HsaINT0091016 @ hg19
Intron Retention
Gene
ENSG00000184925 | LCN12
Description
lipocalin 12 [Source:HGNC Symbol;Acc:28733]
Coordinates
chr9:139848300-139848707:+
Coord C1 exon
chr9:139848300-139848416
Coord A exon
chr9:139848417-139848605
Coord C2 exon
chr9:139848606-139848707
Length
189 bp
Sequences
Splice sites
5' ss Seq
TGGGTGAGC
5' ss Score
7.23
3' ss Seq
CTGGGCTCCCTGGGCTGCAGGCA
3' ss Score
4.64
Exon sequences
Seq C1 exon
AGCCCGGGGCGGACAGAGAGGAGACCCGGGTGGTGGACAGCGACTACACCCAGTTCGCCCTGATGCTGTCCCGCAGACACACGAGCAGGCTGGCCGTCCTCAGGATCAGCCTGCTGG
Seq A exon
GTGAGCCTCCCACCCCGTCCTGGGCCCGTGTGTGGCCCTGGAGGCACCTCCTTCCAGGCTTTGGGTCAGACCCTGCCTCCCCACCCCGCCTGGAGTGACTTGGGGGTACAGATAGTTCAATCTCCCACCTACCCAGCCCCCAACCCCCTGCCAAGTGCACAGACCCATGCTGGGCTCCCTGGGCTGCAG
Seq C2 exon
GCAGGAGCTGGTTGCTGCCTCCCGGGACGCTGGACCAGTTCATCTGCCTGGGCAGAGCTCAGGGCCTCTCGGATGACAACATCGTCTTCCCAGATGTGACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000184925-LCN12:NM_178536:4
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.146 A=NA C2=0.020
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(26.9=100)
A:
NA
C2:
PF0006118=Lipocalin=FE(23.4=100)
Main Inclusion Isoform:
NA
Other Inclusion 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:
CGGACAGAGAGGAGACCCG
R:
CAGTCACATCTGGGAAGACGA
Band lengths:
210-399
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Genotype-Tissue Expression Project (GTEx)
- 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)