RnoALTA0026946-2/2 @ rn6
Alternative 3'ss
Gene
ENSRNOG00000005600 | Nr4a2
Description
nuclear receptor subfamily 4, group A, member 2 [Source:RGD Symbol;Acc:3202]
Coordinates
chr3:43113002-43113705:-
Coord C1 exon
chr3:43113503-43113705
Coord A exon
chr3:43113060-43113126
Coord C2 exon
chr3:43113002-43113059
Length
67 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
AATGGGGTGGTCTTGCACAGGTT
3' ss Score
5.26
Exon sequences
Seq C1 exon
TTCCAGGCAAACCCTGACTATCAGATGAGTGGAGATGATACTCAACATATCCAGCAGTTCTACGATCTCCTGACTGGCTCTATGGAGATCATCAGAGGGTGGGCAGAGAAGATTCCTGGCTTTGCTGACCTGCCCAAAGCCGATCAGGACCTGCTTTTTGAATCAGCTTTCTTAGAATTATTTGTTCTACGCTTAGCATACAG
Seq A exon
GTTGCAATGCGTGCGTGGCTTTGGGGAATGGATTGATTCCATTGTTGAATTCTCCTCCAACTTGCAG
Seq C2 exon
AATATGAACATCGACATTTCTGCCTTCTCCTGCATTGCTGCCCTGGCTATGGTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSRNOG00000005600-12-12,12-11-2/2
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=0.022 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(33.8=100)
A:
NA
C2:
PF0010425=Hormone_recep=PD(16.5=75.0)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Associated events
Conservation
Mouse
(mm9)
No conservation detected
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
ACGATCTCCTGACTGGCTCTA
R:
GCAATGCAGGAGAAGGCAGAA
Band lengths:
180-247
Functional annotations
There are 1 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.
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]