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    SEPSECS Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase [ Homo sapiens (human) ]

    Gene ID: 51091, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SEPSECSprovided by HGNC
    Official Full Name
    Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthaseprovided by HGNC
    Primary source
    HGNC:HGNC:30605
    See related
    Ensembl:ENSG00000109618 MIM:613009; AllianceGenome:HGNC:30605
    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
    LP; SLA; SecS; PCH2D; SLA/LP; SLA-p35
    Summary
    The amino acid selenocysteine is the only amino acid that does not have its own tRNA synthetase. Instead, this amino acid is synthesized on its cognate tRNA in a three step process. The protein encoded by this gene catalyzes the third step in the process, the conversion of O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec).[provided by RefSeq, Mar 2011]
    Expression
    Ubiquitous expression in liver (RPKM 7.2), duodenum (RPKM 5.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    4p15.2
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (25120014..25160582, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (25101930..25142501, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (25121636..25162071, complement)

    Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene leucine rich repeat LGI family member 2 Neighboring gene uncharacterized LOC124900684 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:25086876-25087376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr4:25087377-25087877 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:25089726-25090269 Neighboring gene uncharacterized LOC105374534 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:25133175-25133701 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:25133702-25134228 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15319 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21370 Neighboring gene SEPSECS antisense RNA 1 (head to head) Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21371 Neighboring gene uncharacterized LOC105374535 Neighboring gene H3K27ac hESC enhancers GRCh37_chr4:25235481-25235982 and GRCh37_chr4:25235983-25236482 Neighboring gene uncharacterized LOC124900916 Neighboring gene phosphatidylinositol 4-kinase type 2 beta

    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. Biallelic SEPSECS variants in two siblings with pontocerebellar hypoplasia type 2D underscore the relevance of splice-disrupting synonymous variants in disease. Ramadesikan S, et al. Cold Spring Harb Mol Case Stud, 2022 Feb. PMID 35091508, Free PMC Article
    2. Structural basis for early-onset neurological disorders caused by mutations in human selenocysteine synthase. Puppala AK, et al. Sci Rep, 2016 Aug 31. PMID 27576344, Free PMC Article
    3. Milder progressive cerebellar atrophy caused by biallelic SEPSECS mutations. Iwama K, et al. J Hum Genet, 2016 Jun. PMID 26888482
    4. Selenoprotein biosynthesis defect causes progressive encephalopathy with elevated lactate. Anttonen AK, et al. Neurology, 2015 Jul 28. PMID 26115735, Free PMC Article
    5. Structural asymmetry of the terminal catalytic complex in selenocysteine synthesis. French RL, et al. J Biol Chem, 2014 Oct 17. PMID 25190812, Free PMC Article

    See all (43) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Integrative Analysis Unveils the Correlation of Aminoacyl-tRNA Biosynthesis Metabolites with the Methylation of the SEPSECS Gene in Huntington's Disease Brain Tissue.
      Title: Integrative Analysis Unveils the Correlation of Aminoacyl-tRNA Biosynthesis Metabolites with the Methylation of the SEPSECS Gene in Huntington's Disease Brain Tissue.
    2. Biallelic SEPSECS variants in two siblings with pontocerebellar hypoplasia type 2D underscore the relevance of splice-disrupting synonymous variants in disease.
      Title: Biallelic SEPSECS variants in two siblings with pontocerebellar hypoplasia type 2D underscore the relevance of splice-disrupting synonymous variants in disease.
    3. Human Genetic Disorders Resulting in Systemic Selenoprotein Deficiency.
      Title: Human Genetic Disorders Resulting in Systemic Selenoprotein Deficiency.
    4. Structural basis for early-onset neurological disorders caused by mutations in human selenocysteine synthase has been described.
      Title: Structural basis for early-onset neurological disorders caused by mutations in human selenocysteine synthase.
    5. Epileptic encephalopathy with burst suppression without brain malformations is associated with pathogenic variation in SEPSECS.
      Title: Genetics and genotype-phenotype correlations in early onset epileptic encephalopathy with burst suppression.
    6. The progression of clinical symptoms in these families is evidently slower than in previously reported cases, and the cerebellar atrophy milder by brain MRI, indicating that SEPSECS mutations are also involved in milder late-onset cerebellar atrophy.
      Title: Milder progressive cerebellar atrophy caused by biallelic SEPSECS mutations.
    7. results suggest SEPSECS as a candidate gene for progressive encephalopathies with lactate elevation.
      Title: Selenoprotein biosynthesis defect causes progressive encephalopathy with elevated lactate.
    8. structural analysis of the terminal catalytic complex in selenocysteine synthesis
      Title: Structural asymmetry of the terminal catalytic complex in selenocysteine synthesis.
    9. Data suggest SEPSECS silencing in placental trophoblasts inhibits proliferation, induces apoptosis, and reduces production of progesterone/chorionic gonadotropin (P/hCG); SEPSECS over-expression promotes cell proliferation and secretion of P/hCG.
      Title: The role of Sep (O-phosphoserine) tRNA: Sec (selenocysteine) synthase (SEPSECS) in proliferation, apoptosis and hormone secretion of trophoblast cells.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    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

    Associated conditions

    Description Tests
    Pontocerebellar hypoplasia type 2D
    MedGen: C3151140 OMIM: 613811 GeneReviews: Not available
    		Compare labs

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag HIV-1 Gag is identified to have a physical interaction with Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase (SEPSECS) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed
    matrix gag HIV-1 MA is identified to have a physical interaction with Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase (SEPSECS) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    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

    • MGC161491, DKFZp434B1417

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables O-phosphoseryl-tRNA(Sec) selenium transferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables tRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables tRNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    involved_in conversion of seryl-tRNAsec to selenocys-tRNAsec IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in selenocysteine incorporation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in selenocysteine incorporation ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    O-phosphoseryl-tRNA(Sec) selenium transferase
    Names
    SLA/LP autoantigen
    UGA suppressor tRNA-associated protein
    liver-pancreas antigen
    soluble liver antigen
    soluble liver antigen/liver pancreas antigen
    tRNA(Ser/Sec)-associated antigenic protein
    NP_001397643.1
    NP_058651.3
    XP_011512148.1
    XP_011512149.1
    XP_011512150.1
    XP_047271718.1
    XP_054206119.1
    XP_054206120.1
    XP_054206121.1
    XP_054206122.1

    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.

    Genomic

    1. NG_028222.1 RefSeqGene

      Range
      5134..45569
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001410714.1 → NP_001397643.1  O-phosphoseryl-tRNA(Sec) selenium transferase isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC007073, AC104662
      Consensus CDS
      CCDS93487.1
      UniProtKB/TrEMBL
      A0A7P0TA23
      Related
      ENSP00000505991.1, ENST00000681948.1

    2. NM_016955.4 → NP_058651.3  O-phosphoseryl-tRNA(Sec) selenium transferase isoform 1

      See identical proteins and their annotated locations for NP_058651.3

      Status: REVIEWED

      Source sequence(s)
      AC007073, AK292476, AW515989, BX648976, CN429794, DA155173
      Consensus CDS
      CCDS3432.2
      UniProtKB/Swiss-Prot
      A8K8W1, Q0D2P3, Q17RT1, Q9HD40, Q9NXZ5, Q9UGM9, Q9Y353
      UniProtKB/TrEMBL
      B7Z8P7
      Related
      ENSP00000371535.2, ENST00000382103.7
      Conserved Domains (1) summary
      TIGR03531
      Location:12 → 458
      selenium_SpcS; O-phosphoseryl-tRNA(Sec) selenium transferase

    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_000004.12 Reference GRCh38.p14 Primary Assembly

      Range
      25120014..25160582 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047415762.1 → XP_047271718.1  O-phosphoseryl-tRNA(Sec) selenium transferase isoform X3

      UniProtKB/TrEMBL
      A1A4F3

    2. XM_011513846.3 → XP_011512148.1  O-phosphoseryl-tRNA(Sec) selenium transferase isoform X1

      See identical proteins and their annotated locations for XP_011512148.1

      UniProtKB/TrEMBL
      B7Z8P7
      Conserved Domains (1) summary
      TIGR03531
      Location:38 → 457
      selenium_SpcS; O-phosphoseryl-tRNA(Sec) selenium transferase

    3. XM_011513847.3 → XP_011512149.1  O-phosphoseryl-tRNA(Sec) selenium transferase isoform X2

      UniProtKB/TrEMBL
      B7Z8P7
      Related
      ENST00000680824.1
      Conserved Domains (1) summary
      TIGR03531
      Location:27 → 447
      selenium_SpcS; O-phosphoseryl-tRNA(Sec) selenium transferase

    4. XM_011513848.2 → XP_011512150.1  O-phosphoseryl-tRNA(Sec) selenium transferase isoform X3

      See identical proteins and their annotated locations for XP_011512150.1

      UniProtKB/TrEMBL
      A1A4F3, B7Z8P7
      Related
      ENST00000681071.1
      Conserved Domains (1) summary
      TIGR03531
      Location:1 → 398
      selenium_SpcS; O-phosphoseryl-tRNA(Sec) selenium transferase

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060928.1 Alternate T2T-CHM13v2.0

      Range
      25101930..25142501 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054350146.1 → XP_054206121.1  O-phosphoseryl-tRNA(Sec) selenium transferase isoform X3

      UniProtKB/TrEMBL
      A1A4F3

    2. XM_054350145.1 → XP_054206120.1  O-phosphoseryl-tRNA(Sec) selenium transferase isoform X2

    3. XM_054350144.1 → XP_054206119.1  O-phosphoseryl-tRNA(Sec) selenium transferase isoform X1

    4. XM_054350147.1 → XP_054206122.1  O-phosphoseryl-tRNA(Sec) selenium transferase isoform X3

      UniProtKB/TrEMBL
      A1A4F3

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001159728.1: Suppressed sequence

      Description
      NM_001159728.1: This RefSeq was permanently suppressed because currently there is support for the transcript but not for the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HD40.2 GenPept UniProtKB/Swiss-Prot:Q9HD40

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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