HsaINT0095588 @ hg38
Intron Retention
Gene
ENSG00000115318 | LOXL3
Description
lysyl oxidase like 3 [Source:HGNC Symbol;Acc:HGNC:13869]
Coordinates
chr2:74535588-74536150:-
Coord C1 exon
chr2:74535996-74536150
Coord A exon
chr2:74535756-74535995
Coord C2 exon
chr2:74535588-74535755
Length
240 bp
Sequences
Splice sites
5' ss Seq
AGGGTCAGT
5' ss Score
5.85
3' ss Seq
TCCATTCTGTGTCACTACAGATC
3' ss Score
9.04
Exon sequences
Seq C1 exon
GCATGGGTGCTATCCACCTGAGTGAAGTTCGCTGCTCTGGACAGGAGCTCTCCCTCTGGAAGTGCCCCCACAAGAACATCACAGCTGAGGATTGTTCACATAGCCAGGATGCCGGGGTCCGGTGCAACCTACCTTACACTGGGGCAGAGACCAGG
Seq A exon
GTCAGTCATCCTCTCTACCTTGGTTGAGGTCTCTTTCATCCTATCCAGGTCTGGTCTCCAATCTACAGTCCAATGGCCCCCAGCCCATTGCCCCAGGCCCCTGCCCTCCTGCAGCTCCCACCTGACCCATCACTTGCTAGCCCATTATGTGCCTGAGTCACGCTTCAGCCACATCTGTTAGAGACTCCCACTACCTCACCCCAAAGCTTTCTCCAGCGCTTCCATTCTGTGTCACTACAG
Seq C2 exon
ATCCGACTCAGTGGGGGCCGCAGCCAACATGAGGGGCGAGTCGAGGTGCAAATAGGGGGACCTGGGCCCCTTCGCTGGGGCCTCATCTGTGGGGATGACTGGGGGACCCTGGAGGCCATGGTGGCCTGTAGGCAACTGGGTCTGGGCTACGCCAACCACGGCCTGCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000115318:ENST00000264094:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.151
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PD(42.9=80.8),PF0053013=SRCR=PU(12.9=15.4)
A:
NA
C2:
PF0053013=SRCR=PU(49.1=92.9)
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:
CCTGAGTGAAGTTCGCTGCTC
R:
CCAGACCCAGTTGCCTACAGG
Band lengths:
284-524
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