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    SPATA2 spermatogenesis associated 2 [ Homo sapiens (human) ]

    Gene ID: 9825, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SPATA2provided by HGNC
    Official Full Name
    spermatogenesis associated 2provided by HGNC
    Primary source
    HGNC:HGNC:14681
    See related
    Ensembl:ENSG00000158480 MIM:607662; AllianceGenome:HGNC:14681
    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
    PD1; tamo; PPP1R145
    Summary
    Enables signaling receptor complex adaptor activity and ubiquitin-specific protease binding activity. Involved in several processes, including protein deubiquitination; regulation of necroptotic process; and regulation of tumor necrosis factor-mediated signaling pathway. Located in cytoplasm; fibrillar center; and nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 8.7), brain (RPKM 8.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SPATA2 in Genome Data Viewer
    Location:
    20q13.13
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (49903391..49915529, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (51672830..51685863, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (48519928..48532066, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene solute carrier family 9 member A8 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:48452608-48453108 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:48453109-48453609 Neighboring gene GLYR1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18075 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18076 Neighboring gene microRNA 12122 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48504605-48505416 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48505417-48506228 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_60689 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_60693 Neighboring gene Sharpr-MPRA regulatory region 10189 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_60705 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13006 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18077 Neighboring gene uncharacterized LOC105372653 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_60723 Neighboring gene Sharpr-MPRA regulatory region 9917 Neighboring gene MPRA-validated peak4247 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13007 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:48552583-48553188 Neighboring gene Sharpr-MPRA regulatory region 103 Neighboring gene Sharpr-MPRA regulatory region 7979 Neighboring gene Sharpr-MPRA regulatory region 5689 Neighboring gene small nucleolar RNA U13 Neighboring gene ring finger protein 114

    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. PD-1(+) CD8(+) T cells are exhausted in tumours and functional in draining lymph nodes of colorectal cancer patients. Wu X, et al. Br J Cancer, 2014 Sep 23. PMID 25093496, Free PMC Article
    2. Tumor necrosis factor receptor modulator spermatogenesis-associated protein 2 is a novel predictor of outcome in ovarian cancer. Wieser V, et al. Cancer Sci, 2019 Mar. PMID 30697874, Free PMC Article
    3. Cloning and characterization of the promoter region of human spata2 (spermatogenesis-associated protein 2) gene. Liliana Slongo M, et al. Biochim Biophys Acta, 2003 Jan 27. PMID 12531478
    4. cDNA cloning and characterization of PD1: a novel human testicular protein with different expressions in various testiculopathies. Graziotto R, et al. Exp Cell Res, 1999 May 1. PMID 10222154
    5. Tumor-infiltrating NY-ESO-1-specific CD8+ T cells are negatively regulated by LAG-3 and PD-1 in human ovarian cancer. Matsuzaki J, et al. Proc Natl Acad Sci U S A, 2010 Apr 27. PMID 20385810, Free PMC Article

    See all (60) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A role of SPATA2 in tumorigenesis.
      Title: Tumor necrosis factor receptor modulator spermatogenesis-associated protein 2 is a novel predictor of outcome in ovarian cancer.
    2. SPATA2 has been described as a previously unrecognized factor in the linear ubiquitin chain assembly complex-dependent signaling pathways that serves as an adaptor between HOIP and CYLD, thereby enabling recruitment of CYLD to signaling complexes.
      Title: SPATA2-Mediated Binding of CYLD to HOIP Enables CYLD Recruitment to Signaling Complexes.
    3. The data reveal SPATA2 as a high-affinity binding partner of CYLD and HOIP, and a regulatory component of linear ubiquitin chain assembly complex-mediated NF-kappaB signaling.
      Title: SPATA2 Links CYLD to LUBAC, Activates CYLD, and Controls LUBAC Signaling.
    4. this study identifies SPATA2 as an important factor in the TNF signaling pathway with a substantial role for the effects mediated by the cytokine.
      Title: SPATA2 promotes CYLD activity and regulates TNF-induced NF-κB signaling and cell death.
    5. The predicted PUB domain in the N-terminus of SPATA2 interacts with the USP domain of CYLD and SPATA2 is required for recruitment of CYLD to the TNF-alpha receptor-associated signaling complexes.
      Title: SPATA2 links CYLD to the TNF-α receptor signaling complex and modulates the receptor signaling outcomes.
    6. The aim of this study was to investigate whether the HCP5, TNIP1, TNFAIP3, SPATA2 and COG6 genes were genetic risk factors for psoriasis in Chinese population.
      Title: Investigating the genetic association of HCP5, SPATA2, TNIP1, TNFAIP3 and COG6 with psoriasis in Chinese population.
    7. PD-L1 is highly expressed in tumours rather than tumour-free lymph nodes, which is closely correlated with the impairment of IFN-gamma production of tumour-infiltrating T-cells.
      Title: PD-1(+) CD8(+) T cells are exhausted in tumours and functional in draining lymph nodes of colorectal cancer patients.
    8. Tumor-infiltrating NY-ESO-1-specific CD8+ T cells are negatively regulated by LAG-3 and PD-1 in human ovarian cancer.
      Title: Tumor-infiltrating NY-ESO-1-specific CD8+ T cells are negatively regulated by LAG-3 and PD-1 in human ovarian cancer.
    9. disappearance of TLD epitope reactivity from an otherwise stable EBV-specific response reflects selective loss of cognate antigen restimulation, not IL-7-dependent signals, and is immediately preceded by PD-1 upregulation to unprecedented levels.
      Title: Upregulation of interleukin 7 receptor alpha and programmed death 1 marks an epitope-specific CD8+ T-cell response that disappears following primary Epstein-Barr virus infection.
    10. cloning and base sequence of the promoter region
      Title: Cloning and characterization of the promoter region of human spata2 (spermatogenesis-associated protein 2) gene.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Genome-wide association analysis identifies three psoriasis susceptibility loci.
    EBI GWAS Catalog
    Identification of ZNF313/RNF114 as a novel psoriasis susceptibility gene.
    EBI GWAS Catalog

    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ13167, KIAA0757

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables signaling receptor complex adaptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables signaling receptor complex adaptor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ubiquitin-specific protease binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in necroptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein K63-linked deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein linear deubiquitination IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of inflammatory response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of inflammatory response IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of necroptotic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of necroptotic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of tumor necrosis factor-mediated signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of tumor necrosis factor-mediated signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in seminiferous tubule development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spermatogenesis NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in fibrillar center IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    spermatogenesis-associated protein 2
    Names
    protein phosphatase 1, regulatory subunit 145
    spermatogenesis associated PD1
    spermatogenesis-associated protein PD1

    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_001135773.2 → NP_001129245.1  spermatogenesis-associated protein 2

      See identical proteins and their annotated locations for NP_001129245.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) has an alternate 5' UTR exon, as compared to variant 1.
      Source sequence(s)
      AK289644, AL031685, BC009481, N62318
      Consensus CDS
      CCDS13422.1
      UniProtKB/Swiss-Prot
      E1P626, O94857, Q9UM82
      UniProtKB/TrEMBL
      A8K0S9
      Related
      ENSP00000416799.1, ENST00000422556.1
      Conserved Domains (2) summary
      cl15262
      Location:88 → 176
      PUB; PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins
      cl22851
      Location:459 → 511
      PHD_SF; PHD finger superfamily

    2. NM_006038.4 → NP_006029.1  spermatogenesis-associated protein 2

      See identical proteins and their annotated locations for NP_006029.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) and variant 2 encode the same protein.
      Source sequence(s)
      AK295536, AL031685, BC009481, N62318
      Consensus CDS
      CCDS13422.1
      UniProtKB/Swiss-Prot
      E1P626, O94857, Q9UM82
      UniProtKB/TrEMBL
      A8K0S9
      Related
      ENSP00000289431.5, ENST00000289431.10
      Conserved Domains (2) summary
      cl15262
      Location:88 → 176
      PUB; PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins
      cl22851
      Location:459 → 511
      PHD_SF; PHD finger superfamily

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      49903391..49915529 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006723894.2 → XP_006723957.1  spermatogenesis-associated protein 2 isoform X1

      See identical proteins and their annotated locations for XP_006723957.1

      UniProtKB/Swiss-Prot
      E1P626, O94857, Q9UM82
      UniProtKB/TrEMBL
      A8K0S9
      Conserved Domains (2) summary
      cl15262
      Location:88 → 176
      PUB; PNGase/UBA or UBX (PUB) domain of p97 adaptor proteins
      cl22851
      Location:459 → 511
      PHD_SF; PHD finger superfamily

    2. XM_047440624.1 → XP_047296580.1  spermatogenesis-associated protein 2 isoform X1

      UniProtKB/Swiss-Prot
      E1P626, O94857, Q9UM82

    3. XM_047440623.1 → XP_047296579.1  spermatogenesis-associated protein 2 isoform X1

      UniProtKB/Swiss-Prot
      E1P626, O94857, Q9UM82

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      51672830..51685863 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054324293.1 → XP_054180268.1  spermatogenesis-associated protein 2 isoform X1

      UniProtKB/Swiss-Prot
      E1P626, O94857, Q9UM82

    2. XM_054324295.1 → XP_054180270.1  spermatogenesis-associated protein 2 isoform X1

      UniProtKB/Swiss-Prot
      E1P626, O94857, Q9UM82

    3. XM_054324294.1 → XP_054180269.1  spermatogenesis-associated protein 2 isoform X1

      UniProtKB/Swiss-Prot
      E1P626, O94857, Q9UM82
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UM82.2 GenPept UniProtKB/Swiss-Prot:Q9UM82

    Gene LinkOut

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

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