HsaINT0091013 @ hg19
Intron Retention
Gene
ENSG00000184925 | LCN12
Description
lipocalin 12 [Source:HGNC Symbol;Acc:28733]
Coordinates
chr9:139846768-139847480:+
Coord C1 exon
chr9:139846768-139846893
Coord A exon
chr9:139846894-139847343
Coord C2 exon
chr9:139847344-139847480
Length
450 bp
Sequences
Splice sites
5' ss Seq
CAGGTACAG
5' ss Score
8.68
3' ss Seq
GCCCACCACCGCCTCTGTAGTTC
3' ss Score
3.7
Exon sequences
Seq C1 exon
GCAGCTGCCAGGATGAGGCTGCTGTGTGGCCTGTGGCTGTGGCTCTCCTTGCTGAAAGTCCTGCAGGCCCAGACCCCAACCCCCCTGCCACTCCCGCCCCCGATGCAGAGCTTCCAAGGAAACCAG
Seq A exon
GTACAGGGGTTTTGACGGAAGGAGAAGCAGCCGGCTGGGTCTGAGTGCAGGGAGAGGCTGGTGGCTGAGCAGGCCTGGGGATGCTGCCCAGAGAGCCAGGACCAGCCGTGCTTCCAGGAGCCCCCAGGCGGGCCCCTGACCTCCAGCAGAGGAGGGCCCAGCGCAGACCTTCCTGGCACCCATTCCCTGCCGTCAGCCCAGCCCATCGCTCCCTCTGTGCGTGAGGGGAAACAGGCTCGGGAAGGCCGCACAGCCACTGGCCAGGGTCACCATGTCCCTGCCAGACCCAGAGTAGGCTCTGGTTCTTGCCAGTGTCCCTGGCGCCGGCCCAGCCAGGAGCACTGCTCTGTGAGGGGTCCAGAAGCTGCCAGGGAGGGCGGGAGGGGGCTCCTGACCCTGCCCACTGCCACCCCTGCCCACCGCCGCCCCTGCCCACCACCGCCTCTGTAG
Seq C2 exon
TTCCAGGGGGAATGGTTCGTCCTGGGCCTGGCGGGCAACAGCTTCAGGCCGGAGCACAGGGCGCTGCTGAACGCTTTCACCGCAACTTTTGAGCTAAGTGATGATGGCCGCTTTGAGGTGTGGAATGCGATGACTCG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000184925-LCN12:NM_178536:1
Average complexity
IR-S
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion (1st CDS intron)
No structure available
Features
Disorder rate (Iupred):
C1=0.184 A=NA C2=0.000
Domain overlap (PFAM):
C1:
NO
A:
NA
C2:
PF0006118=Lipocalin=PU(30.3=95.7)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Rat
(rn6)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCAGCTGCCAGGATGAGG
R:
GAGTCATCGCATTCCACACCT
Band lengths:
262-712
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)