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SPATA2 spermatogenesis associated 2 [ Homo sapiens (human) ]

Gene ID: 9825, updated on 3-Apr-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, Apr 2022]
Expression
Broad expression in testis (RPKM 8.7), brain (RPKM 8.4) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (49903391..49915529, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (51672830..51685863, complement)
105.20220307 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
  • 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. 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
  2. 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
  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. 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
  5. 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. Sauce D, et al. J Virol, 2009 Sep. PMID 19605492, Free PMC Article

See all (56) 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 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 IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein K63-linked deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein linear deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein linear deubiquitination IDA
Inferred from Direct Assay
more info
 PubMed 
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_2023_10

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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