HsaINT0091016 @ hg38
Intron Retention
Gene
ENSG00000184925 | LCN12
Description
lipocalin 12 [Source:HGNC Symbol;Acc:HGNC:28733]
Coordinates
chr9:136953924-136954255:+
Coord C1 exon
chr9:136953924-136953964
Coord A exon
chr9:136953965-136954153
Coord C2 exon
chr9:136954154-136954255
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
ACACACGAGCAGGCTGGCCGTCCTCAGGATCAGCCTGCTGG
Seq A exon
GTGAGCCTCCCACCCCGTCCTGGGCCCGTGTGTGGCCCTGGAGGCACCTCCTTCCAGGCTTTGGGTCAGACCCTGCCTCCCCACCCCGCCTGGAGTGACTTGGGGGTACAGATAGTTCAATCTCCCACCTACCCAGCCCCCAACCCCCTGCCAAGTGCACAGACCCATGCTGGGCTCCCTGGGCTGCAG
Seq C2 exon
GCAGGAGCTGGTTGCTGCCTCCCGGGACGCTGGACCAGTTCATCTGCCTGGGCAGAGCTCAGGGCCTCTCGGATGACAACATCGTCTTCCCAGATGTGACTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000184925:ENST00000491316:4
Average complexity
IR
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.123 A=NA C2=0.015
Domain overlap (PFAM):
C1:
NO
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:
ACACACGAGCAGGCTGGC
R:
CAGTCACATCTGGGAAGACGA
Band lengths:
143-332
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