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

Summary

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

Location:: 4p15.2

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	4	NC_000004.12 (25120014..25160582, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	4	NC_060928.1 (25101930..25142501, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	4	NC_000004.11 (25121636..25162071, complement)

Chromosome 4 - NC_000004.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
Human Genetic Disorders Resulting in Systemic Selenoprotein Deficiency.
Title: Human Genetic Disorders Resulting in Systemic Selenoprotein Deficiency.
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.
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.
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.
results suggest SEPSECS as a candidate gene for progressive encephalopathies with lactate elevation.
Title: Selenoprotein biosynthesis defect causes progressive encephalopathy with elevated lactate.
structural analysis of the terminal catalytic complex in selenocysteine synthesis
Title: Structural asymmetry of the terminal catalytic complex in selenocysteine synthesis.
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.
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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-105226 (e-PCR)
- UniSTS:169267

SHGC-64855 (e-PCR)
- UniSTS:24634

SHGC-79143 (e-PCR)
- UniSTS:95851

RH46210 (e-PCR)
- UniSTS:28332

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

EC 2.9.1.2

NP_058651.3

EC 2.9.1.2

XP_011512148.1

EC 2.9.1.2

XP_011512149.1

EC 2.9.1.2

XP_011512150.1

EC 2.9.1.2

XP_047271718.1

EC 2.9.1.2

XP_054206119.1

EC 2.9.1.2

XP_054206120.1

EC 2.9.1.2

XP_054206121.1

EC 2.9.1.2

XP_054206122.1

EC 2.9.1.2

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

NG_028222.1 RefSeqGene

Range

5134..45569

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000004.12 Reference GRCh38.p14 Primary Assembly

Range

25120014..25160582 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A1A4F3
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
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
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

NC_060928.1 Alternate T2T-CHM13v2.0

Range

25101930..25142501 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A1A4F3
XM_054350145.1 → XP_054206120.1 O-phosphoseryl-tRNA(Sec) selenium transferase isoform X2
XM_054350144.1 → XP_054206119.1 O-phosphoseryl-tRNA(Sec) selenium transferase isoform X1
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

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.