HsaALTA0005820-1/3 @ hg38
Alternative 3'ss
Gene
ENSG00000153234 | NR4A2
Description
nuclear receptor subfamily 4 group A member 2 [Source:HGNC Symbol;Acc:HGNC:7981]
Coordinates
chr2:156329914-156330791:-
Coord C1 exon
chr2:156330668-156330791
Coord A exon
NA
Coord C2 exon
chr2:156329914-156330010
Length
0 bp
Sequences
Splice sites
5' ss Seq
AAGGTTAGT
5' ss Score
8.54
3' ss Seq
GCCACCACTTCTCTCCCCAGCTT
3' ss Score
7.43
Exon sequences
Seq C1 exon
GGAGGAGATTGGACAGGCTGGACTCCCCATTGCTTTTCTAAAAATCTTGGAAACTTTGTCCTTCATTGAATTACGACACTGTCCACCTTTAATTTCCTCGAAAACGCCTGTAACTCGGCTGAAG
Seq A exon
NA
Seq C2 exon
CTTCAGTACCTTTATGGACAACTACAGCACAGGCTACGACGTCAAGCCACCTTGCTTGTACCAAATGCCCCTGTCCGGACAGCAGTCCTCCATTAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSG00000153234-5-15,5-13,5-12-1/3
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
Protein isoform when splice site is used (No Ref, Alt. ATG)
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.558
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0010513=zf-C4=PU(38.6=12.0)
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GAGGAGATTGGACAGGCTGGA
R:
GTCCGGACAGGGGCATTTG
Band lengths:
203-364
Functional annotations
There are 2 annotated functions for this event
PMID: 16313515
Formed by alternative RNA splicing in exon 7 (HsaALTA1036233), nurr1a has a truncated carboxy-terminus, nurr1b has an internal deletion in the ligand-binding domain and nurr1c, newly identified in this study, has a novel carboxy-terminus produced by a frame shift downstream of the splice junction. Alternative RNA splicing in exon 3 (HsaALTA0005820) produces the isoform known as the transcriptionally-inducible nuclear receptor (TINUR), lacking the amino-terminus (when the internal Alt3 is used). Nurr2 and the newly identified nurr2c are produced by utilization of both exon 3 and exon 7 alternative splice sites. Transfection studies in dopaminergic SK-N-AS cells demonstrate that nurr1a, nurr1b, nurr1c and TINUR have significantly reduced transcriptional activities compared with full-length nurr1, while nurr2 and nurr2c are inactive. Furthermore, in these experiments, nurr2 and nurr2c both act as dominant negatives.
PMID: 16313515
Formed by alternative RNA splicing in exon 7 (HsaALTA1036233), nurr1a has a truncated carboxy-terminus, nurr1b has an internal deletion in the ligand-binding domain and nurr1c, newly identified in this study, has a novel carboxy-terminus produced by a frame shift downstream of the splice junction. Alternative RNA splicing in exon 3 (HsaALTA0005820) produces the isoform known as the transcriptionally-inducible nuclear receptor (TINUR), lacking the amino-terminus (when the internal Alt3 is used). Nurr2 and the newly identified nurr2c are produced by utilization of both exon 3 and exon 7 alternative splice sites. Transfection studies in dopaminergic SK-N-AS cells demonstrate that nurr1a, nurr1b, nurr1c and TINUR have significantly reduced transcriptional activities compared with full-length nurr1, while nurr2 and nurr2c are inactive. Furthermore, in these experiments, nurr2 and nurr2c both act as dominant negatives.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]
SPECIAL DATASETS
- Autistic and control brains