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    SEPHS1 selenophosphate synthetase 1 [ Homo sapiens (human) ]

    Gene ID: 22929, updated on 3-Dec-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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SEPHS1 in Genome Data Viewer
    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_000010.11Genomic 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 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

    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_2024_08

    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

      UniProtKB/TrEMBL
      B4DLS1
    2. XM_047424840.1XP_047280796.1  selenide, water dikinase 1 isoform X2

      UniProtKB/TrEMBL
      B4DLS1
    3. XM_047424839.1XP_047280795.1  selenide, water dikinase 1 isoform X1

      UniProtKB/Swiss-Prot
      B4DWK0, D3DRS9, D6PSQ9, P49903, Q5T5U8, Q5T5U9, Q9BVT4
      UniProtKB/TrEMBL
      B4DLS1

    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

      UniProtKB/TrEMBL
      B4DLS1
    2. XM_054365233.1XP_054221208.1  selenide, water dikinase 1 isoform X1

      UniProtKB/Swiss-Prot
      B4DWK0, D3DRS9, D6PSQ9, P49903, Q5T5U8, Q5T5U9, Q9BVT4
      UniProtKB/TrEMBL
      B4DLS1
    3. XM_054365234.1XP_054221209.1  selenide, water dikinase 1 isoform X2

      UniProtKB/TrEMBL
      B4DLS1

    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.