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EEFSEC eukaryotic elongation factor, selenocysteine-tRNA specific [ Homo sapiens (human) ]

Gene ID: 60678, updated on 13-Apr-2024

Summary

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Official Symbol
EEFSECprovided by HGNC
Official Full Name
eukaryotic elongation factor, selenocysteine-tRNA specificprovided by HGNC
Primary source
HGNC:HGNC:24614
See related
Ensembl:ENSG00000132394 MIM:607695; AllianceGenome:HGNC:24614
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SELB; EFSEC
Summary
Predicted to enable translation elongation factor activity. Predicted to be involved in selenocysteine incorporation. Predicted to be located in cytoplasm and nucleus. Predicted to be part of ribonucleoprotein complex. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 3.1), kidney (RPKM 2.8) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
3q21.3
Exon count:
12
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (128153481..128426223)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (130895120..131167807)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (127872324..128127489)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14700 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14701 Neighboring gene RUVBL1 antisense RNA 1 Neighboring gene RuvB like AAA ATPase 1 Neighboring gene NANOG hESC enhancer GRCh37_chr3:127819055-127819574 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20476 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14702 Neighboring gene Sharpr-MPRA regulatory region 11416 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:127865444-127866013 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20477 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14703 Neighboring gene RNA, U6 small nuclear 823, pseudogene Neighboring gene Sharpr-MPRA regulatory region 8761 Neighboring gene CRISPRi-FlowFISH-validated H1-10 regulatory element 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20478 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20479 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:127945585-127946085 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:127999447-127999964 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128001517-128002034 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128004261-128004760 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:128005625-128006126 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128035068-128035620 Neighboring gene Sharpr-MPRA regulatory region 3031 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128053445-128054066 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128054067-128054686 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:128062271-128062684 Neighboring gene Sharpr-MPRA regulatory regions 13692 and 14760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128087685-128088185 Neighboring gene Sharpr-MPRA regulatory region 10596 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128107303-128107892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128107893-128108480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128118070-128118864 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128118865-128119659 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128120455-128121248 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128126077-128126958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128128140-128128788 Neighboring gene CRISPRi-validated cis-regulatory element chr3.3676 Neighboring gene CRISPRi-validated cis-regulatory element chr3.3677 Neighboring gene CRISPRi-validated cis-regulatory element chr3.3678 Neighboring gene CRISPRi-validated cis-regulatory element chr3.3679 Neighboring gene CRISPRi-FlowFISH-validated RPN1 regulatory element 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128146331-128146889 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128150709-128151289 Neighboring gene uncharacterized LOC124909428 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128151290-128151869 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:128151870-128152450 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128154435-128155122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20483 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:128170962-128171462 Neighboring gene uncharacterized LOC124909429

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. [EEFSEC knockdown inhibits proliferation, migration and invasion of prostate cancer cells in vitro]. Xu B, et al. Nan Fang Yi Ke Da Xue Xue Bao, 2021 Dec 20. PMID 35012909, Free PMC Article
  2. Crystal structures of the human elongation factor eEFSec suggest a non-canonical mechanism for selenocysteine incorporation. Dobosz-Bartoszek M, et al. Nat Commun, 2016 Oct 6. PMID 27708257, Free PMC Article
  3. A novel protein domain induces high affinity selenocysteine insertion sequence binding and elongation factor recruitment. Donovan J, et al. J Biol Chem, 2008 Dec 12. PMID 18948268, Free PMC Article
  4. Efficiency of mammalian selenocysteine incorporation. Mehta A, et al. J Biol Chem, 2004 Sep 3. PMID 15229221, Free PMC Article
  5. Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation. Fagegaltier D, et al. EMBO J, 2000 Sep 1. PMID 10970870, Free PMC Article

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Association of rs142548867 (EEFSEC) and periodontitis Grade C in a young Brazilian population.
    Title: Association of rs142548867 (EEFSEC) and periodontitis Grade C in a young Brazilian population.
  2. [EEFSEC knockdown inhibits proliferation, migration and invasion of prostate cancer cells in vitro].
    Title: [EEFSEC knockdown inhibits proliferation, migration and invasion of prostate cancer cells in vitro].
  3. eEFSec employs a non-canonical mechanism involving the distinct C-terminal domain 4 for the release of the selenocysteinyl-tRNA during decoding on the ribosome
    Title: Crystal structures of the human elongation factor eEFSec suggest a non-canonical mechanism for selenocysteine incorporation.
  4. EEFSEC, which encodes selenocysteine-tRNA specific eukaryotic elongation factor, participates in the incorporation of selenocysteine into selenoproteins. Selenoproteins serve critical cellular homeostatic functions in maintaining redox status and antioxidant defenses, as well as modulating inflammatory responses. These physiologic functions have been linked to the parturition process and preterm birth.
    Title: Genetic Associations with Gestational Duration and Spontaneous Preterm Birth.
  5. In this genomewide association study, we found that variants at the EBF1, EEFSEC, AGTR2, WNT4, ADCY5, and RAP2C loci were associated with gestational duration and variants at the EBF1, EEFSEC, and AGTR2 loci with preterm birth.
    Title: Genetic Associations with Gestational Duration and Spontaneous Preterm Birth.
  6. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Inherited genetic markers discovered to date are able to identify a significant number of men at considerably elevated risk for prostate cancer.
  7. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  8. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  9. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility.
  10. SECIS binding induces a conformational change in SBP2 that recruits eEFSec, which in concert with the Sec incorporation domain gains access to the ribosomal A site
    Title: A novel protein domain induces high affinity selenocysteine insertion sequence binding and elongation factor recruitment.
Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Genome-wide association analyses identify variants in developmental genes associated with hypospadias.
EBI GWAS Catalog
Genome-wide association and replication studies identify four variants associated with prostate cancer susceptibility.
EBI GWAS Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
EBI GWAS Catalog
Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.
EBI GWAS Catalog

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

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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables GTP binding IEA
Inferred from Electronic Annotation
more info
  
enables GTPase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables ribonucleoprotein complex binding IEA
Inferred from Electronic Annotation
more info
  
enables selenocysteine insertion sequence binding IEA
Inferred from Electronic Annotation
more info
  
enables tRNA binding IEA
Inferred from Electronic Annotation
more info
  
enables translation elongation factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in selenocysteine incorporation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in selenocysteine incorporation IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
part_of ribonucleoprotein complex IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
selenocysteine-specific elongation factor
Names
elongation factor for selenoprotein translation
elongation factor sec
selenocysteine (Sec)-specific eukaryotic elongation factor

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.

mRNA and Protein(s)

  1. NM_021937.5 → NP_068756.2  selenocysteine-specific elongation factor

    See identical proteins and their annotated locations for NP_068756.2

    Status: VALIDATED

    Source sequence(s)
    AF268872, AL449217, BC007933, DB454660
    Consensus CDS
    CCDS33849.1
    UniProtKB/Swiss-Prot
    P57772, Q96HZ6
    Related
    ENSP00000254730.5, ENST00000254730.11
    Conserved Domains (5) summary
    cd01889
    Location:8 → 209
    SelB_euk; SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome
    pfam00009
    Location:8 → 213
    GTP_EFTU; Elongation factor Tu GTP binding domain
    cd03696
    Location:224 → 306
    SelB_II; Domain II of elongation factor SelB
    cd04094
    Location:311 → 450
    eSelB_III; Domain III of eukaryotic and archaeal elongation factor SelB
    cl02916
    Location:505 → 571
    POLO_box; Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    128153481..128426223
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024453695.2 → XP_024309463.1  selenocysteine-specific elongation factor isoform X3

    Conserved Domains (3) summary
    cd01889
    Location:8 → 209
    SelB_euk; SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome
    cd03696
    Location:224 → 357
    SelB_II; Domain II of elongation factor SelB
    cd04094
    Location:362 → 501
    eSelB_III; Domain III of eukaryotic and archaeal elongation factor SelB

  2. XM_024453692.2 → XP_024309460.1  selenocysteine-specific elongation factor isoform X1

    Conserved Domains (4) summary
    cd01889
    Location:8 → 209
    SelB_euk; SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome
    cd03696
    Location:224 → 357
    SelB_II; Domain II of elongation factor SelB
    cd04094
    Location:362 → 501
    eSelB_III; Domain III of eukaryotic and archaeal elongation factor SelB
    cl02916
    Location:556 → 622
    POLO_box; Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases

  3. XM_024453693.2 → XP_024309461.1  selenocysteine-specific elongation factor isoform X2

    Conserved Domains (4) summary
    cd01889
    Location:8 → 209
    SelB_euk; SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome
    cd03696
    Location:224 → 356
    SelB_II; Domain II of elongation factor SelB
    cd04094
    Location:361 → 500
    eSelB_III; Domain III of eukaryotic and archaeal elongation factor SelB
    cl02916
    Location:555 → 621
    POLO_box; Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases

  4. XM_047448659.1 → XP_047304615.1  selenocysteine-specific elongation factor isoform X8

  5. XM_005247696.4 → XP_005247753.1  selenocysteine-specific elongation factor isoform X6

    Conserved Domains (5) summary
    cd01889
    Location:8 → 210
    SelB_euk; SelB, the dedicated elongation factor for delivery of selenocysteinyl-tRNA to the ribosome
    pfam00009
    Location:8 → 209
    GTP_EFTU; Elongation factor Tu GTP binding domain
    cd04094
    Location:256 → 395
    eSelB_III; Domain III of eukaryotic and archaeal elongation factor SelB
    cl02787
    Location:206 → 251
    Translation_Factor_II_like; Domain II of Elongation factor Tu (EF-Tu)-like proteins
    cl02916
    Location:450 → 516
    POLO_box; Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases

  6. XM_047448660.1 → XP_047304616.1  selenocysteine-specific elongation factor isoform X9

    UniProtKB/TrEMBL
    C9J8T0
    Related
    ENSP00000417660.1, ENST00000483457.1

  7. XM_047448656.1 → XP_047304612.1  selenocysteine-specific elongation factor isoform X4

  8. XM_047448657.1 → XP_047304613.1  selenocysteine-specific elongation factor isoform X5

  9. XM_047448658.1 → XP_047304614.1  selenocysteine-specific elongation factor isoform X7

  10. XM_024453696.2 → XP_024309464.1  selenocysteine-specific elongation factor isoform X10

    Conserved Domains (3) summary
    cd04094
    Location:62 → 201
    eSelB_III; Domain III of eukaryotic and archaeal elongation factor SelB
    cl02787
    Location:13 → 57
    Translation_Factor_II_like; Domain II of Elongation factor Tu (EF-Tu)-like proteins
    cl02916
    Location:256 → 322
    POLO_box; Polo-box domain (PBD), a C-terminal tandemly repeated region of polo-like kinases

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_019805490.1 Reference GRCh38.p14 PATCHES

    Range
    22577..295325
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054332377.1 → XP_054188352.1  selenocysteine-specific elongation factor isoform X3

  2. XM_054332375.1 → XP_054188350.1  selenocysteine-specific elongation factor isoform X1

  3. XM_054332376.1 → XP_054188351.1  selenocysteine-specific elongation factor isoform X2

  4. XM_054332383.1 → XP_054188358.1  selenocysteine-specific elongation factor isoform X8

  5. XM_054332380.1 → XP_054188355.1  selenocysteine-specific elongation factor isoform X6

  6. XM_054332384.1 → XP_054188359.1  selenocysteine-specific elongation factor isoform X9

    UniProtKB/TrEMBL
    C9J8T0

  7. XM_054332378.1 → XP_054188353.1  selenocysteine-specific elongation factor isoform X4

  8. XM_054332379.1 → XP_054188354.1  selenocysteine-specific elongation factor isoform X5

  9. XM_054332381.1 → XP_054188356.1  selenocysteine-specific elongation factor isoform X7

  10. XM_054332382.1 → XP_054188357.1  selenocysteine-specific elongation factor isoform X11

  11. XM_054332385.1 → XP_054188360.1  selenocysteine-specific elongation factor isoform X10

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    130895120..131167807
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054347433.1 → XP_054203408.1  selenocysteine-specific elongation factor isoform X3

  2. XM_054347431.1 → XP_054203406.1  selenocysteine-specific elongation factor isoform X1

  3. XM_054347432.1 → XP_054203407.1  selenocysteine-specific elongation factor isoform X2

  4. XM_054347440.1 → XP_054203415.1  selenocysteine-specific elongation factor isoform X8

  5. XM_054347436.1 → XP_054203411.1  selenocysteine-specific elongation factor isoform X6

  6. XM_054347441.1 → XP_054203416.1  selenocysteine-specific elongation factor isoform X9

    UniProtKB/TrEMBL
    C9J8T0

  7. XM_054347434.1 → XP_054203409.1  selenocysteine-specific elongation factor isoform X4

  8. XM_054347435.1 → XP_054203410.1  selenocysteine-specific elongation factor isoform X5

  9. XM_054347437.1 → XP_054203412.1  selenocysteine-specific elongation factor isoform X7

  10. XM_054347438.1 → XP_054203413.1  selenocysteine-specific elongation factor isoform X12

  11. XM_054347439.1 → XP_054203414.1  selenocysteine-specific elongation factor isoform X13

  12. XM_054347442.1 → XP_054203417.1  selenocysteine-specific elongation factor isoform X10

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P57772.4 GenPept UniProtKB/Swiss-Prot:P57772

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