HsaINT0091038 @ hg19
Intron Retention
Gene
ENSG00000204001 | LCN8
Description
lipocalin 8 [Source:HGNC Symbol;Acc:27038]
Coordinates
chr9:139649696-139649968:-
Coord C1 exon
chr9:139649864-139649968
Coord A exon
chr9:139649786-139649863
Coord C2 exon
chr9:139649696-139649785
Length
78 bp
Sequences
Splice sites
5' ss Seq
TTAGTAAGC
5' ss Score
4.41
3' ss Seq
AGCCCCCCTGTGCCCCACAGCTC
3' ss Score
7.43
Exon sequences
Seq C1 exon
GCCACAGAGAGATCCACGTGCTGGACACCGACTACGAGGGCTACGCCATCCTGCGGGTGTCCCTGATGTGGCGGGGCAGGAACTTTCGCGTCCTCAAGTACTTTA
Seq A exon
GTAAGCTTGGCCCTGGGGGGCTCTGCCCAGCTGCTGCTCTCCCAGGGACTGCCCGCCCAGCCCCCCTGTGCCCCACAG
Seq C2 exon
CTCGGAGCCTTGAGGACAAGGACCGGCTGGGGTTCTGGAAGTTTCGGGAGCTGACAGCAGACACTGGTCTCTACCTGGCGGCCCGGCCTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204001-LCN8:NM_178469:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
Alternative protein isoforms
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(27.8=100)
A:
NA
C2:
PF0006118=Lipocalin=PD(19.0=77.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CACAGAGAGATCCACGTGCTG
R:
GACCAGTGTCTGCTGTCAGC
Band lengths:
172-250
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)