HsaINT0095583 @ hg19
Intron Retention
Gene
ENSG00000115318 | LOXL3
Description
lysyl oxidase-like 3 [Source:HGNC Symbol;Acc:13869]
Coordinates
chr2:74777312-74779773:-
Coord C1 exon
chr2:74779449-74779773
Coord A exon
chr2:74777476-74779448
Coord C2 exon
chr2:74777312-74777475
Length
1973 bp
Sequences
Splice sites
5' ss Seq
CAGGTGAGC
5' ss Score
9.6
3' ss Seq
CTTCATCTCCCCTTCCACAGGCC
3' ss Score
10.89
Exon sequences
Seq C1 exon
GCCTTCCCTGCCATGCGACCTGTCAGTGTCTGGCAGTGGAGCCCCTGGGGGCTGCTGCTGTGCCTGCTGTGCAGTTCGTGCTTGGGGTCTCCGTCCCCTTCCACGGGCCCTGAGAAGAAGGCCGGGAGCCAGGGGCTTCGGTTCCGGCTGGCTGGCTTCCCCAGGAAGCCCTACGAGGGCCGCGTGGAGATACAGCGAGCTGGTGAATGGGGCACCATCTGCGATGATGACTTCACGCTGCAGGCTGCCCACATCCTCTGCCGGGAGCTGGGCTTCACAGAGGCCACAGGCTGGACCCACAGTGCCAAATATGGCCCTGGAACAG
Seq A exon
GTGAGCAATGATCCAGGCATATCCTAGATATTTCCTATGTGTGGCCAAAGTGCAGGGAAAGGGAACACGAGGATGGCACAGCCATAGGGACACACGACACCAAGAACAGCCAGCATTGAGTAAATCCATGGATGACAAACCAAGCAACATAGTTACTTCCCAGAGCTGTGTGACCTTAGGCTAGTCAGTGCTTTCTCTGAGCCTCAGATGCCCTGTATGCAAAATGACTAGATGATGTCTAAGTTCTTTTCTGCTGCAAAAGTATGATCCTACAAAGCCATCCACAAAACAGCCCAGATACAGGTGAGCCCTGTACAAATAAAGTACAGTTAGTCTCATGGGACGCTAAGAGCAGGTAAATGATATCTGGATGTCCCAAAGTCACAAGGGGTCACAGACACTGCAGCTAACAAAATCAGGTTATGGGCCAGAGCTAAAACTAACAAGGTGGTACTGTCTAAGGACAAGTATAAAATCTAGGACAAGTATGAGTGTGGGTGGTGGAGGCTTAAGAGCAGTTCCCTAGGTGAGGCCTAGGACTGTGCCCATGGTATGAACCCACAGTGGGAATGATGGACAGAAGCAGGTGCAACCTGCAGCTGATTCCCCAGTTCCCACTGGCTAGACCACCTGTGGAATTAAGTGTCATTTGTAGATGCTGTGTTTTAAGAGGGACAGTAGAAAATGGAAATACTTTCAGAGGAGAGCTGCCTAGATGTGAAAGATTCAGAAGCCAAGTTTCAAGGAGGAATTGCTGAAGAATCAGGGGATTGATATGGAAAGTAAAAACCTTGCATAGCAATGGCGTAATGGTTGTTTTTAAATATGGGAAGGACAGTCGTGTGGCTGAAGGATTTTTCTGGTTGGCACCAAAGGAATGAATCAGATGTGGTAGGGGAAAGTCATGAAGAGTCACAAGGACTTTGATGGTTACACAGTCTGGTGGGGCAGGAGCTAGGTGTCTCCGCAACAACTGGGTAAGTCCTGTTGGGATGTGAATGAGATGTCCTTGAACATTGGCTAGGACAGATGACCTTTGAGGCTGCGCCCAATTCTGAGAGGAAGCCAGTGATACTCCACAGGGTTCAGGCCGGGCTCAGTGGCTCACGCCTATAATCCCAGCACTTTGGGAGGCTGAGGTGGGTGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGCCAACATGGTTGAAACCCTGTCTCTACTACAAATACAAAAATTAGCCAGGTATGGTGGCACATGCTTGTAGCCCCAGCTACTTGGGAGGCTAAGGCAGGAGAATTGCTTGAACCTGGGAGACAGAGGTTGCAGTGAGCTGAGATCATGCCACTGCATTTCAGCCTAGGCAACAGGGCAAGACTTCGTTTCAAAAAAAAAAAAAAAACAGGTTTCAGACAGAGAGAAGAACAAGGGGCTATATGGCAGCACAGACAGGGCGGGCACAAGAGAGAATGCAAGGATGTGAAGAAAGGATCTTAGACATCCAAGCCTCACAGATAGATCAAACTCCTAAGCCCCCACGTATTGGCTTTATGGTCTTAAGCAAGTTGCTCAGCTTCTCTAAACCCCAGTTTCTTTATATAAAACAGTGTTCTGGCAGCTCTGTTCTAAGAATGATCACATATGTGCACACCATGGCAGAGCACCTGGCACACAGTAGGTACCTGATTAATTGTAGCTATCAATGAATGGGTAGAGACTGATCAGAACTTCAGGGTTGATTCTTGGTTTTTTATTCACCGTATCAGGTTCTTGAGTATCCCCAGATCACACCAATTTTCCCTCAATCTTATGCCCCCTTCCTATTCCCTGCCAGGGTCCCCTGTCCCGTCTCCACCCCTTATCATACCAGAAAGATGGGATCATCATGGCCAAGTGGGAGGCCTCAGCACTCACTCTTCCCTACATCCCCATTACTCCCCCATCCTCCCTCCCCAAGCTTCTCTGTCCCTTCATCTCCCCTTCCACAG
Seq C2 exon
GCCGCATCTGGCTGGACAACTTGAGCTGCAGTGGGACCGAGCAGAGTGTGACTGAATGTGCCTCCCGGGGCTGGGGGAACAGTGACTGTACGCACGATGAGGATGCTGGGGTCATCTGCAAAGACCAGCGCCTCCCTGGCTTCTCGGACTCCAATGTCATTGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000115318-LOXL3:NM_032603:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.076 A=NA C2=0.012
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PU(57.3=52.4)
A:
NA
C2:
PF0053013=SRCR=PD(41.7=72.7)
Main Inclusion Isoform:
NA
Other Skipping Isoforms:
Associated events
Other assemblies
Conservation
Chicken
(galGal4)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CATGCGACCTGTCAGTGTCTG
R:
CACTGCAGCTCAAGTTGTCCA
Band lengths:
347-2320
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)