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SEPHS1 selenophosphate synthetase 1 [ Homo sapiens (human) ]

Gene ID: 22929, updated on 7-Apr-2024

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
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Genomic context

See SEPHS1 in Genome Data Viewer
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

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 Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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)

NEW Try the new Transcript table

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_001195602.2NP_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: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_001195604.2NP_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_001375769.1NP_001362698.1  selenide, water dikinase 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AL138764, AL355870
    UniProtKB/TrEMBL
    B4DLS1
    Conserved Domains (1) summary
    TIGR00476
    Location:19331
    selD; selenium donor protein
  4. 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
    B4DWK0, D3DRS9, D6PSQ9, P49903, Q5T5U8, Q5T5U9, Q9BVT4
    UniProtKB/TrEMBL
    B4DLS1
    Related
    ENSP00000367893.3, ENST00000327347.10
    Conserved Domains (1) summary
    TIGR00476
    Location:19333
    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_047424841.1XP_047280797.1  selenide, water dikinase 1 isoform X3

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

  3. XM_047424839.1XP_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_054365235.1XP_054221210.1  selenide, water dikinase 1 isoform X3

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

    UniProtKB/Swiss-Prot
    B4DWK0, D3DRS9, D6PSQ9, P49903, Q5T5U8, Q5T5U9, Q9BVT4
  3. XM_054365234.1XP_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.