DreALTA0018783-2/2 @ danRer10
Alternative 3'ss
Gene
ENSDARG00000044532 | nr4a2b
Description
nuclear receptor subfamily 4, group A, member 2b [Source:ZFIN;Acc:ZDB-GENE-040718-103]
Coordinates
chr6:12227656-12228857:+
Coord C1 exon
chr6:12227656-12227754
Coord A exon
chr6:12228007-12228023
Coord C2 exon
chr6:12228024-12228857
Length
17 bp
Sequences
Splice sites
5' ss Seq
GAGGTAAAC
5' ss Score
7.2
3' ss Seq
TGAGTTTTCTAACACTGCAGCCA
3' ss Score
5.14
Exon sequences
Seq C1 exon
AAAAGCAAGCGAACGAAGAGACGCTCTGACATCAACCGGTACAAGAGCCCTGACTTCAGAGATTGTTCCACGAGAGATAAAAGTAGCAGGTGTGCGGAG
Seq A exon
CCATGCCCTGCGTCCAG
Seq C2 exon
GCTCAGTATGGGACATCACCTCCAGGAGCCAGCCCTGCATCTCAGAGTTACAGCTACAACACCACGGGAGAGTACAACTGCGACTTCTTAACGCCGGAGTTTGTCAAGTTTAGCATGGACCTGACTAACGCAGAGATAGCTGTCACTTCTTCGCTCCCCAGTTTCAGCACCTTCGTGGACACCTACAACTCCAACTACGACGTGAAGCCTCCCTGCCTCTACCAAATGGCCCACTCTGGGGATCAGCTGTCCATCAAGGTGGAGGAGATACCCGCACACGGCTACCATCAGCAGCAGCACCATCAGCCGCATCAGGCTGAGGAGAGCATACCCCATACCGGAGCTATATACTATAAACCATCCACTCCAAACATCTCCCAGTCCCCCAGTTACCCAACGGCTCCACATCATACGTGGGAAGACACCGGATCCCTTCACAGCTTTCACCAGAACTACCTGGCGACGTCACATATTATGGACCAGCAGCGGAAAAACGCGAT
VastDB Features
Vast-tools module Information
Secondary ID
ENSDARG00000044532-2-2,2-1-2/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
5' UTR
No structure available
Features
Disorder rate (Iupred):
C1=NA A=NA C2=0.403
Domain overlap (PFAM):
C1:
NA
A:
NA
C2:
PF0010513=zf-C4=PU(38.6=9.5)
Main Skipping Isoform:
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:
CGAACGAAGAGACGCTCTGAC
R:
CTCCTGGAGGTGATGTCCCAT
Band lengths:
118-135
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]