SPATA2 spermatogenesis associated 2 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

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_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
cloning and base sequence of the promoter region
Title: Cloning and characterization of the promoter region of human spata2 (spermatogenesis-associated protein 2) gene.

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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 EBI GWAS CatalogPubMed
Identification of ZNF313/RNF114 as a novel psoriasis susceptibility gene. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AL034507 (e-PCR)
- UniSTS:94259

RH12086 (e-PCR)
- UniSTS:9340

SPATA2_8999 (e-PCR)
- UniSTS:468712

STS-D25902 (e-PCR)
- UniSTS:4849

RH79044 (e-PCR)
- UniSTS:50421

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)

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
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

NC_000020.11 Reference GRCh38.p14 Primary Assembly

Range

49903391..49915529 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

E1P626, O94857, Q9UM82
XM_047440623.1 → XP_047296579.1 spermatogenesis-associated protein 2 isoform X1

UniProtKB/Swiss-Prot

E1P626, O94857, Q9UM82

Alternate T2T-CHM13v2.0

Genomic

NC_060944.1 Alternate T2T-CHM13v2.0

Range

51672830..51685863 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

E1P626, O94857, Q9UM82
XM_054324295.1 → XP_054180270.1 spermatogenesis-associated protein 2 isoform X1

UniProtKB/Swiss-Prot

E1P626, O94857, Q9UM82
XM_054324294.1 → XP_054180269.1 spermatogenesis-associated protein 2 isoform X1

UniProtKB/Swiss-Prot

E1P626, O94857, Q9UM82