HsaINT0095569 @ hg19
Intron Retention
Gene
ENSG00000134013 | LOXL2
Description
lysyl oxidase-like 2 [Source:HGNC Symbol;Acc:6666]
Coordinates
chr8:23154410-23156460:-
Coord C1 exon
chr8:23156349-23156460
Coord A exon
chr8:23155636-23156348
Coord C2 exon
chr8:23154410-23155635
Length
713 bp
Sequences
Splice sites
5' ss Seq
TAGGTAAGG
5' ss Score
9.31
3' ss Seq
ACCCGATTCTCGCTCTTCAGGTG
3' ss Score
9.44
Exon sequences
Seq C1 exon
GTTGTTATTAACCCCAACTTCGAGGTTGCAGAATCCGATTACTCCAACAACATCATGAAATGCAGGAGCCGCTATGACGGCCACCGCATCTGGATGTACAACTGCCACATAG
Seq A exon
GTAAGGCCAGGCCGCCCCCACTCCAGGAAGCAGGCGGGAGCTGCCCTACTTTCTCAAGGACCCAGAGGCAGCTTCCTAATTTGGGTAAAGAGCTCGGGGAATGCAGCCAGCATCACATTTCCACATTCAGGACAGAAGCCACAGACACACAGGCCTGGATGGAGACTGAGTTTTTACAGCCAGCTCCGGCCACGGATAGAGGATGGTACAGGACCAGGCCAGCCCAGTGCAGACCCCAAGGCTTTTTAAGGGTTGGAGCTGAGGCCACTGGCTCATTATGTATGTGACCTCAAAAATGTGGGCATCAGCAATCTGTGGGCTCTGCCTATCAGGTTTTTCTGTCGAGAGCTGGAAGCTAGCAAACTACTGTTATTTCTAGTCTCCAATAAAGACACTTTTTTCCTTGGATGATAGGACTTGGGGAACAAAAGGGAAGGCAGAGCTTTTTCCTCTGCAGGAAAAGTCATGGGCCTCACTCTTGGCAAAAGGTTAAAATTAAAGGCGCTATATTTATTCACTCGTTCACTCAACTTTGACAGAGCACCTGCTATGTGCCCAGCCCTAGAGATGGCCAGTGCCTGGCACCTGTCCTTTTGAGGAGGGCACACACAGGTGGCCCCAGCAGCCCCTGAGGCCCACTCCCCTGGCTCAGGGTCAGGCAAGGCCCGAGCATCTCATTTGTCCACTCTCTCTACCCGATTCTCGCTCTTCAG
Seq C2 exon
GTGGTTCCTTCAGCGAAGAGACGGAAAAAAAGTTTGAGCACTTCAGCGGGCTCTTAAACAACCAGCTGTCCCCGCAGTAAAGAAGCCTGCGTGGTCAACTCCTGTCTTCAGGCCACACCACATCTTCCATGGGACTTCCCCCCAACAACTGAGTCTGAACGAATGCCACGTGCCCTCACCCAGCCCGGCCCCCACCCTGTCCAGACCCCTACAGCTGTGTCTAAGCTCAGGAGGAAAGGGACCCTCCCATCATTCATGGGGGGCTGCTACCTGACCCTTGGGGCCTGAGAAGGCCTTGCGGGGGTGGGGTTTGTCCACAGAGCTGCTGGAGCAGCACCAAGAGCCAGTCTTGACCGGGATGAGGCCCACAGACAGGTTGTCATCAGCTTGTCCCATTCAAGCCACCGAGCTCACCACAGACACAGTGGAGCCGCGCTCTTCTCCAGTGACACGTGGACAAATGCGGGCTCATCAGCCCCCCCAGAGAGGGTCAGGCCGAACCCCATTTCTCCTCCTCTTAGGTCATTTTCAGCAAACTTGAATATCTAGACCTCTCTTCCAATGAAACCCTCCAGTCTATTATAGTCACATAGATAATGGTGCCACGTGTTTTCTGATTTGGTGAGCTCAGACTTGGTGCTTCCCTATCCACAGCCCCCACCCCTTGTTTTTCAAGATACTATTATTATATTTTCACAGACTTTTGAAGCACAAATTTATTGGCATTTAATATTGGACATCTGGGCCCTTGGAAGTACAAATCTAAGGAAAAACCAACCCACTGTGTAAGTGACTCATCTTCCTGTTGTTCCAATTCTGTGGGTTTTTGATTCAACGGTGCTATAACCAGGGTCCTGGGTGACAGGGCGCTCACTGAGCACCATGTGTCATCACAGACACTTACACATACTTGAAACTTGGAATAAAAGAAAGATTTATGAAACGTGTCTGTGTTTCCTTTGACCCACAGCACCTGGGCCCTGAGCAGCAGGCTTCCTATGTTCAGTGGCCAGAAGCAGAGCTTCAGGTACATTCGTGGTTTTCTCCGGTGGACATGGGTCCTCAGATCCCCTCCAGCCCAGTGTGGCCACCAGGGCACCTCCTTCAATAGACTCCAAAAGGGGCAGCTCCTACCATCTGGGAGAAGCAATCTAAGGAGATCACAAAAAGTAACGGAACAGGAGTCATAATCTTTCTTGAACTCCTGTGGTTTTTACTGAAACTTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000134013-LOXL2:NM_002318:13
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=0.000
Domain overlap (PFAM):
C1:
PF0118612=Lysyl_oxidase=FE(18.1=100)
A:
NA
C2:
PF0118612=Lysyl_oxidase=PD(1.0=7.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCCAACTTCGAGGTTGCAGAA
R:
GAGGGTCCCTTTCCTCCTGAG
Band lengths:
346-1059
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)