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    THRAP3 thyroid hormone receptor associated protein 3 [ Homo sapiens (human) ]

    Gene ID: 9967, updated on 3-Nov-2024

    Summary

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    Official Symbol
    THRAP3provided by HGNC
    Official Full Name
    thyroid hormone receptor associated protein 3provided by HGNC
    Primary source
    HGNC:HGNC:22964
    See related
    Ensembl:ENSG00000054118 MIM:603809; AllianceGenome:HGNC:22964
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    BCLAF2; TRAP150
    Summary
    Enables nuclear thyroid hormone receptor binding activity; phosphoprotein binding activity; and transcription coactivator activity. Involved in positive regulation of circadian rhythm and regulation of gene expression. Acts upstream of or within positive regulation of transcription by RNA polymerase II. Located in exon-exon junction complex and nuclear speck. Part of mediator complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in lymph node (RPKM 27.3), thyroid (RPKM 26.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See THRAP3 in Genome Data Viewer
    Location:
    1p34.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (36207637..36305357)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (36070513..36168203)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (36690044..36770958)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 655 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 656 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36625977-36626754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 745 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 746 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:36638149-36639348 Neighboring gene MAP7 domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 657 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36643121-36643768 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36643769-36644414 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36644415-36645060 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36653458-36654156 Neighboring gene RNA, 7SL, cytoplasmic 131, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr1:36680691-36680811 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 747 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:36689434-36689961 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:36689962-36690490 Neighboring gene Sharpr-MPRA regulatory regions 10257 and 14041 Neighboring gene ubiquitin conjugating enzyme E2 V2 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 659 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:36726300-36726456 Neighboring gene Sharpr-MPRA regulatory region 2392 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 660 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36772217-36773017 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36786744-36787628 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36788515-36789399 Neighboring gene SH3 domain containing 21 Neighboring gene eva-1 homolog B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36823274-36823774 Neighboring gene serine/threonine kinase 40 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36834695-36835363 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36835364-36836031 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36837681-36838244 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:36838245-36838808 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr1:36839045-36840244 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:36844393-36844892 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 666 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 667 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 668

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Proteomic investigations reveal a role for RNA processing factor THRAP3 in the DNA damage response. Beli P, et al. Mol Cell, 2012 Apr 27. PMID 22424773, Free PMC Article
    2. Thrap3 promotes osteogenesis by inhibiting the degradation of Runx2. Zhou L, et al. FASEB J, 2022 Apr. PMID 35230719
    3. Thrap3 promotes R-loop resolution via interaction with methylated DDX5. Kang HJ, et al. Exp Mol Med, 2021 Oct. PMID 34697388, Free PMC Article
    4. The RNA processing factors THRAP3 and BCLAF1 promote the DNA damage response through selective mRNA splicing and nuclear export. Vohhodina J, et al. Nucleic Acids Res, 2017 Dec 15. PMID 29112714, Free PMC Article
    5. Btf and TRAP150 have distinct roles in regulating subcellular mRNA distribution. Varia S, et al. Nucleus, 2013 May-Jun. PMID 23778535, Free PMC Article

    See all (247) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Thrap3 promotes nonalcoholic fatty liver disease by suppressing AMPK-mediated autophagy.
      Title: Thrap3 promotes nonalcoholic fatty liver disease by suppressing AMPK-mediated autophagy.
    2. Thrap3 promotes R-loop resolution via interaction with methylated DDX5.
      Title: Thrap3 promotes R-loop resolution via interaction with methylated DDX5.
    3. Thrap3 promotes osteogenesis by inhibiting the degradation of Runx2.
      Title: Thrap3 promotes osteogenesis by inhibiting the degradation of Runx2.
    4. These results indicate that THRAP3 negatively regulates SOX9 transcriptional activity as a cofactor of a SOX9 transcriptional complex during chondrogenesis.
      Title: THRAP3 interacts with and inhibits the transcriptional activity of SOX9 during chondrogenesis.
    5. Results indicate a role for the RNA processing factors THRAP3 and BCLAF1 in the regulation of the cellular DNA damage response (DDR) pathway.
      Title: The RNA processing factors THRAP3 and BCLAF1 promote the DNA damage response through selective mRNA splicing and nuclear export.
    6. The data suggest a model in which TRAP150 interacts with dimeric PSF to block access of RNA to RRM2, thereby regulating the activity of PSF toward a broad set of splicing events in T cells.
      Title: TRAP150 interacts with the RNA-binding domain of PSF and antagonizes splicing of numerous PSF-target genes in T cells.
    7. Thrap3 plays a crucial role in controlling diabetic gene programming and may provide opportunities for the development of new therapeutics for obesity and type 2 diabetes.
      Title: Thrap3 docks on phosphoserine 273 of PPARγ and controls diabetic gene programming.
    8. BTF has functions distinct from TRAP150 in regulating the subcellular distribution of mRNAs in human cells.
      Title: Btf and TRAP150 have distinct roles in regulating subcellular mRNA distribution.
    9. Thrap3 could play indispensable roles in terminal differentiation of adipocytes by enhancing PPARgamma-mediated gene activation cooperatively with Helz2.
      Title: THRAP3 interacts with HELZ2 and plays a novel role in adipocyte differentiation.
    10. Data indicate that distinct differences in proteins becoming Poly(ADP-ribose) PARylated upon various genotoxic insults are observed, exemplified by the PARylation of RNA-processing factors THRAP3 and TAF15 under oxidative stress.
      Title: Proteome-wide identification of poly(ADP-Ribosyl)ation targets in different genotoxic stress responses.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag HIV-1 Gag is identified to have a physical interaction with thyroid hormone receptor associated protein 3 (THRAP3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
    integrase gag-pol Using acetylated HIV-1 IN as bait in yeast two-hybrid screening identifies transcription regulatory and chromatin remodeling factors LEDGF/p75, KAP1, BTF3b, THRAP3, and HMGN2 as IN-binding partners PubMed
    retropepsin gag-pol Positional proteomics analysis identifies the cleavage of human thyroid hormone receptor associated protein 3 (THRAP3) at amino acid residues 473-474 by the HIV-1 protease PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ22082, MGC133082, MGC133083

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding HDA PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables nuclear receptor coactivator activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables nuclear thyroid hormone receptor binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables nuclear vitamin D receptor binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    enables phosphoprotein binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables transcription coactivator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription coregulator activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables transcription coregulator activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in circadian rhythm IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA stabilization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in nuclear-transcribed mRNA catabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of circadian rhythm IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of alternative mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of exon-exon junction complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    part_of mediator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of mediator complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    thyroid hormone receptor-associated protein 3
    Names
    BCLAF1 and THRAP3 family member 2
    TR-associated protein, 150-kDa
    thyroid hormone receptor-associated protein complex 150 kDa component
    thyroid hormone receptor-associated protein, 150 kDa subunit

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001321471.2 → NP_001308400.1  thyroid hormone receptor-associated protein 3 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC114484, AI754117, AK025735, BC112350, HY001123
      Consensus CDS
      CCDS405.1
      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1
      UniProtKB/TrEMBL
      A0A3B3ITZ9
      Related
      ENSP00000433825.1, ENST00000469141.6
      Conserved Domains (1) summary
      pfam15440
      Location:191 → 769
      THRAP3_BCLAF1; THRAP3/BCLAF1 family

    2. NM_001321473.2 → NP_001308402.1  thyroid hormone receptor-associated protein 3 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AI754117, AK025735, BC112330, HY001123
      UniProtKB/TrEMBL
      A0A3B3ITZ9
      Conserved Domains (1) summary
      pfam15440
      Location:191 → 769
      THRAP3_BCLAF1; THRAP3/BCLAF1 family

    3. NM_005119.4 → NP_005110.2  thyroid hormone receptor-associated protein 3 isoform 1

      See identical proteins and their annotated locations for NP_005110.2

      Status: VALIDATED

      Source sequence(s)
      AI754117, AK025735, BC112350, BG572651
      Consensus CDS
      CCDS405.1
      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1
      UniProtKB/TrEMBL
      A0A3B3ITZ9
      Related
      ENSP00000346634.5, ENST00000354618.10
      Conserved Domains (1) summary
      pfam15440
      Location:191 → 769
      THRAP3_BCLAF1; THRAP3/BCLAF1 family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      36207637..36305357
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047436227.1 → XP_047292183.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    2. XM_047436226.1 → XP_047292182.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    3. XM_047436246.1 → XP_047292202.1  thyroid hormone receptor-associated protein 3 isoform X2

    4. XM_047436215.1 → XP_047292171.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    5. XM_047436245.1 → XP_047292201.1  thyroid hormone receptor-associated protein 3 isoform X2

    6. XM_047436212.1 → XP_047292168.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1
      Related
      ENSP00000498001.1, ENST00000648638.1

    7. XM_047436243.1 → XP_047292199.1  thyroid hormone receptor-associated protein 3 isoform X2

    8. XM_047436222.1 → XP_047292178.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    9. XM_047436252.1 → XP_047292208.1  thyroid hormone receptor-associated protein 3 isoform X2

    10. XM_047436233.1 → XP_047292189.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    11. XM_047436218.1 → XP_047292174.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    12. XM_047436250.1 → XP_047292206.1  thyroid hormone receptor-associated protein 3 isoform X2

    13. XM_047436232.1 → XP_047292188.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    14. XM_047436254.1 → XP_047292210.1  thyroid hormone receptor-associated protein 3 isoform X2

    15. XM_047436271.1 → XP_047292227.1  thyroid hormone receptor-associated protein 3 isoform X3

    RNA

    1. XR_007065302.1 RNA Sequence

    2. XR_007065301.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      36070513..36168203
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339973.1 → XP_054195948.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    2. XM_054339972.1 → XP_054195947.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    3. XM_054339978.1 → XP_054195953.1  thyroid hormone receptor-associated protein 3 isoform X2

    4. XM_054339969.1 → XP_054195944.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    5. XM_054339977.1 → XP_054195952.1  thyroid hormone receptor-associated protein 3 isoform X2

    6. XM_054339968.1 → XP_054195943.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    7. XM_054339976.1 → XP_054195951.1  thyroid hormone receptor-associated protein 3 isoform X2

    8. XM_054339971.1 → XP_054195946.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    9. XM_054339980.1 → XP_054195955.1  thyroid hormone receptor-associated protein 3 isoform X2

    10. XM_054339975.1 → XP_054195950.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    11. XM_054339970.1 → XP_054195945.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    12. XM_054339979.1 → XP_054195954.1  thyroid hormone receptor-associated protein 3 isoform X2

    13. XM_054339974.1 → XP_054195949.1  thyroid hormone receptor-associated protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DPS5, Q5VTK6, Q9Y2W1

    14. XM_054339981.1 → XP_054195956.1  thyroid hormone receptor-associated protein 3 isoform X2

    15. XM_054339982.1 → XP_054195957.1  thyroid hormone receptor-associated protein 3 isoform X3

    RNA

    1. XR_008486223.1 RNA Sequence

    2. XR_008486222.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y2W1.2 GenPept UniProtKB/Swiss-Prot:Q9Y2W1

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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