HsaINT0090838 @ hg19
Intron Retention
Gene
ENSG00000090661 | LASS4
Description
ceramide synthase 4 [Source:HGNC Symbol;Acc:23747]
Coordinates
chr19:8319383-8320609:+
Coord C1 exon
chr19:8319383-8319500
Coord A exon
chr19:8319501-8320490
Coord C2 exon
chr19:8320491-8320609
Length
990 bp
Sequences
Splice sites
5' ss Seq
GAGGTGAGA
5' ss Score
7.66
3' ss Seq
CCTCATCACCCCCTCCCCAGCCC
3' ss Score
6.83
Exon sequences
Seq C1 exon
ATTCATTGGCCTGCCCCTGAGCCGGTGGCTGGGTGTGAGGGATCAGACCAGGAGGCAAGTGAAGCCCAACGCCACGCTGGAGAAACACTTCCTCACGGAAGGGCACAGGCCCAAGGAG
Seq A exon
GTGAGAGCCCCCCATGCCCTCCGACCCGCACTACTGCCCTGGGGGTGGGGCGTGGGGATGGTGTGTGGCCCATTTGTTGGGGCAGGAGAAGCCAAGGTGGCTGCAGGCACCCCTGCAATGCCCCTACTTTCCACTCTTCATCCTCAATTCCCTGGGAAAGGGCTCTACCCCCCAGCCTCCCTGGGAAACGACGCCCCACCCCTCCCAGCATCCCTGGGACATGGAGCCCCACCCTTCCAGCCTCCCTGGGAGATGAGGACCCCCCCCTTCCCAGCCTCCTTGGGAGATGGGGCCCCTCCCCTCCCAGCCTCCCTGAGCCTTAGTGGGCACAGTTGCACAATGGACAGATTCTAGGAGAGTGAGAGTAGTTGCTTGCTCTCCTATCCTGGGGAGGAATGGAAGGTCTGAGCTGATAGGGAATGGAGTAACAGAAGCAGCCCTGTGACCCTCCCTCCATTCCCGTCTCTGGTGTGGCTGCCCGCTGGACAGGGTCTGTGCTGTGGAGGCGTGGCTGCGTCCTGAGTGGGGTGGGGAATGGTGAAGACCACATACCCTAGAGGCGACAGGGCAGCTTCCGCAGAGCTAGACGTGACTCCCCCTTTACTTGTCAATTTCCCTCTTCAGGTAGGGCTTGGGGCTGGGGCAAGGTCTCAACTGCCTGTCTAGGTTGGAGGTGAGAACTGACCGTTCTGGAGGGACGCAGGGAAGCCTATCCGGGGGTAGGGGATGCTGCACGCCAGCATCTCTCTTAATCCCATCCCCGTCAGCGACCTGCCTGCCCTATGAACAGGATTTGCTTCTCTTAGGGCCCAAGTGTTCTGCAGGGCCCCACGCTGGGACCCCCAACACTGCCCCTCCATATAGACATGGTCACCCTGTAGGCAAGATGTGGGCCTGCAGTGGAGAGGGCAGAGCCAAGTCCTGTCTGGGGACATGGGGGAAGCCACCACAGGGCCTCTGTGACCCTTGTCCTCATCACCCCCTCCCCAG
Seq C2 exon
CCCCAGCTGTCTCTCCTGGCCGCCCAGTGTGGCCTCACGCTGCAGCAGACCCAGCGATGGTTCCGGAGACGCCGGAACCAGGATCGACCCCAGCTGACCAAGAAGTTCTGTGAGGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000090661-LASS4:NM_024552:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.025 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0004624=Homeobox=PU(45.6=65.0),PF067288=PIG-U=FE(25.5=100)
A:
NA
C2:
PF0004624=Homeobox=PD(50.9=72.5),PF067288=PIG-U=FE(25.5=100),PF0379811=TRAM_LAG1_CLN8=PU(8.2=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:
ATTCATTGGCCTGCCCCTGAG
R:
GGCCTCACAGAACTTCTTGGT
Band lengths:
235-1225
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)