SEPHS1 selenophosphate synthetase 1 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

Location:: 10p13

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (13317428..13348293, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (13330509..13361341, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (13359428..13390293, complement)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

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.
Selenophosphate synthetase 1 deficiency exacerbates osteoarthritis by dysregulating redox homeostasis.
Title: Selenophosphate synthetase 1 deficiency exacerbates osteoarthritis by dysregulating redox homeostasis.
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.
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.
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.
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.
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.
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.
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.

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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
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. 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

RH27227 (e-PCR)
- UniSTS:88327

RH36724 (e-PCR)
- UniSTS:86308

RH48902 (e-PCR)
- UniSTS:7994

WI-22046 (e-PCR)
- UniSTS:40771

G42936 (e-PCR)
- UniSTS:94831

SEPHS1_9288 (e-PCR)
- UniSTS:467877

RH11181 (e-PCR)
- UniSTS:86472

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 protein heterodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables selenide, water dikinase activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
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 cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear membrane	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
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

EC 2.7.9.3

NP_001182533.1

EC 2.7.9.3

NP_001362698.1

EC 2.7.9.3

NP_036379.2

EC 2.7.9.3

XP_047280795.1

EC 2.7.9.3

XP_047280796.1

EC 2.7.9.3

XP_047280797.1

EC 2.7.9.3

XP_054221208.1

EC 2.7.9.3

XP_054221209.1

EC 2.7.9.3

XP_054221210.1

EC 2.7.9.3

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_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 ...
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 ...
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
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

NR_164738.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL138764, AL355870

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

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

13317428..13348293 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047424841.1 → XP_047280797.1 selenide, water dikinase 1 isoform X3
XM_047424840.1 → XP_047280796.1 selenide, water dikinase 1 isoform X2
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

NC_060934.1 Alternate T2T-CHM13v2.0

Range

13330509..13361341 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054365235.1 → XP_054221210.1 selenide, water dikinase 1 isoform X3
XM_054365233.1 → XP_054221208.1 selenide, water dikinase 1 isoform X1

UniProtKB/Swiss-Prot

B4DWK0, D3DRS9, D6PSQ9, P49903, Q5T5U8, Q5T5U9, Q9BVT4
XM_054365234.1 → XP_054221209.1 selenide, water dikinase 1 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001375770.1: Suppressed sequence

Description

NM_001375770.1: This RefSeq was removed because it is a nonsense-mediated mRNA decay (NMD) candidate.