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SEPHS1 selenophosphate synthetase 1 [ Homo sapiens (human) ]

Gene ID: 22929, updated on 7-Dec-2018

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
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

Genomic context

See SEPHS1 in Genome Data Viewer
Location:
10p13
Exon count:
10
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 10 NC_000010.11 (13317428..13348298, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (13359428..13390298, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene phytanoyl-CoA 2-hydroxylase Neighboring gene chromosome 8 open reading frame 59 pseudogene 1 Neighboring gene uncharacterized LOC105376419 Neighboring gene uncharacterized LOC105376420

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC4980

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
GTP binding TAS
Traceable Author Statement
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
selenide, water dikinase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
cellular protein modification process TAS
Traceable Author Statement
more info
PubMed 
phosphorylation IEA
Inferred from Electronic Annotation
more info
 
selenium compound metabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
selenocysteine biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
tRNA seleno-modification IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 

General protein information

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_036379.2
XP_016871432.1
XP_016871433.1
XP_016871434.1

NCBI Reference Sequences (RefSeq)

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_001195602.1NP_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/Swiss-Prot
    P49903
    Related
    ENSP00000441119.2, ENST00000545675.5
    Conserved Domains (1) summary
    cd02195
    Location:1290
    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_001195604.1NP_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:20286
    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_012247.5NP_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
    P49903
    Related
    ENSP00000367893.3, ENST00000327347.9
    Conserved Domains (1) summary
    TIGR00476
    Location:19333
    selD; selenium donor protein

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p12 Primary Assembly

    Range
    13317428..13348298 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017015944.2XP_016871433.1  selenide, water dikinase 1 isoform X2

    Conserved Domains (1) summary
    TIGR00476
    Location:19331
    selD; selenium donor protein
  2. XM_017015943.2XP_016871432.1  selenide, water dikinase 1 isoform X1

    UniProtKB/Swiss-Prot
    P49903
    Conserved Domains (1) summary
    TIGR00476
    Location:19333
    selD; selenium donor protein
  3. XM_017015945.2XP_016871434.1  selenide, water dikinase 1 isoform X3

    UniProtKB/Swiss-Prot
    P49903
    Conserved Domains (1) summary
    cd02195
    Location:1290
    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 ...
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