HsaEX0036149 @ hg19
Exon Skipping
Gene
ENSG00000134013 | LOXL2
Description
lysyl oxidase-like 2 [Source:HGNC Symbol;Acc:6666]
Coordinates
chr8:23225510-23261753:-
Coord C1 exon
chr8:23261467-23261753
Coord A exon
chr8:23228156-23228275
Coord C2 exon
chr8:23225510-23225947
Length
120 bp
Sequences
Splice sites
3' ss Seq
GGTCCCTTTGTCCTTGGCAGGTT
3' ss Score
9.1
5' ss Seq
AAAGTGAGC
5' ss Score
5.89
Exon sequences
Seq C1 exon
ACAACAAAAGAGGCCGGAGGCCGGGCCTGCTGCGGCGGCCGCCTTCGGGGAAGGGGGTGGGTCCGGGGAGGGGTTTGCCATCCTCCTCTAGTTAAAAGTAAGGGGGAAAAGAGTAAACGCGCGACTCCAGCGCGCGGCTACCTACGCTTGGTGCTTGCTTTCTCCAGCCATCGGAGACCAGAGCCGCCCCCTCTGCTCGAGAAAGGGGCTCAGCGGCGGCGGAAGCGGAGGGGGACCACCGTGGAGAGCGCGGTCCCAGCCCGGCCACTGCGGATCCCTGAAACCAA
Seq A exon
GTTCTGAACTCCCGGTCTCCCCAGTCCCTGGAGGCTGCCTGCAGCTTTGCTTAGCTTCTCAGCCTGTTGATCACTGCCGTGGAATTGGCGAGTATCTTCCGGGGGAAAGCAGAGACAAAA
Seq C2 exon
AAAGCTCCTGCTGCTTCTGTACCCCGCCTGTCCCTCCCAGCTGCGCAGGGCCCCTTCGTGGGATCATCAGCCCGAAGACAGGGATGGAGAGGCCTCTGTGCTCCCACCTCTGCAGCTGCCTGGCTATGCTGGCCCTCCTGTCCCCCCTGAGCCTGGCACAGTATGACAGCTGGCCCCATTACCCCGAGTACTTCCAGCAACCGGCTCCTGAGTATCACCAGCCCCAGGCCCCCGCCAACGTGGCCAAGATTCAGCTGCGCCTGGCTGGGCAGAAGAGGAAGCACAGCGAGGGCCGGGTGGAGGTGTACTATGATGGCCAGTGGGGCACCGTGTGCGATGACGACTTCTCCATCCACGCTGCCCACGTCGTCTGCCGGGAGCTGGGCTACGTGGAGGCCAAGTCCTGGACTGCCAGCTCCTCCTACGGCAAGGGAGAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000134013-'1-11,'1-8,5-11
Average complexity
S
Mappability confidence:
100%=100=100%
Protein Impact
ORF disruption upon sequence inclusion
Show structural model
Features
Disorder rate (Iupred):
C1=0.512 A=0.000 C2=0.009
Domain overlap (PFAM):
C1:
NO
A:
NO
C2:
PF0053013=SRCR=PU(58.2=47.9)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Rat
(rn6)
No conservation detected
Chicken
(galGal4)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
AAAGAGTAAACGCGCGACTCC
R:
TCTTCGGGCTGATGATCCCAC
Band lengths:
258-378
Functional annotations
There are 1 annotated functions for this event
PMID: 31721164
This event
Expression of a novel LOXL2 variant was found to be upregulated in The Cancer Genome Atlas HPV-negative HNSCC, and confirmed in the separate primary tumor validation set. Analyses of loss and gain of function demonstrated that this LOXL2 variant enhanced proliferation, migration, and invasion in HPV-negative HNSCC cells and activated the FAK/AKT pathway. A total of 837 upregulated and 820 downregulated genes and 526 upregulated and 124 downregulated pathways associated with LOXL2 variant expression were identified using gene set enrichment analysis, which helped in developing a better understanding of the networks activated by this LOXL2 variant in patients with HPV-negative HNSCC. Note: no comparison between isoforms has been done.
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)