HsaINT0091014 @ hg19
Intron Retention
Gene
ENSG00000184925 | LCN12
Description
lipocalin 12 [Source:HGNC Symbol;Acc:28733]
Coordinates
chr9:139847344-139848231:+
Coord C1 exon
chr9:139847344-139847480
Coord A exon
chr9:139847481-139848151
Coord C2 exon
chr9:139848152-139848231
Length
671 bp
Sequences
Splice sites
5' ss Seq
TCGGTGAGT
5' ss Score
11.11
3' ss Seq
CCACCTGTCCCCTCCTACAGAGG
3' ss Score
10.19
Exon sequences
Seq C1 exon
TTCCAGGGGGAATGGTTCGTCCTGGGCCTGGCGGGCAACAGCTTCAGGCCGGAGCACAGGGCGCTGCTGAACGCTTTCACCGCAACTTTTGAGCTAAGTGATGATGGCCGCTTTGAGGTGTGGAATGCGATGACTCG
Seq A exon
GTGAGTGGCTGTCCCTGCCGTTCCAAGCGGGTGAGGAGGATCCCGGGCCTGGGTCCCAGCCGCCAGTGGCTCAGGTGCGCCATGGGCCCTGTCCCAGCACAGGCAGCTTCATGACTCTGCCTGCCAATGACCAAACCCAGCTGGGGAGTATACAAAAAAGTGTGGGCAGCTGGGCGCGCTGGCTCACACCTGTAATCCTAGCACTTCGGGGGCCGGGTGCGCTGGCTCACACCTGTAATCCCAGCACTTCCGGGGCTGGGCGCGCTGGCTCACACCTGTAATCCCAGGACTTCAGGGGCCGGGCGCGCTGGCTCACACCTGTAATCCTAGCACTTTGGGGGCCGGGCGCGGTCGCGCACACCTGTAATCCTAGCACTTTGGGGGCCGGGCGCGGTGGCGCACACCTGTAATCCCAGCACTTTAGGGGCCGGGCGCAGTGGCGCACACCTGTAATCCCAGTACTTCAGGAGGCAGAGGCAGAAGGATCACTTGAACTCAGGAGTTTGAGACCAGCCTGAGCAACATAGTTAGACACCATCTCCACTCATGACGCTTGGCCACTCCCGCCGTGGGTCCCTCTGAATAAGTGGCTGAAATCTCCTGAGGGGCCCACCTCAGCATGGACCTGCCAGCTTCCGGAGCCTTCCGCCTCCACCTGTCCCCTCCTACAG
Seq C2 exon
AGGCCAGCACTGTGACACATGGTCTTATGTGCTGATACCGGCAGCCCAGCCTGGGCAGTTCACTGTGGACCACGGTGTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000184925-LCN12:NM_178536:2
Average complexity
IR-C
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.202
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=PU(30.3=95.7)
A:
NA
C2:
PF0006118=Lipocalin=FE(55.1=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:
TCCAGGGGGAATGGTTCGTC
R:
ACACCGTGGTCCACAGTGAA
Band lengths:
214-885
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)