HsaINT0090813 @ hg19
Intron Retention
Gene
ENSG00000143418 | LASS2
Description
ceramide synthase 2 [Source:HGNC Symbol;Acc:14076]
Coordinates
chr1:150937649-150939105:-
Coord C1 exon
chr1:150938952-150939105
Coord A exon
chr1:150938765-150938951
Coord C2 exon
chr1:150937649-150938764
Length
187 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAAG
5' ss Score
5.73
3' ss Seq
TTCTTGTCCCTTTTCCACAGCTG
3' ss Score
10.83
Exon sequences
Seq C1 exon
GATCCTGCATTGCACCCTGGTGTACCCACTGGAGCTCTATCCTGCCTTCTTTGGCTATTACTTCTTCAATTCCATGATGGGAGTTCTACAGCTGCTGCATATCTTCTGGGCCTACCTCATTTTGCGCATGGCCCACAAGTTCATAACTGGAAAG
Seq A exon
GTGAAGCCCTGTTCCCATTGTGTAGGCCTTACTACTCTCTACAACTTCCTGAACTCCCATCTTGCCAGTAACTCTCTAAAAAACTAGTGTGGAGCCCTGGGTATAACAGGAACAAGCCCTCAGAGAGAAGCAGTACTTAGGGGTTTGAGGATCTCATGTAATAACCCTTCTTGTCCCTTTTCCACAG
Seq C2 exon
CTGGTAGAAGATGAACGCAGTGACCGGGAAGAAACAGAGAGCTCAGAGGGGGAGGAGGCTGCAGCTGGGGGAGGAGCAAAGAGCCGGCCCCTAGCCAATGGCCACCCCATCCTCAATAACAACCATCGTAAGAATGACTGAACCATTACTCCAGCTGCCTCCCAGATTAATGCATAAAGCCAAGGAACTACCCCGCTCCCTGCGCTATAGGGTCACTTTAAGCTCTGGGGAAAAAGGAGAAAGTGAGAGGAGAGTTCTCTGCATCCTCCCTCCTTGCTTGTCACCCAGTTGCCTTTAAACCAAATTCTAACCAGCCTATCCCCAGGTAGGGGGACGTTGGTTATATTCTGTTAGAGGGGGACGGTCGTATTTTCCTCCCTACCCGCCAAGTCATCCTTTCTACTGCTTTTGAGGCCCTCCCTCAGCTCTCTGTGGGTAGGGGTTACAATTCACATTCCTTATTCTGAGAATTTGGCCCCAGCTGTTTGCCTTTGACTCCCTGACCTCCAGAGCCAGGGTTGTGCCTTATTGTCCCATCTGTGGGCCTCATTCTGCCAAAGCTGGACCAAGGCTAACCTTTCTAAGCTCCCTAACTTGGGCCAGAAACCAAAGCTGAGCTTTTAACTTTCTCCCTCTATGACACAAATGAATTGAGGGTAGGAGGAGGGTGCACATAACCCTTACCCTACCTCTGCCAAAAAGTGGGGGCTGTACTGGGGACTGCTCGGATGATCTTTCTTAGTGCTACTTCTTTCAGCTGTCCCTGTAGCGACAGGTCTAAGATCTGACTGCCTCCTCCTTTCTCTGGCCTCTTCCCCCTTCCCTCTTCTCTTCAGCTAGGCTAGCTGGTTTGGAGTAGAATGGCAACTAATTCTAATTTTTATTTATTAAATATTTGGGGTTTTGGTTTTAAAGCCAGAATTACGGCTAGCACCTAGCATTTCAGCAGAGGGACCATTTTAGACCAAAATGTACTGTTAATGGGTTTTTTTTAAAAATTAAAAGATTAAATAAAAAATATTAAATAAAACATGGCAATAAGTGTCAGACTATTAGGAATTGAGAAGGGGGATCAACTAAATAAACGAAGAGAGTCTTTCTTATGCCTTCCTTGCA
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000143418-LASS2:NM_181746:10
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.478
Domain overlap (PFAM):
C1:
PF0379811=TRAM_LAG1_CLN8=PD(24.0=80.8),PF116763=DUF3272=PU(84.3=82.7)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACTGGAGCTCTATCCTGCCT
R:
TATTGAGGATGGGGTGGCCAT
Band lengths:
246-433
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)