GgaINT1016864 @ galGal4
Intron Retention
Gene
ENSGALG00000013254 | LOXL3
Description
lysyl oxidase-like 3 [Source:HGNC Symbol;Acc:HGNC:13869]
Coordinates
JH375171.1:162838-163328:+
Coord C1 exon
JH375171.1:162838-162993
Coord A exon
JH375171.1:162994-163165
Coord C2 exon
JH375171.1:163166-163328
Length
172 bp
Sequences
Splice sites
5' ss Seq
ACGGTAGGT
5' ss Score
10.15
3' ss Seq
GGCCTTCTCCCCCACCCCAGGAG
3' ss Score
7.93
Exon sequences
Seq C1 exon
ATCCGCCTGGCCGGGGGGAGGACAGAGTTCGAGGGCCGCGTGGAGGTGAAGCGCGGCAGTAAGTGGGGCACTGTGTGCAGCGACGGCTGGACCACCAAGGAGGCGATGGTGGTCTGTCGCCAGCTGGGCCTGGGCTACTCCCTGCACGCGGTGACG
Seq A exon
GTAGGTGCGGTGCGGTGCGGTGTGGTGGCCCTCGTGCTTCCCTGACAGCCACGGGGCGATGGGATGTGGCTGATACATGCCGTGAGATGGGGTCGCTGTGGGTGTGTGGGTGCACAGGCTGGGGGTACTGCAGCATGCATGGCGTCCTGCCCGGCCTTCTCCCCCACCCCAG
Seq C2 exon
GAGACGTGGTACTGGGATGCCAGCAACGTGACAGAAATGGTGCTGAGTGGTGTGAAGTGCGCTGGCCATGAGCTGTCCCTGAGCCACTGCCAGCACCACGGCAGCAGCCTGAACTGCAGGAACACGGGAACGCGCTTCGCTGCCGGTGTCATCTGCTCTGAAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000013254:ENSGALT00000021647:17
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=0.000
Domain overlap (PFAM):
C1:
PF0053013=SRCR=PD(0.1=0.0),PF0053013=SRCR=PU(47.1=92.3)
A:
NA
C2:
PF0053013=SRCR=PD(51.0=94.5)
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:
CAGTAAGTGGGGCACTGTGTG
R:
GAGCAGATGACACCGGCAG
Band lengths:
258-430
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]