HsaINT0095599 @ hg19
Intron Retention
Gene
ENSG00000138131 | LOXL4
Description
lysyl oxidase-like 4 [Source:HGNC Symbol;Acc:17171]
Coordinates
chr10:100019148-100020884:-
Coord C1 exon
chr10:100020679-100020884
Coord A exon
chr10:100019187-100020678
Coord C2 exon
chr10:100019148-100019186
Length
1492 bp
Sequences
Splice sites
5' ss Seq
CAGGTAGGA
5' ss Score
9.79
3' ss Seq
TCTGTTTTCTCCCATAACAGGAA
3' ss Score
9.9
Exon sequences
Seq C1 exon
GGCCGGCGGCTGGAGGAGGTGCGGCTCAAGCCCATCCTTGCCAGTGCCAAGCAGCATAGCCCAGTGACCGAGGGAGCCGTGGAGGTGAAGTATGAGGGCCACTGGCGGCAGGTGTGTGACCAGGGCTGGACCATGAACAACAGCAGGGTGGTGTGCGGGATGCTGGGCTTCCCCAGCGAGGTGCCTGTCGACAGCCACTACTACAG
Seq A exon
GTAGGAGGGCGGCTGGCGTAGGCCCCACAGGAGGCAGGGTTGTGGGGCAGGGACTGAGTGTGTGTTCATGTGCGTGCATGTGATGTAGGGTGTGTGCATGAGTCTGAGTGTGGACTCATGTGAGGGGCAAGTAAGTATGCACACAGGCGAGTGTGTGATGTGTGTGGCATGTGGGACCTCGCAGAGTTCAGTGAGTACTGACTGGCAGTGGTGTTGTCTGTGGCAGGACATCCAGCAGGTGTTGGGATTGGGGGAGAGAAAACAGGCCCTACTGAGGAATGTGCCCAGATTTCTTGCTTCACGGGTGCCTCAGAATAATAAACAGGAAAGTGAATAAGGAGGACCTTCAGGATCCTGGGAAATACCTAGAAACAGTCAGAAAACAAACACTGCACTCTCGAATTATGTAAACAGAATTAACTAGGTACAGAACGCCCCCCCACCCCCCGCCCCCGGTGAAAACAGTTGAACATAAAACCGCGTGTCCTTGGTTAAAACACTAGACTTTCCTGCAGATACTTGCAGTGACACCCACGTGTAGAGTTTAGACAAACTGTTCTGGCCTCAGCTCAGCCAGTGACTGGCGTTAGGGCTTTGGGGAGGGCCTCTGAGCCTCCATCCTCAATTCCACTGCGAATATCCCAACGCTTCCCTCCTGAATTTCCTCAGCTCTGATCAAGCCAGGCTGTGACTGGGTTGTGTGTAAGTGAGGCGTGGGGTGGGGCACCTGGAGAGAGGAGACATAAAAATATTCTGTCAGAAACAAGGCGGAACTGTCACAACTGATTGCATCAACCAGTAAACGACAGCCACAGTCATGGTTCTGCCAGATCCGTGTCAGGGAGGACTTGTGTGTTTCCCATCAAGTGAGAAGTCTCCCGTAGTACGTCTGAGTCATCTGCCACCCCAATCAGTTTGATCCTGCTTCCCTAAAGGGTTAGAAGGCCCTTGTTGCAGTGACTTAGAGGAACCCCGTTCTGAGGAAACAGGGGTGCTGGTCAGCCTCTGGCTCCATCCTTGGGGATCCTGGGATGCAGCCTGACTCCCCCTGCCTGGTAATTGCACACCTGGGTCTCGCTGACTTGCCTGCCACCCATGAGGAGGGCAGGCCTGATGGTAGCCTGGGTGTCTCTGGGCGGGCCGCCCCCACCAGCAAGGCCTTCACCTCCCACCTGTCCCCAGAGGGCCCCTTCTCTTGGGCCCTCCCTAAATGCTCCCCTTCCTCTGGACTTCGGAGAGGGCAAGCCTGATCCACCTGCCCCCACTCTAGGACTGGCCGAGGGACCTTGCTTGCCTTCCTTGTAAAATGGTTATTTGTGAGGTGGCCACCCCGTCAGGGCTGCTGTGAAGCTCAGCATTGAAATCAGATTAGTGAATAAGTTTACAAAATGTAAAGTCCTGTGCAAACTTAAGGACAACTATGAGGAACCAGGTGGCAGGGGGTGGGACTTCCACACCCCTTCCACCTCCTATCTGTTTTCTCCCATAACAG
Seq C2 exon
GAAAGTCTGGGATCTGAAGATGAGGGACCCTAAGTCTAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000138131-LOXL4:NM_032211:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.014 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PU(43.2=73.9)
A:
NA
C2:
PF0053013=SRCR=FE(11.0=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGAGGAGGTGCGGCTCAAG
R:
ACTTAGGGTCCCTCATCTTCAGA
Band lengths:
230-1722
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)