HsaINT0095587 @ hg19
Intron Retention
Gene
ENSG00000115318 | LOXL3
Description
lysyl oxidase-like 3 [Source:HGNC Symbol;Acc:13869]
Coordinates
chr2:74763123-74763598:-
Coord C1 exon
chr2:74763418-74763598
Coord A exon
chr2:74763278-74763417
Coord C2 exon
chr2:74763123-74763277
Length
140 bp
Sequences
Splice sites
5' ss Seq
AGGGTGAGG
5' ss Score
7.13
3' ss Seq
TCTTTGCCATCTGGCCCTAGGCA
3' ss Score
9.16
Exon sequences
Seq C1 exon
GCCCGTGTCCGTCTAAAGGGCGGCGCCCACCCTGGAGAGGGCCGGGTAGAAGTCCTGAAGGCCAGCACATGGGGCACAGTCTGTGACCGCAAGTGGGACCTGCATGCAGCCAGCGTGGTGTGTCGGGAGCTGGGCTTCGGGAGTGCTCGAGAAGCTCTGAGTGGCGCTCGCATGGGGCAGG
Seq A exon
GTGAGGTGGCATGGAGGTGGGAGGGAGAGGGAAGGAGGTACATGCTCCTGGGGGGCATATTCCTTCGGAAGGTTAGGTGTCCCCTGGGCAGACAATATATGCTTAATTACAACTTCCTGATCTTTGCCATCTGGCCCTAG
Seq C2 exon
GCATGGGTGCTATCCACCTGAGTGAAGTTCGCTGCTCTGGACAGGAGCTCTCCCTCTGGAAGTGCCCCCACAAGAACATCACAGCTGAGGATTGTTCACATAGCCAGGATGCCGGGGTCCGGTGCAACCTACCTTACACTGGGGCAGAGACCAGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000115318-LOXL3:NM_032603:6
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.124 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PU(67.9=90.2),PF0118612=Lysyl_oxidase=PU(23.9=44.3)
A:
NA
C2:
PF0053013=SRCR=PD(42.9=80.8),PF0053013=SRCR=PU(12.9=15.4)
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:
TAGAAGTCCTGAAGGCCAGCA
R:
CGGCATCCTGGCTATGTGAAC
Band lengths:
249-389
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)