HsaINT0090820 @ hg19
Intron Retention
Gene
ENSG00000143418 | LASS2
Description
ceramide synthase 2 [Source:HGNC Symbol;Acc:14076]
Coordinates
chr1:150938952-150939338:-
Coord C1 exon
chr1:150939232-150939338
Coord A exon
chr1:150939106-150939231
Coord C2 exon
chr1:150938952-150939105
Length
126 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGT
5' ss Score
10.1
3' ss Seq
CTCTCTCCTTGAATCCTCAGGAT
3' ss Score
9.61
Exon sequences
Seq C1 exon
TCAGCCAAGATGTTTAACTACGCGGGATGGAAGAACACCTGCAACAACATCTTCATCGTCTTCGCCATTGTTTTTATCATCACCCGACTGGTCATCCTGCCCTTCTG
Seq A exon
GTGAGTAGGCAGCTAGGCTACACTCCTGTTCTGAAGAAATCAGGAGCCTTGCCTTTCTTCCCCTCCTGTATCTCCCCGGTGTCTGACCTGCTCTTGTCCACGTTCTCTCTCTCCTTGAATCCTCAG
Seq C2 exon
GATCCTGCATTGCACCCTGGTGTACCCACTGGAGCTCTATCCTGCCTTCTTTGGCTATTACTTCTTCAATTCCATGATGGGAGTTCTACAGCTGCTGCATATCTTCTGGGCCTACCTCATTTTGCGCATGGCCCACAAGTTCATAACTGGAAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143418-LASS2:NM_181746:9
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:
PF0379811=TRAM_LAG1_CLN8=FE(18.0=100)
A:
NA
C2:
PF0379811=TRAM_LAG1_CLN8=PD(24.0=80.8),PF116763=DUF3272=PU(84.3=82.7)
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:
AACTACGCGGGATGGAAGAAC
R:
CCAGTTATGAACTTGTGGGCCA
Band lengths:
242-368
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)