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SEPHS1 selenophosphate synthetase 1 [ Homo sapiens (human) ]

Gene ID: 22929, updated on 16-Apr-2024

Summary

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Official Symbol
SEPHS1provided by HGNC
Official Full Name
selenophosphate synthetase 1provided by HGNC
Primary source
HGNC:HGNC:19685
See related
Ensembl:ENSG00000086475 MIM:600902; AllianceGenome:HGNC:19685
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SPS; SELD; SPS1
Summary
This gene encodes an enzyme that synthesizes selenophosphate from selenide and ATP. Selenophosphate is the selenium donor used to synthesize selenocysteine, which is co-translationally incorporated into selenoproteins at in-frame UGA codons. [provided by RefSeq, Sep 2010]
Expression
Ubiquitous expression in thyroid (RPKM 16.5), kidney (RPKM 11.8) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
10p13
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (13317428..13348293, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (13330509..13361341, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (13359428..13390293, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3051 Neighboring gene uncharacterized LOC124902377 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:13343766-13344266 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3053 Neighboring gene RBIS pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:13371420-13371920 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:13371921-13372421 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:13376783-13377284 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:13377285-13377784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:13383617-13384469 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2153 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2154 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13390478-13391268 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13391269-13392060 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:13397412-13397565 Neighboring gene uncharacterized LOC105376419 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:13437106-13438069 Neighboring gene Sharpr-MPRA regulatory region 1825 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:13452136-13452642 Neighboring gene uncharacterized LOC105376420 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3054

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. The role of selenium-mediated redox signaling by selenophosphate synthetase 1 (SEPHS1) in hESCs. Lee MO, et al. Biochem Biophys Res Commun, 2019 Dec 3. PMID 31607477
  2. Cloning and functional characterization of human selenophosphate synthetase, an essential component of selenoprotein synthesis. Low SC, et al. J Biol Chem, 1995 Sep 15. PMID 7665581
  3. Selenium, selenoprotein genes and Crohn's disease in a case-control population from Auckland, New Zealand. Gentschew L, et al. Nutrients, 2012 Sep. PMID 23112913, Free PMC Article
  4. Human selenophosphate synthetase 1 has five splice variants with unique interactions, subcellular localizations and expression patterns. Kim JY, et al. Biochem Biophys Res Commun, 2010 Jun 18. PMID 20471958, Free PMC Article
  5. p53-Mediated enhancement of radiosensitivity by selenophosphate synthetase 1 overexpression. Chung HJ, et al. J Cell Physiol, 2006 Oct. PMID 16786570

See all (36) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. De novo missense variants in exon 9 of SEPHS1 cause a neurodevelopmental condition with developmental delay, poor growth, hypotonia, and dysmorphic features.
    Title: De novo missense variants in exon 9 of SEPHS1 cause a neurodevelopmental condition with developmental delay, poor growth, hypotonia, and dysmorphic features.
  2. Selenophosphate synthetase 1 deficiency exacerbates osteoarthritis by dysregulating redox homeostasis.
    Title: Selenophosphate synthetase 1 deficiency exacerbates osteoarthritis by dysregulating redox homeostasis.
  3. SEPHS1 expression is high in undifferentiated embryonic stem cells.SEPHS1 expression is required to obtain pluripotency.SEPHS1 plays a role in the embryonic stem cell survival via reactive oxygen species signaling and apoptosis.
    Title: The role of selenium-mediated redox signaling by selenophosphate synthetase 1 (SEPHS1) in hESCs.
  4. Data confirm interactions among components of the early steps of the selenocysteine biosynthesis pathway (SEPSECS, SECP43, SEPHS1, and SEPHS2); SECP43, which interacts with SEPSECS and SEPHS1, is a globular protein that forms oligomers in vivo.
    Title: Analysis of Novel Interactions between Components of the Selenocysteine Biosynthesis Pathway, SEPHS1, SEPHS2, SEPSECS, and SECp43.
  5. Three SNPs in SEPSECS and SEPHS1 were found to significantly interact with serum selenium level and Crohn's Disease.
    Title: Selenium, selenoprotein genes and Crohn's disease in a case-control population from Auckland, New Zealand.
  6. Five alternative splice variants of human SPS1 (major type, DeltaE2, DeltaE8, +E9, +E9a) were identified wherein +E9 and +E9a make the same protein.
    Title: Human selenophosphate synthetase 1 has five splice variants with unique interactions, subcellular localizations and expression patterns.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
  8. the Sps1-encoded enzyme depends on a selenium salvage system that recycles l-selenocysteine, whereas the Sps2 enzyme can function with a selenite assimilation system
    Title: Selenophosphate synthetase genes from lung adenocarcinoma cells: Sps1 for recycling L-selenocysteine and Sps2 for selenite assimilation.
  9. Sps1 affect cell viability upon ionizing radiation via modulation of p53 activity. Sps1 and its product selenophosphate might be involved in cancer prevention in a p53-dependent manner and could be applied to development of a novel cancer therapy.
    Title: p53-Mediated enhancement of radiosensitivity by selenophosphate synthetase 1 overexpression.
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
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
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

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

  • MGC4980

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables GTP binding TAS
Traceable Author Statement
more info
 PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables selenide, water dikinase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in phosphorylation IEA
Inferred from Electronic Annotation
more info
  
involved_in protein modification process TAS
Traceable Author Statement
more info
 PubMed 
involved_in selenocysteine biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nuclear membrane IEA
Inferred from Electronic Annotation
more info
  
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
selenide, water dikinase 1
Names
selenium donor protein 1
selenophosphate synthase 1
selenophosphate synthetase 1 +E9
selenophosphate synthetase 1 +E9a
selenophosphate synthetase 1 delta E2
selenophosphate synthetase 1 delta E8
selenophosphate synthetase 1 major
NP_001182531.1
NP_001182533.1
NP_001362698.1
NP_036379.2
XP_047280795.1
XP_047280796.1
XP_047280797.1
XP_054221208.1
XP_054221209.1
XP_054221210.1

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_001195602.2 → NP_001182531.1  selenide, water dikinase 1 isoform 2

    See identical proteins and their annotated locations for NP_001182531.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' region and uses a downstream start codon, compared to variant 1. Isoform 2 (also called Delta E2) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AK301568, AL138764, BC064610, CT000832, GU954546
    Consensus CDS
    CCDS55702.1
    UniProtKB/TrEMBL
    B4DLS1
    Related
    ENSP00000441119.2, ENST00000545675.5
    Conserved Domains (1) summary
    cd02195
    Location:1 → 290
    SelD; Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The ...

  2. NM_001195604.2 → NP_001182533.1  selenide, water dikinase 1 isoform 3

    See identical proteins and their annotated locations for NP_001182533.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an exon in the coding region, compared to variant 1. Isoform 3 (also called Delta E8) is shorter, compared to isoform 1.
    Source sequence(s)
    AK301568, AL138764, BC064610, CT000832, GU954547
    Consensus CDS
    CCDS55703.1
    UniProtKB/Swiss-Prot
    P49903
    Related
    ENSP00000367877.3, ENST00000378614.8
    Conserved Domains (1) summary
    cd02195
    Location:20 → 286
    SelD; Selenophosphate synthetase (SelD) catalyzes the conversion of selenium to selenophosphate which is required by a number of bacterial, archaeal and eukaryotic organisms for synthesis of Secys-tRNA, the precursor of selenocysteine in selenoenzymes. The ...

  3. NM_001375769.1 → NP_001362698.1  selenide, water dikinase 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL138764, AL355870
    UniProtKB/TrEMBL
    B4DLS1
    Conserved Domains (1) summary
    TIGR00476
    Location:19 → 331
    selD; selenium donor protein

  4. NM_012247.5 → NP_036379.2  selenide, water dikinase 1 isoform 1

    See identical proteins and their annotated locations for NP_036379.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK301568, AL138764, BC064610, CT000832, GU954545
    Consensus CDS
    CCDS7098.1
    UniProtKB/Swiss-Prot
    B4DWK0, D3DRS9, D6PSQ9, P49903, Q5T5U8, Q5T5U9, Q9BVT4
    UniProtKB/TrEMBL
    B4DLS1
    Related
    ENSP00000367893.3, ENST00000327347.10
    Conserved Domains (1) summary
    TIGR00476
    Location:19 → 333
    selD; selenium donor protein

RNA

  1. NR_164738.1 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AL138764, AL355870

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    13317428..13348293 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047424841.1 → XP_047280797.1  selenide, water dikinase 1 isoform X3

  2. XM_047424840.1 → XP_047280796.1  selenide, water dikinase 1 isoform X2

  3. XM_047424839.1 → XP_047280795.1  selenide, water dikinase 1 isoform X1

    UniProtKB/Swiss-Prot
    B4DWK0, D3DRS9, D6PSQ9, P49903, Q5T5U8, Q5T5U9, Q9BVT4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    13330509..13361341 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054365235.1 → XP_054221210.1  selenide, water dikinase 1 isoform X3

  2. XM_054365233.1 → XP_054221208.1  selenide, water dikinase 1 isoform X1

    UniProtKB/Swiss-Prot
    B4DWK0, D3DRS9, D6PSQ9, P49903, Q5T5U8, Q5T5U9, Q9BVT4

  3. XM_054365234.1 → XP_054221209.1  selenide, water dikinase 1 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001375770.1: Suppressed sequence

    Description
    NM_001375770.1: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P49903.2 GenPept UniProtKB/Swiss-Prot:P49903

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