGTCTCCTCAAGAAGTTCCGAGAAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143418-LASS2:NM_181746:3
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=0.002
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(46.6=67.5)
A:
NA
C2:
PF0004624=Homeobox=PD(50.0=72.5),PF0379811=TRAM_LAG1_CLN8=PU(2.6=12.5)
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:
CTACACCACTGGCTGCCCTC
R:
GGCTTCTCGGAACTTCTTGAGG
Band lengths:
227-420
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- 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)