Human Gene TRA2A (uc003swi.3) Description and Page Index
  Description: Homo sapiens transformer 2 alpha homolog (Drosophila) (TRA2A), mRNA.
RefSeq Summary (NM_013293): This gene is a member of the transformer 2 homolog family and encodes a protein with several RRM (RNA recognition motif) domains. This phosphorylated nuclear protein binds to specific RNA sequences and plays a role in the regulation of pre-mRNA splicing. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2013].
Transcript (Including UTRs)
   Position: hg19 chr7:23,544,401-23,571,656 Size: 27,256 Total Exon Count: 8 Strand: -
Coding Region
   Position: hg19 chr7:23,545,178-23,571,443 Size: 26,266 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:23,544,401-23,571,656)mRNA (may differ from genome)Protein (282 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: TRA2A_HUMAN
DESCRIPTION: RecName: Full=Transformer-2 protein homolog alpha; Short=TRA-2 alpha; Short=TRA2-alpha; AltName: Full=Transformer-2 protein homolog A;
FUNCTION: Sequence-specific RNA-binding protein which participates in the control of pre-mRNA splicing.
SUBUNIT: Binds to A3 enhancer proteins SRp75, SRp55, SRp40 and SRp30.
SUBCELLULAR LOCATION: Nucleus.
PTM: Phosphorylated in the RS domains.
SIMILARITY: Belongs to the splicing factor SR family.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): TRA2A
CDC HuGE Published Literature: TRA2A
Positive Disease Associations: Iron
Related Studies:
  1. Iron
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 49.15 RPKM in Ovary
Total median expression: 1492.32 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -91.00213-0.427 Picture PostScript Text
3' UTR -171.25777-0.220 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

ModBase Predicted Comparative 3D Structure on Q13595
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
 Protein SequenceProtein Sequence   
 AlignmentAlignment   

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing

Cellular Component:
GO:0005634 nucleus
GO:0005730 nucleolus
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  AB097048 - Homo sapiens mRNA for putative MAPK activating protein, complete cds, clone: PM24.
BC017094 - Homo sapiens transformer 2 alpha homolog (Drosophila), mRNA (cDNA clone MGC:10169 IMAGE:3907327), complete cds.
U53209 - Human transformer-2 alpha (htra-2 alpha) mRNA, complete cds.
AK300741 - Homo sapiens cDNA FLJ50689 complete cds, highly similar to Transformer-2 protein homolog.
AK298815 - Homo sapiens cDNA FLJ50614 complete cds, highly similar to Transformer-2 protein homolog.
AK300565 - Homo sapiens cDNA FLJ50682 complete cds, highly similar to Transformer-2 protein homolog.
AK314801 - Homo sapiens cDNA, FLJ95674, Homo sapiens transformer-2 alpha (htra-2 alpha) (HSU53209), mRNA.
CU677835 - Synthetic construct Homo sapiens gateway clone IMAGE:100018717 5' read TRA2A mRNA.
DQ892442 - Synthetic construct clone IMAGE:100005072; FLH186353.01X; RZPDo839D0871D transformer-2 alpha (TRA2A) gene, encodes complete protein.
DQ895653 - Synthetic construct Homo sapiens clone IMAGE:100010113; FLH186349.01L; RZPDo839D0861D transformer-2 alpha (TRA2A) gene, encodes complete protein.
KJ893705 - Synthetic construct Homo sapiens clone ccsbBroadEn_03099 TRA2A gene, encodes complete protein.
AB528532 - Synthetic construct DNA, clone: pF1KE0693, Homo sapiens TRA2A gene for transformer 2 alpha homolog, without stop codon, in Flexi system.
AK310719 - Homo sapiens cDNA, FLJ17761.
AK311687 - Homo sapiens cDNA, FLJ18729.
BC069011 - Homo sapiens cDNA clone IMAGE:5924874, with apparent retained intron.
DQ589264 - Homo sapiens piRNA piR-56376, complete sequence.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome

-  Other Names for This Gene
  Alternate Gene Symbols: NM_013293, NP_037425, Q13595, TRA2A_HUMAN
UCSC ID: uc003swi.3
RefSeq Accession: NM_013293
Protein: Q13595 (aka TRA2A_HUMAN or TR2A_HUMAN)
CCDS: CCDS5383.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_013293.3
exon count: 8CDS single in 3' UTR: no RNA size: 1852
ORF size: 849CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1049.00frame shift in genome: no % Coverage: 99.30
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.