GgaINT1016954 @ galGal4
Intron Retention
Gene
ENSGALG00000023172 | LRP5L
Description
low density lipoprotein receptor-related protein 5-like [Source:HGNC Symbol;Acc:HGNC:25323]
Coordinates
chr4:48989500-48990107:+
Coord C1 exon
chr4:48989500-48989708
Coord A exon
chr4:48989709-48989934
Coord C2 exon
chr4:48989935-48990107
Length
226 bp
Sequences
Splice sites
5' ss Seq
AGTCTACTA
5' ss Score
-16.19
3' ss Seq
CCCCCCACTCCACTCTTTGGGCC
3' ss Score
-0.8
Exon sequences
Seq C1 exon
GGGACAGCCCCAAATCCAGGCTCATGTTCCAGTGCCTGTGCCTCTGCCAGTGCCAGCAAGCAAAGGACCTGCCCTGCCACTCCCTCCACCTGTGACCACCACTACGAGGACAACCACAGCCACATCTGCTCAGCCCACCACCTCCACCACACAGCTCCCACTGAGCAAGACCACTGCTGCGCCTACCACGCCTGCAACAACCACCAAGT
Seq A exon
CTACTACAACACTGACCACCACCAGCCTGTCCGCCACAACCACAACCGCCTCTGCACCAACCACCACATGGACAACCTCAAACAAAACAACCACCGTGCAGGTAGCCACCACCAGCACCGCCACCACCCGGTCCTTGCCAACCAAGCCTGCTGTCCCACAGCTAAGCACTAGCACCCAACCCCCAACCACTCCTGCACTGGCAGTTCCCCCCACTCCACTCTTTGG
Seq C2 exon
GCCCAGCCCTCCACACCCCCCAACCCGGTTCTCCCATCTCTCCTGTCCTCGCACACACATGCCCTGCCGTGACGGCGCTGAGTGCGTGGCCCAGGAGTACGTGTGTGATGGAGAGAAGGACTGTGCGGATGGCTCTGACGAGGATGAGTGTGCCCAGCTCTGTGACGCCCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSGALG00000023172:ENSGALT00000037928:17
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=0.017
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0005713=Ldl_recept_a=WD(100=64.4),PF0005713=Ldl_recept_a=PU(15.4=10.2)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Human
(hg19)
No conservation detected
Mouse
(mm9)
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:
CTCATGTTCCAGTGCCTGTGC
R:
CATCACACACGTACTCCTGGG
Band lengths:
299-525
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]