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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
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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
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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

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