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

    Gene ID: 60678, updated on 3-Nov-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
    Enables GTPase activity. 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, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 3.1), kidney (RPKM 2.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See EEFSEC in Genome Data Viewer
    Location:
    3q21.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (128153481..128426223)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (130895120..131167807)
    RS_2024_09 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 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. Association of rs142548867 (EEFSEC) and periodontitis Grade C in a young Brazilian population. Stolf CS, et al. J Appl Oral Sci, 2023. PMID 37466550, 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. [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
    4. Efficiency of mammalian selenocysteine incorporation. Mehta A, et al. J Biol Chem, 2004 Sep 3. PMID 15229221, Free PMC Article
    5. 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

    See all (52) 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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    NEW Try the new Transcript table

    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_2024_08

    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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