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    EFL1 elongation factor like GTPase 1 [ Homo sapiens (human) ]

    Gene ID: 79631, updated on 3-Apr-2024

    Summary

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    Official Symbol
    EFL1provided by HGNC
    Official Full Name
    elongation factor like GTPase 1provided by HGNC
    Primary source
    HGNC:HGNC:25789
    See related
    Ensembl:ENSG00000140598 MIM:617538; AllianceGenome:HGNC:25789
    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
    RIA1; SDS2; EFTUD1; FAM42A; HsT19294
    Summary
    Enables GTPase activity and ribosome binding activity. Involved in GTP metabolic process and mature ribosome assembly. Predicted to be part of ribonucleoprotein complex. Implicated in Shwachman-Diamond syndrome. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 7.4), small intestine (RPKM 6.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    15q25.2
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (82130233..82262734, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (79994284..80126851, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (82422574..82555075, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6744 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:82338662-82339608 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:82350032-82350532 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:82350533-82351033 Neighboring gene mex-3 RNA binding family member B Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6746 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:82375549-82375651 Neighboring gene uncharacterized LOC105370924 Neighboring gene long intergenic non-protein coding RNA 1583 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr15:82392793-82393305 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6747 Neighboring gene RNA, U1 small nuclear 77, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9960 Neighboring gene MPRA-validated peak2402 silencer Neighboring gene ReSE screen-validated silencer GRCh37_chr15:82553005-82553191 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9961 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9962 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:82559427-82559987 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9963 Neighboring gene stabilizer of axonemal microtubules 2 Neighboring gene ADAMTS7 pseudogene 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:82611132-82611632 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:82611633-82612133 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:82621782-82622282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:82622283-82622783

    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. Exploring the role of elongation Factor-Like 1 (EFL1) in Shwachman-Diamond syndrome through molecular dynamics. Delre P, et al. J Biomol Struct Dyn, 2020 Oct. PMID 31838967
    2. Mutations in EFL1, an SBDS partner, are associated with infantile pancytopenia, exocrine pancreatic insufficiency and skeletal anomalies in aShwachman-Diamond like syndrome. Stepensky P, et al. J Med Genet, 2017 Aug. PMID 28331068
    3. Functional analysis of a novel glioma antigen, EFTUD1. Saito K, et al. Neuro Oncol, 2014 Dec. PMID 25015090, Free PMC Article
    4. EFL1 mutations impair eIF6 release to cause Shwachman-Diamond syndrome. Tan S, et al. Blood, 2019 Jul 18. PMID 31151987, Free PMC Article
    5. Defective Guanine Nucleotide Exchange in the Elongation Factor-like 1 (EFL1) GTPase by Mutations in the Shwachman-Diamond Syndrome Protein. García-Márquez A, et al. J Biol Chem, 2015 Jul 17. PMID 25991726, Free PMC Article

    See all (40) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Somatic uniparental disomy mitigates the most damaging EFL1 allele combination in Shwachman-Diamond syndrome.
      Title: Somatic uniparental disomy mitigates the most damaging EFL1 allele combination in Shwachman-Diamond syndrome.
    2. Exploring the role of elongation Factor-Like 1 (EFL1) in Shwachman-Diamond syndrome through molecular dynamics.
      Title: Exploring the role of elongation Factor-Like 1 (EFL1) in Shwachman-Diamond syndrome through molecular dynamics.
    3. Whole exome sequencing discloses heterozygous variants in the DNAJC21 and EFL1 genes but not in SRP54 in 6 out of 16 patients with Shwachman-Diamond Syndrome carrying biallelic SBDS mutations.
      Title: Whole exome sequencing discloses heterozygous variants in the DNAJC21 and EFL1 genes but not in SRP54 in 6 out of 16 patients with Shwachman-Diamond Syndrome carrying biallelic SBDS mutations.
    4. we report biallelic mutations in EFL1 in 3 unrelated individuals with clinical features of SDS. Cellular defects in these individuals include impaired ribosomal subunit joining and attenuated global protein translation as a consequence of defective eIF6 eviction.
      Title: EFL1 mutations impair eIF6 release to cause Shwachman-Diamond syndrome.
    5. the effect of SBDS mutations on the interaction with EFL1were tested, and showed that all tested mutations disrupted the binding to EFL1.
      Title: Interaction of the GTPase Elongation Factor Like-1 with the Shwachman-Diamond Syndrome Protein and Its Missense Mutations.
    6. Mutations in EFL1 clinically manifest phenotypes of infantile pancytopenia, exocrine pancreatic insufficiency and skeletal anomalies. Mutant EFL1 proteins do not promote the release of yeast cytoplasmic Tif6 from the 60S subunit, likely preventing the formation of mature ribosomes.
      Title: Mutations in EFL1, an SBDS partner, are associated with infantile pancytopenia, exocrine pancreatic insufficiency and skeletal anomalies in aShwachman-Diamond like syndrome.
    7. Association of Elongation Factor-like 1 (EFL1) GTPase to SBDS did not modify the affinity for GTP but dramatically decreased that for GDP by increasing the dissociation rate of the nucleotide.
      Title: Defective Guanine Nucleotide Exchange in the Elongation Factor-like 1 (EFL1) GTPase by Mutations in the Shwachman-Diamond Syndrome Protein.
    8. Upon EFL1 binding, SBDS is repositioned around helix 69, thus facilitating a conformational switch in EFL1 that displaces eIF6 by competing for an overlapping binding site on the 60S ribosomal subunit.
      Title: Mechanism of eIF6 release from the nascent 60S ribosomal subunit.
    9. Downregulation of EFTUD1 induced cell-cycle arrest and apoptosis in gliomas by impairing ribosome biogenesis
      Title: Functional analysis of a novel glioma antigen, EFTUD1.
    10. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genomewide linkage and peakwide association analyses of carotid plaque in Caribbean Hispanics.
    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

    Associated conditions

    Description Tests
    Shwachman-Diamond syndrome 2
    MedGen: C4693704 OMIM: 617941 GeneReviews: Shwachman-Diamond Syndrome
    		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)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat HIV-1 Tat downregulates the expression of elongation factor Tu GTP binding domain containing 1 (EFTUD1) in human primary T cells 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

    Homology

    Clone Names

    • FLJ13119

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables GTP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables GTPase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables GTPase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables ribosome binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ribosome binding IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables translation elongation factor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in GTP metabolic process IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cytosolic ribosome assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cytosolic ribosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in translational elongation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of ribonucleoprotein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    elongation factor-like GTPase 1
    Names
    elongation factor Tu GTP binding domain containing 1
    elongation factor Tu GTP-binding domain-containing protein 1
    elongation factor-like 1
    ribosome assembly 1 homolog

    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_001040610.3 → NP_001035700.1  elongation factor-like GTPase 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two in-frame exons in the 5' coding region, compared to variant 1, which results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AC026624, AC026956, BC014628
      Consensus CDS
      CCDS42070.1
      UniProtKB/TrEMBL
      H0YKI9
      Related
      ENSP00000352418.3, ENST00000359445.8
      Conserved Domains (6) summary
      cd01681
      Location:636 → 935
      aeEF2_snRNP_like_IV; This family represents domain IV of archaeal and eukaryotic elongation factor 2 (aeEF-2) and of an evolutionarily conserved U5 snRNP-specific protein. U5 snRNP is a GTP-binding factor closely related to the ribosomal translocase EF-2. In complex with GTP, ...
      cd04096
      Location:932 → 1010
      eEF2_snRNP_like_C; eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart ...
      PTZ00416
      Location:1 → 1052
      PTZ00416; elongation factor 2; Provisional
      cd16268
      Location:451 → 549
      EF2_II; Domain II of Elongation Factor 2
      cd16261
      Location:565 → 636
      EF2_snRNP_III; Domain III of Elongation Factor 2 (EF2)
      cl21455
      Location:20 → 202
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    2. NM_001322844.2 → NP_001309773.1  elongation factor-like GTPase 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC026624, AC026956
      UniProtKB/TrEMBL
      B3KPR5
      Conserved Domains (4) summary
      cd01681
      Location:424 → 723
      aeEF2_snRNP_like_IV; This family represents domain IV of archaeal and eukaryotic elongation factor 2 (aeEF-2) and of an evolutionarily conserved U5 snRNP-specific protein. U5 snRNP is a GTP-binding factor closely related to the ribosomal translocase EF-2. In complex with GTP, ...
      cd04096
      Location:720 → 798
      eEF2_snRNP_like_C; eEF2_snRNP_like_C: this family represents a C-terminal domain of eukaryotic elongation factor 2 (eEF-2) and a homologous domain of the spliceosomal human 116kD U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116 kD) and, its yeast counterpart ...
      cd16268
      Location:239 → 337
      EF2_II; Domain II of Elongation Factor 2
      cd16261
      Location:353 → 424
      EF2_snRNP_III; Domain III of Elongation Factor 2 (EF2)

    3. NM_001322845.2 → NP_001309774.1  elongation factor-like GTPase 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC026624, AC026956
      Consensus CDS
      CCDS42071.1
      UniProtKB/Swiss-Prot
      A6NKY5, B7Z6I0, Q7Z2Z2, Q9H8Z6
      UniProtKB/TrEMBL
      H0YKI9
      Related
      ENSP00000512564.1, ENST00000696330.1
      Conserved Domains (1) summary
      cl30786
      Location:1 → 1103
      FusA; Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]

    4. NM_024580.6 → NP_078856.4  elongation factor-like GTPase 1 isoform 1

      See identical proteins and their annotated locations for NP_078856.4

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the the longest isoform (1).
      Source sequence(s)
      AC026624, AC026956, BC014628
      Consensus CDS
      CCDS42071.1
      UniProtKB/Swiss-Prot
      A6NKY5, B7Z6I0, Q7Z2Z2, Q9H8Z6
      UniProtKB/TrEMBL
      H0YKI9
      Related
      ENSP00000268206.7, ENST00000268206.12
      Conserved Domains (1) summary
      cl30786
      Location:1 → 1103
      FusA; Translation elongation factor EF-G, a GTPase [Translation, ribosomal structure and biogenesis]

    RNA

    1. NR_136410.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC026624, AC026956
      Related
      ENST00000696336.1

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      82130233..82262734 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_024450048.2 → XP_024305816.1  elongation factor-like GTPase 1 isoform X1

      UniProtKB/TrEMBL
      A0A8Q3SIM9
      Related
      ENSP00000512563.1, ENST00000696327.1
      Conserved Domains (1) summary
      cl27769
      Location:29 → 567
      GTP_EFTU; Elongation factor Tu GTP binding domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      79994284..80126851 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054378772.1 → XP_054234747.1  elongation factor-like GTPase 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q7Z2Z2.2 GenPept UniProtKB/Swiss-Prot:Q7Z2Z2

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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