HsaALTA0004718-2/2 @ hg38
Alternative 3'ss
Gene
ENSG00000184925 | LCN12
Description
lipocalin 12 [Source:HGNC Symbol;Acc:HGNC:28733]
Coordinates
chr9:136953700-136953964:+
Coord C1 exon
chr9:136953700-136953779
Coord A exon
chr9:136953848-136953923
Coord C2 exon
chr9:136953924-136953964
Length
76 bp
Sequences
Splice sites
5' ss Seq
TGGGTAAGC
5' ss Score
8.84
3' ss Seq
TGACGTCTGTGCCGCCTCAGAGC
3' ss Score
6.92
Exon sequences
Seq C1 exon
AGGCCAGCACTGTGACACATGGTCTTATGTGCTGATACCGGCAGCCCAGCCTGGGCAGTTCACTGTGGACCACGGTGTGG
Seq A exon
AGCCCGGGGCGGACAGAGAGGAGACCCGGGTGGTGGACAGCGACTACACCCAGTTCGCCCTGATGCTGTCCCGCAG
Seq C2 exon
ACACACGAGCAGGCTGGCCGTCCTCAGGATCAGCCTGCTGG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000184925-14-22,14-20-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
ORF disruption when splice site is used (sequence inclusion)
No structure available
Features
Disorder rate (Iupred):
C1=0.152 A=NA C2=0.138
Domain overlap (PFAM):
C1:
PF0006118=Lipocalin=FE(18.6=100)
A:
NA
C2:
NO
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCAGCACTGTGACACATGGT
R:
AGGCTGATCCTGAGGACGG
Band lengths:
113-189
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- Autistic and control brains
- Pre-implantation embryo development