GgaINT1016859 @ galGal4
Intron Retention
Gene
ENSGALG00000013254 | LOXL3
Description
lysyl oxidase-like 3 [Source:HGNC Symbol;Acc:HGNC:13869]
Coordinates
JH375171.1:160636-161112:+
Coord C1 exon
JH375171.1:160636-160695
Coord A exon
JH375171.1:160696-160892
Coord C2 exon
JH375171.1:160893-161112
Length
197 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAT
5' ss Score
8.39
3' ss Seq
GCTCTGGTCTCTCCTTGCAGGCT
3' ss Score
10.86
Exon sequences
Seq C1 exon
GCTGGCCTCCAAATCTCAGCCTAAACAAAAGCGCAGGGAGGACGTAGGGTCCAGGAAGAG
Seq A exon
GTAAATGGCTCCCGTGGAGAGCCTGAGTGCCAGGATCCCAGCTCAGCACTGCCAAAGCCGTGTGTGTCCCTGCACTGCTGGGACGTGGGGAATGGAGCAGGCAGGGGTGGGATCCCAGGGGCAGGGACCGTACAGCTGCAGGCAGGTGACACCTCTGCTCTGCTGGCTGTTGCTCAGGCTCTGGTCTCTCCTTGCAG
Seq C2 exon
GCTGTTTGCGGAGCGGCAGCAGCTCAACTACCGCCTGCACTCAGTGTCCTGCACAGGGACAGAGGTGCACATCTCCATGTGCACGTTCCAGTTCTACCGGGGCAACTCCTCAGCAGCCTGCAGCACTGGCATGCCCGCTGTTGTCAGCTGCCTGCCCGGGCCCCTCTTTGCTACCAGCAGCACCCAGAAGAAGAAGCAGCGCCAGCAGCAGCAGAGCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013254:ENSGALT00000021647:12
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.952 A=NA C2=0.203
Domain overlap (PFAM):
C1:
PF0053013=SRCR=FE(14.3=100)
A:
NA
C2:
PF0053013=SRCR=PD(36.4=68.9)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg38)
No conservation detected
Human
(hg19)
No conservation detected
Mouse
(mm10)
No conservation detected
Mouse
(mm9)
No conservation detected
Rat
(rn6)
No conservation detected
Cow
(bosTau6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGGCCTCCAAATCTCAGCCTA
R:
TTCTTCTGGGTGCTGCTGGTA
Band lengths:
250-447
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]