HsaINT0091017 @ hg38
Intron Retention
Gene
ENSG00000184925 | LCN12
Description
lipocalin 12 [Source:HGNC Symbol;Acc:HGNC:28733]
Coordinates
chr9:136954154-136954826:+
Coord C1 exon
chr9:136954154-136954255
Coord A exon
chr9:136954256-136954723
Coord C2 exon
chr9:136954724-136954826
Length
468 bp
Sequences
Splice sites
5' ss Seq
CTGGTAACA
5' ss Score
4.6
3' ss Seq
GGAGCTTGGACTCATCCCAGGAG
3' ss Score
0.76
Exon sequences
Seq C1 exon
GCAGGAGCTGGTTGCTGCCTCCCGGGACGCTGGACCAGTTCATCTGCCTGGGCAGAGCTCAGGGCCTCTCGGATGACAACATCGTCTTCCCAGATGTGACTG
Seq A exon
GTAACATGGTTCACCTGCAGGCATGCTGGGCAGTAGGCACGGGGCCCGCAGGAATGAGTTTGGTTGACCCTAGAGGAGCTGGACCCAGTGTCTACCCAGGGAGCTCAGCCCCAGCCTGCGCTCAGGGGTCTCCAGGCTCCTGGGTCCCTGTGCTCAACCCAGGCTCTGAGCCACCTCCTGCCGCCCCGGGTCCCCTGTCCTGGGCCACCTCCTCCCACCCCGGGTCTCCTGTCCCGGGCCACCTCCTCCCGCCCCAGGTCCCCTGTCCCGGGCCACCTCCCCCTGCCCCTCCCGCCCCAGGTCCCCTGTCCCGGCCCACCTCCTCCCACCCCGGGTCTCCTGTCCTGGGCTACCTCCTCCCACCCCAGGTCCCCTGTCCCGGGCCATCTCCTCCCTCTGGGTCCCCTGTCCTGGGCCACCTCCTCCCCTCACCCATCCCTGCTCACAAGGAGCTTGGACTCATCCCAG
Seq C2 exon
GAGGTGCCCTGGACCTCAGCAGCCTGCCCTGGGTGGCAGCCCCAGCCTGACCACTCAGACAGCCGCGGCCCCCAAGGCCTGACTCTTCTTGTGGGAGGGCGAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000184925:ENST00000491316:5
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.015 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(23.4=100)
A:
NA
C2:
NO
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Other assemblies
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGACGCTGGACCAGTTCAT
R:
CTCGCCCTCCCACAAGAAGAG
Band lengths:
182-650
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