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Aliases for SEPSECS Gene

Aliases for SEPSECS Gene

  • Sep (O-Phosphoserine) TRNA:Sec (Selenocysteine) TRNA Synthase 2 3 5
  • Soluble Liver Antigen/Liver Pancreas Antigen 2 3
  • TRNA(Ser/Sec)-Associated Antigenic Protein 3 4
  • UGA Suppressor TRNA-Associated Protein 3 4
  • Liver-Pancreas Antigen 3 4
  • Soluble Liver Antigen 3 4
  • SLA/LP Autoantigen 3 4
  • SLA-P35 3 4
  • SLA 3 4
  • LP 3 4
  • O-Phosphoseryl-TRNA(Sec) Selenium Transferase 3
  • Selenocysteinyl-TRNA(Sec) Synthase 4
  • Sep-TRNA:Sec-TRNA Synthase 4
  • Selenocysteine Synthase 4
  • Sec Synthase 4
  • EC 2.9.1.n1 58
  • EC 4
  • SepSecS 4
  • SLA/LP 3
  • TRNP48 4
  • PCH2D 3

External Ids for SEPSECS Gene

Previous GeneCards Identifiers for SEPSECS Gene

  • GC04M024730
  • GC04M024462

Summaries for SEPSECS Gene

Entrez Gene Summary for SEPSECS Gene

  • 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]

GeneCards Summary for SEPSECS Gene

SEPSECS (Sep (O-Phosphoserine) TRNA:Sec (Selenocysteine) TRNA Synthase) is a Protein Coding gene. Diseases associated with SEPSECS include Pontocerebellar Hypoplasia Type 2D and Pontocerebellar Hypoplasia, Type 2E. Among its related pathways are Metabolism and Selenium Metabolism and Selenoproteins. GO annotations related to this gene include transferase activity and tRNA binding.

UniProtKB/Swiss-Prot for SEPSECS Gene

  • Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis.

Gene Wiki entry for SEPSECS Gene

Additional gene information for SEPSECS Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SEPSECS Gene

Genomics for SEPSECS Gene

Regulatory Elements for SEPSECS Gene

Enhancers for SEPSECS Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH04H025912 1.1 ENCODE 10.3 -753.7 -753697 3 HDGF PKNOX1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF143 SMIM20 SEL1L3 ANAPC4 ZCCHC4 PI4K2B SEPSECS LOC105374538 PIR49686
GH04H025107 0.6 ENCODE 10.4 +52.9 52942 0.9 PKNOX1 HLF CEBPB USF2 ZNF354B RAD51 POLR2A ZNF512 ANAPC4 DHX15 ZCCHC4 LGI2 SEPSECS LOC105374534 GC04M024941
GH04H025158 1.1 ENCODE 0.7 +0.0 23 3.8 HDGF FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF207 ZNF143 ANAPC4 PI4K2B DHX15 SEPSECS PIR60918
GH04H025132 0.5 ENCODE 0.3 +27.4 27410 1.7 SOX5 SOX13 FOXA2 SAP130 MIXL1 ANAPC4 CCDC149 PI4K2B PIR60918 SEPSECS
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around SEPSECS on UCSC Golden Path with GeneCards custom track

Promoters for SEPSECS Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000166874 -18 2401 HDGF FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF207 ZNF143

Transcription factor binding sites by QIAGEN in the SEPSECS gene promoter:

Genomic Locations for SEPSECS Gene

Genomic Locations for SEPSECS Gene
40,578 bases
Minus strand

Genomic View for SEPSECS Gene

Genes around SEPSECS on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SEPSECS Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SEPSECS Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SEPSECS Gene

Proteins for SEPSECS Gene

  • Protein details for SEPSECS Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    O-phosphoseryl-tRNA(Sec) selenium transferase
    Protein Accession:
    Secondary Accessions:
    • A8K8W1
    • Q0D2P3
    • Q17RT1
    • Q9NXZ5
    • Q9UGM9
    • Q9Y353

    Protein attributes for SEPSECS Gene

    501 amino acids
    Molecular mass:
    55726 Da
    Name=pyridoxal 5-phosphate; Xref=ChEBI:CHEBI:597326;
    Quaternary structure:
    • Homotetramer formed by a catalytic dimer and a non-catalytic dimer serving as a binding platform that orients tRNASec for catalysis. Each tetramer binds the CCA ends of two tRNAs which point to the active sites of the catalytic dimer.
    • Possible diagnostic marker for autoimmune hepatitis (AIH).
    • Sequence=AAD33963.2; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305}; Sequence=AAH23539.1; Type=Erroneous translation; Note=Wrong choice of CDS.; Evidence={ECO:0000305}; Sequence=CAB62209.1; Type=Erroneous initiation; Note=Translation N-terminally shortened.; Evidence={ECO:0000305}; Sequence=CAB89517.1; Type=Frameshift; Positions=39; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SEPSECS Gene

    Alternative splice isoforms for SEPSECS Gene


neXtProt entry for SEPSECS Gene

Selected DME Specific Peptides for SEPSECS Gene


Post-translational modifications for SEPSECS Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Domains & Families for SEPSECS Gene

Gene Families for SEPSECS Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

Suggested Antigen Peptide Sequences for SEPSECS Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the SepSecS family.
  • Belongs to the SepSecS family.
genes like me logo Genes that share domains with SEPSECS: view

Function for SEPSECS Gene

Molecular function for SEPSECS Gene

UniProtKB/Swiss-Prot CatalyticActivity:
O-phospho-L-seryl-tRNA(Sec) + selenophosphate + H(2)O = L-selenocysteinyl-tRNA(Sec) + 2 phosphate.
UniProtKB/Swiss-Prot Function:
Converts O-phosphoseryl-tRNA(Sec) to selenocysteinyl-tRNA(Sec) required for selenoprotein biosynthesis.

Enzyme Numbers (IUBMB) for SEPSECS Gene

Phenotypes From GWAS Catalog for SEPSECS Gene

Gene Ontology (GO) - Molecular Function for SEPSECS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000049 tRNA binding ISS --
GO:0003723 RNA binding IEA --
GO:0003824 catalytic activity IEA --
GO:0005515 protein binding IPI 22190034
GO:0016740 transferase activity IEA --
genes like me logo Genes that share ontologies with SEPSECS: view

Phenotypes for SEPSECS Gene

GenomeRNAi human phenotypes for SEPSECS:
genes like me logo Genes that share phenotypes with SEPSECS: view

Human Phenotype Ontology for SEPSECS Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for SEPSECS Gene

Localization for SEPSECS Gene

Subcellular locations from UniProtKB/Swiss-Prot for SEPSECS Gene


Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SEPSECS gene
Compartment Confidence
cytosol 5
nucleus 4
mitochondrion 3
plasma membrane 1
cytoskeleton 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for SEPSECS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus ISS --
GO:0005737 cytoplasm ISS --
GO:0005829 cytosol TAS --
genes like me logo Genes that share ontologies with SEPSECS: view

Pathways & Interactions for SEPSECS Gene

genes like me logo Genes that share pathways with SEPSECS: view

Pathways by source for SEPSECS Gene

UniProtKB/Swiss-Prot Q9HD40-SPCS_HUMAN

  • Pathway: Aminoacyl-tRNA biosynthesis; selenocysteinyl-tRNA(Sec) biosynthesis; selenocysteinyl-tRNA(Sec) from L-seryl-tRNA(Sec) (archaeal/eukaryal route): step 2/2.

Gene Ontology (GO) - Biological Process for SEPSECS Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001514 selenocysteine incorporation ISS --
GO:0006412 translation IEA --
GO:0016259 selenocysteine metabolic process TAS --
GO:0097056 selenocysteinyl-tRNA(Sec) biosynthetic process IEA --
genes like me logo Genes that share ontologies with SEPSECS: view

No data available for SIGNOR curated interactions for SEPSECS Gene

Drugs & Compounds for SEPSECS Gene

(9) Drugs for SEPSECS Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Phosphoric acid Approved Pharma 0
Selenium Approved, Vet_approved Pharma 185
Water Approved Pharma 0
Selenocysteine Experimental Pharma 0
Pyridoxal Phosphate Nutra Target, cofactor 16

(4) Additional Compounds for SEPSECS Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Dihydroxy-oxido-selanylidenephosphorane
  • Phosphorus monoselenide
  • Phosphorus selenide (PSe)
  • Selenoxo-phosphino
Phosphoroselenoic acid
  • Monoselenophosphoric acid
  • Selenophosphoric acid
  • SePO3
  • Trihydroxidoselenidophosphorus
  • [P(OH)3Se]
genes like me logo Genes that share compounds with SEPSECS: view

Transcripts for SEPSECS Gene

Unigene Clusters for SEPSECS Gene

Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SEPSECS Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b · 12c
SP1: - - -
SP2: - - - -
SP3: - -
SP4: - - - -
SP5: -

Relevant External Links for SEPSECS Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SEPSECS Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SEPSECS Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SEPSECS Gene

This gene is overexpressed in Liver (x4.1).

Protein differential expression in normal tissues from HIPED for SEPSECS Gene

This gene is overexpressed in Testis (21.8), Peripheral blood mononuclear cells (10.9), and Liver (8.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for SEPSECS Gene

Protein tissue co-expression partners for SEPSECS Gene

NURSA nuclear receptor signaling pathways regulating expression of SEPSECS Gene:


SOURCE GeneReport for Unigene cluster for SEPSECS Gene:


mRNA Expression by UniProt/SwissProt for SEPSECS Gene:

Tissue specificity: Primarily expressed in liver, pancreas, kidney and lung. Overexpressed in PHA-stimulated T-cells.

Evidence on tissue expression from TISSUES for SEPSECS Gene

  • Liver(4.6)
  • Muscle(4.4)
  • Nervous system(4.1)
  • Kidney(2.4)
  • Pancreas(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SEPSECS Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cranial nerve
  • ear
  • eye
  • face
  • forehead
  • head
  • jaw
  • mandible
  • maxilla
  • mouth
  • neck
  • pharynx
  • skull
  • chest wall
  • clavicle
  • heart
  • lung
  • rib
  • rib cage
  • scapula
  • sternum
  • abdominal wall
  • pelvis
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
  • blood vessel
  • peripheral nerve
  • peripheral nervous system
  • spinal column
  • spinal cord
  • vertebrae
genes like me logo Genes that share expression patterns with SEPSECS: view

Primer Products

Orthologs for SEPSECS Gene

This gene was present in the common ancestor of animals.

Orthologs for SEPSECS Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia SEPSECS 33 34
  • 99.73 (n)
(Bos Taurus)
Mammalia SEPSECS 33 34
  • 94 (n)
(Canis familiaris)
Mammalia SEPSECS 33 34
  • 92.47 (n)
(Rattus norvegicus)
Mammalia Sepsecs 33
  • 87.47 (n)
(Mus musculus)
Mammalia Sepsecs 33 16 34
  • 86.65 (n)
(Monodelphis domestica)
Mammalia SEPSECS 34
  • 85 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 76 (a)
-- 34
  • 72 (a)
(Gallus gallus)
Aves SEPSECS 33 34
  • 80.08 (n)
(Anolis carolinensis)
Reptilia SEPSECS 34
  • 78 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia sepsecs 33
  • 72.36 (n)
(Danio rerio)
Actinopterygii sepsecs 33 34
  • 70.49 (n)
zgc55980 33
fruit fly
(Drosophila melanogaster)
Insecta CG1427 33 34
  • 52.92 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP003527 33
  • 51.28 (n)
(Caenorhabditis elegans)
Secernentea secs-1 33 34
  • 50.79 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 53 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.930 33
Species where no ortholog for SEPSECS was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SEPSECS Gene

Gene Tree for SEPSECS (if available)
Gene Tree for SEPSECS (if available)

Paralogs for SEPSECS Gene

genes like me logo Genes that share paralogs with SEPSECS: view

No data available for Paralogs for SEPSECS Gene

Variants for SEPSECS Gene

Sequence variations from dbSNP and Humsavar for SEPSECS Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs267607035 Pathogenic, Pontocerebellar hypoplasia 2D (PCH2D) [MIM:613811] 25,152,049(-) AACTG(A/G)CTGTG reference, missense
rs267607036 Pathogenic, Pontocerebellar hypoplasia 2D (PCH2D) [MIM:613811] 25,144,799(-) TGGCT(A/G)TAAGA reference, missense
VAR_074163 Pontocerebellar hypoplasia 2D (PCH2D) [MIM:613811]
rs773876739 Pathogenic 25,123,971(+) CATTA(A/C/T)CTAGT reference, missense
rs776969714 Pathogenic 25,145,129(+) TCGAG(-/C)CCCCC reference, frameshift-variant

Structural Variations from Database of Genomic Variants (DGV) for SEPSECS Gene

Variant ID Type Subtype PubMed ID
nsv819375 CNV loss 19587683
nsv4277 CNV deletion 18451855
nsv1143080 CNV tandem duplication 24896259
esv3599957 CNV loss 21293372

Variation tolerance for SEPSECS Gene

Residual Variation Intolerance Score: 26.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.12; 75.56% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SEPSECS Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SEPSECS Gene

Disorders for SEPSECS Gene

MalaCards: The human disease database

(13) MalaCards diseases for SEPSECS Gene - From: HGMD, OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
pontocerebellar hypoplasia type 2d
  • progressive cerebello-cerebral atrophy
pontocerebellar hypoplasia, type 2e
  • pontocerebellar hypoplasia type 2a
autoimmune hepatitis
  • autoimmune chronic active hepatitis
  • acute and subacute liver necrosis
amelogenesis imperfecta, type ib
  • amelogenesis imperfecta type 1b
- elite association - COSMIC cancer census association via MalaCards


  • Pontocerebellar hypoplasia 2D (PCH2D) [MIM:613811]: A disorder characterized by postnatal onset of progressive atrophy of the cerebrum and cerebellum, microcephaly, profound mental retardation, spasticity, and variable seizures. {ECO:0000269 PubMed:20920667, ECO:0000269 PubMed:26115735}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for SEPSECS

Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with SEPSECS: view

No data available for Genatlas for SEPSECS Gene

Publications for SEPSECS Gene

  1. Isolation and characterization of cDNA encoding the antigenic protein of the human tRNP(Ser)Sec complex recognized by autoantibodies from patients withtype-1 autoimmune hepatitis. (PMID: 10931155) Costa M … Gelpí C (Clinical and experimental immunology 2000) 2 3 4 22 60
  2. Biosynthesis of selenocysteine on its tRNA in eukaryotes. (PMID: 17194211) Xu XM … Hatfield DL (PLoS biology 2007) 2 3 22 60
  3. RNA-dependent conversion of phosphoserine forms selenocysteine in eukaryotes and archaea. (PMID: 17142313) Yuan J … Söll D (Proceedings of the National Academy of Sciences of the United States of America 2006) 2 3 4 60
  4. Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery. (PMID: 16230358) Xu XM … Hatfield DL (The Journal of biological chemistry 2005) 2 3 22 60
  5. Fine specificity of autoantibodies to soluble liver antigen and liver/pancreas. (PMID: 11826415) Herkel J … Lohse AW (Hepatology (Baltimore, Md.) 2002) 3 4 22 60

Products for SEPSECS Gene

Sources for SEPSECS Gene

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