HsaINT0090815 @ hg19
Intron Retention
Gene
ENSG00000143418 | LASS2
Description
ceramide synthase 2 [Source:HGNC Symbol;Acc:14076]
Coordinates
chr1:150940296-150940677:-
Coord C1 exon
chr1:150940559-150940677
Coord A exon
chr1:150940354-150940558
Coord C2 exon
chr1:150940296-150940353
Length
205 bp
Sequences
Splice sites
5' ss Seq
CAGGTGGGG
5' ss Score
6.92
3' ss Seq
ATTTCTGCTTCCTCTGCCAGCTG
3' ss Score
9.29
Exon sequences
Seq C1 exon
GTGGAAGTAGAGCTTTTGTCCCGGCAGAGCGGGCTCTCTGGCCGCCAGGTAGAGCGTTGGTTCCGTCGCCGCCGCAACCAGGACCGGCCCAGTCTCCTCAAGAAGTTCCGAGAAGCCAG
Seq A exon
GTGGGGGAGGCTGGGGCAGAAGCTGGGTGACAAGGAATATCCTGATGTGTCTTGCTGGGAGGGATAGGCGGTGGCTATACGCAGGGAGATGTGAGGAGGTGAATTCAGTTATTAATGGTATCTTGTGAGGGTATCTGCAGGTATTTGGGGGCTGCTGGGGGACTGTGCTATCCTCTGACCTAGCCATTTCTGCTTCCTCTGCCAG
Seq C2 exon
CTGGAGATTCACATTTTACCTGATTGCCTTCATTGCCGGCATGGCCGTCATTGTGGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143418-LASS2:NM_181746:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.002 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PD(50.0=72.5),PF0379811=TRAM_LAG1_CLN8=PU(2.6=12.5)
A:
NA
C2:
PF0379811=TRAM_LAG1_CLN8=PU(2.9=83.3)
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:
AAGTAGAGCTTTTGTCCCGGC
R:
ATCCACAATGACGGCCATGC
Band lengths:
173-378
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)