BtaALTA0020370-1/2 @ bosTau6
Alternative 3'ss
Gene
ENSBTAG00000003650 | NR4A2
Description
Bos taurus nuclear receptor subfamily 4, group A, member 2 (NR4A2), mRNA. [Source:RefSeq mRNA;Acc:NM_001076208]
Coordinates
chr2:40011367-40012838:+
Coord C1 exon
chr2:40011367-40011490
Coord A exon
NA
Coord C2 exon
chr2:40012151-40012838
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
GGAGGCGATCTGACAGGCTGGGCTCTCCACTGCTCTTCTAAAAATCTTGGAAACTTTGTCCTTCATTGAATTACGACACTGTCCACCTTTAATTTTCTCCAAAACGCCTGTAACTCGGCTGAAG
Seq A exon
NA
Seq C2 exon
CTTCAGTACCTTTATGGACAACTACAGCACAGGCTACGACGTCAAGCCACCTTGCTTGTACCAAATGCCCCTGTCCGGACAGCAGTCCTCCATTAAGGTAGAAGACATTCAGATGCACAACTACCAGCAACACAGCCACCTGCCCCCACAGTCCGAGGAGATGATGCCGCACTCCGGGTCCGTTTACTACAAGCCCTCCTCGCCCCCGACGCCCACCACCCCGGGCTTCCAGGTGCAGCACAGCCCCATGTGGGACGACCCAGGCTCCCTCCACAACTTCCACCAGAACTACGTGGCCACTACCCACATGATCGAACAGAGGAAAACGCCGGTCTCCCGCCTTTCCCTCTTCTCCTTTAAGCAGTCGCCCCCCGGAACCCCCGTGTCTAGCTGCCAGATGCGCTTCGATGGGCCCCTGCACGTCCCCATGAACCCGGAGCCAGCGGGCAGCCACCACGTGGTGGACGGGCAGACCTTCGCCGTGCCCAACCCCATCCGAA
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003650-7-3,7-2-1/2
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=0.507
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0010513=zf-C4=PU(38.6=9.4)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GGGCTCTCCACTGCTCTTCTA
R:
TGGCTGTGTTGCTGGTAGTTG
Band lengths:
243-421
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
- Pre-implantation embryo development