HsaINT0091039 @ hg19
Intron Retention
Gene
ENSG00000204001 | LCN8
Description
lipocalin 8 [Source:HGNC Symbol;Acc:27038]
Coordinates
chr9:139649587-139649785:-
Coord C1 exon
chr9:139649696-139649785
Coord A exon
chr9:139649613-139649695
Coord C2 exon
chr9:139649587-139649612
Length
83 bp
Sequences
Splice sites
5' ss Seq
CTGGTGAGC
5' ss Score
8.05
3' ss Seq
CATGCTGGCCTATCCTGCAGGGC
3' ss Score
8.88
Exon sequences
Seq C1 exon
CTCGGAGCCTTGAGGACAAGGACCGGCTGGGGTTCTGGAAGTTTCGGGAGCTGACAGCAGACACTGGTCTCTACCTGGCGGCCCGGCCTG
Seq A exon
GTGAGCCCAGGGGCCTTGGGGTGGAGGCTGGGCTGGGCCCTGTGGGCTGACTCTGCAGCTCCTCATGCTGGCCTATCCTGCAG
Seq C2 exon
GGCGGTGTGCCGAGCTCCTGAAGGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204001-LCN8:NM_178469:5
Average complexity
IR-S
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:
PF0006118=Lipocalin=PD(19.0=77.4)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CTCGGAGCCTTGAGGACAA
R:
CTTCAGGAGCTCGGCACAC
Band lengths:
113-196
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)