BtaALTA0020369-1/2 @ 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
chr2:40015222-40015995:+
Coord C1 exon
chr2:40015222-40015424
Coord A exon
NA
Coord C2 exon
chr2:40015938-40015995
Length
0 bp
Sequences
Splice sites
5' ss Seq
CAGGTAATG
5' ss Score
9.43
3' ss Seq
AATTCTCCTCCAACTTGCAGAAT
3' ss Score
8.88
Exon sequences
Seq C1 exon
TTCCAGGCGAACCCTGACTATCAGATGAGTGGAGATGACACCCAGCATATCCAGCAATTCTATGATCTCCTGACTGGCTCCATGGAGATCATCAGGGGCTGGGCAGAGAAGATCCCGGGCTTCACTGACCTGCCCAAAGCCGACCAAGACCTGCTTTTCGAATCGGCTTTCTTAGAACTATTTGTGCTGCGATTAGCCTACAG
Seq A exon
NA
Seq C2 exon
AATATGAACATCGACATTTCTGCCTTCTCCTGCATCGCTGCCCTGGCTATGGTCACAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000003650-12-9,12-8-1/2
Average complexity
Alt3
Mappability confidence:
NA
Protein Impact
In the CDS, with uncertain impact
No structure available
Features
Disorder rate (Iupred):
C1=0.015 A=NA C2=NA
Domain overlap (PFAM):
C1:
PF0010425=Hormone_recep=FE(33.8=100)
A:
NA
C2:
NA
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal3)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
CCTGACTGGCTCCATGGAGAT
R:
CGATGCAGGAGAAGGCAGAAA
Band lengths:
172-239
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]
SPECIAL DATASETS
- Pre-implantation embryo development