HsaALTA0007450-2/2 @ hg19
Alternative 3'ss
Gene
ENSG00000204231 | RXRB
Description
retinoid X receptor, beta [Source:HGNC Symbol;Acc:10478]
Coordinates
chr6:33163140-33163479:-
Coord C1 exon
chr6:33163347-33163479
Coord A exon
chr6:33163232-33163243
Coord C2 exon
chr6:33163140-33163231
Length
12 bp
Sequences
Splice sites
5' ss Seq
TCGGTCAGT
5' ss Score
7.03
3' ss Seq
GACCTTTGAGTGACCTGCAGGTC
3' ss Score
3.43
Exon sequences
Seq C1 exon
GCTGGAATGAACTCCTCATTGCCTCCTTCTCACACCGATCCATTGATGTTCGAGATGGCATCCTCCTTGCCACAGGTCTTCACGTGCACCGCAACTCAGCCCATTCAGCAGGAGTAGGAGCCATCTTTGATCG
Seq A exon
GTCCCTCTCCAG
Seq C2 exon
GGTGCTGACAGAGCTAGTGTCCAAAATGCGTGACATGAGGATGGACAAGACAGAGCTTGGCTGCCTGAGGGCAATCATTCTGTTTAATCCAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000204231-7-9,7-8-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref)
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(23.5=100)
A:
NA
C2:
PF0010425=Hormone_recep=FE(16.9=100)
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Other assemblies
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TCAGCAGGAGTAGGAGCCATC
R:
CAGCCAAGCTCTGTCTTGTCC
Band lengths:
92-104
Functional annotations
There are 1 annotated functions for this event
PMID: 9150434
This event
A Four-Amino-Acid Insertion in the Ligand-Binding Domain Inactivates hRXRbeta and Renders Dominant Negative Activity
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- The Cancer Genome Atlas (TCGA)
- 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)