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    ZFYVE1 zinc finger FYVE-type containing 1 [ Homo sapiens (human) ]

    Gene ID: 53349, updated on 28-Oct-2024

    Summary

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    Official Symbol
    ZFYVE1provided by HGNC
    Official Full Name
    zinc finger FYVE-type containing 1provided by HGNC
    Primary source
    HGNC:HGNC:13180
    See related
    Ensembl:ENSG00000165861 MIM:605471; AllianceGenome:HGNC:13180
    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
    SR3; DFCP1; TAFF1; ZNFN2A1; PPP1R172
    Summary
    The FYVE domain mediates the recruitment of proteins involved in membrane trafficking and cell signaling to phosphatidylinositol 3-phosphate-containing membranes. This protein contains two zinc-binding FYVE domains in tandem and is reported to localize to the Golgi apparatus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
    Expression
    Ubiquitous expression in thyroid (RPKM 7.4), kidney (RPKM 6.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZFYVE1 in Genome Data Viewer
    Location:
    14q24.2
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (72969445..73027106, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (67175059..67232660, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (73436153..73493814, complement)

    Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene tRNA-Cys (anticodon GCA) 8-1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:73437151-73437652 Neighboring gene ribosomal protein S12 pseudogene 1 Neighboring gene MPRA-validated peak2195 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5903 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8692 Neighboring gene ReSE screen-validated silencer GRCh37_chr14:73502840-73503013 Neighboring gene RNA, 7SL, cytoplasmic 586, pseudogene Neighboring gene MED14-independent group 3 enhancer GRCh37_chr14:73524555-73525754 Neighboring gene RBM25 antisense RNA 1 Neighboring gene RNA binding motif protein 25

    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. Double FYVE-containing protein 1 (DFCP1): isolation, cloning and characterization of a novel FYVE finger protein from a human bone marrow cDNA library. Derubeis AR, et al. Gene, 2000 Sep 19. PMID 11024279
    2. The role of NSP6 in the biogenesis of the SARS-CoV-2 replication organelle. Ricciardi S, et al. Nature, 2022 Jun. PMID 35551511, Free PMC Article
    3. A subdomain of the endoplasmic reticulum forms a cradle for autophagosome formation. Hayashi-Nishino M, et al. Nat Cell Biol, 2009 Dec. PMID 19898463
    4. Cellular localization and tissue distribution of endogenous DFCP1 protein. Nanao T, et al. Biomed Res, 2015. PMID 25876663
    5. TRIM13 regulates ER stress induced autophagy and clonogenic ability of the cells. Tomar D, et al. Biochim Biophys Acta, 2012 Feb. PMID 22178386

    See all (41) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    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

    Clone Names

    • KIAA1589

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables 1-phosphatidylinositol binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 1-phosphatidylinositol binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-3,4,5-trisphosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-3,4,5-trisphosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-3,4-bisphosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-3,4-bisphosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables phosphatidylinositol-3-phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables phosphatidylinositol-3-phosphate binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to starvation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in lipid droplet formation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in lipid droplet formation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in macroautophagy IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation by host of viral genome replication IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi stack IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in autophagosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extrinsic component of omegasome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in lipid droplet IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lipid droplet IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    colocalizes_with membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondria-associated endoplasmic reticulum membrane contact site IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in mitochondrion IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in omegasome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in perinuclear region of cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in phagophore assembly site IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    zinc finger FYVE domain-containing protein 1
    Names
    double FYVE-containing protein 1
    phosphoinositide-binding protein SR3
    protein phosphatase 1, regulatory subunit 172
    tandem FYVE fingers-1 protein
    zinc finger protein, subfamily 2A, member 1
    zinc finger, FYVE domain containing 1

    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_001281734.2 → NP_001268663.1  zinc finger FYVE domain-containing protein 1 isoform 3

      See identical proteins and their annotated locations for NP_001268663.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 3), compared to isoform 1.
      Source sequence(s)
      AL442663, BC014902, DA324499, DB059103, EL734498
      Consensus CDS
      CCDS61498.1
      UniProtKB/TrEMBL
      G3V5N8
      Related
      ENSP00000326921.5, ENST00000318876.9
      Conserved Domains (3) summary
      cd01851
      Location:174 → 410
      GBP; Guanylate-binding protein (GBP) family (N-terminal domain)
      cd15734
      Location:697 → 757
      FYVE_ZFYV1; FYVE domains found in zinc finger FYVE domain-containing protein 1 (ZFYV1) and similar proteins
      cl22851
      Location:580 → 641
      PHD_SF; PHD finger superfamily

    2. NM_001281735.1 → NP_001268664.1  zinc finger FYVE domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001268664.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) uses an alternate 5' exon structure, and thus differs in the 5' UTR and 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1. Both variants 2 and 4 encode the same isoform (2).
      Source sequence(s)
      AK098542, AL442663, AW070816, BU740588, BX339655, CK005173, HY248287
      Consensus CDS
      CCDS41969.1
      UniProtKB/Swiss-Prot
      Q9HBF4
      Related
      ENSP00000377757.2, ENST00000394207.6
      Conserved Domains (2) summary
      cd15734
      Location:296 → 356
      FYVE_ZFYV1; FYVE domains found in zinc finger FYVE domain-containing protein 1 (ZFYV1) and similar proteins
      cl22851
      Location:179 → 240
      PHD_SF; PHD finger superfamily

    3. NM_021260.4 → NP_067083.1  zinc finger FYVE domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_067083.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AB046809, BC053520, HY248287
      Consensus CDS
      CCDS9811.1
      UniProtKB/Swiss-Prot
      J3KNL9, Q8WYX7, Q96K57, Q9BXP9, Q9HBF4, Q9HCI3
      UniProtKB/TrEMBL
      G3V5N8
      Related
      ENSP00000450742.1, ENST00000556143.6
      Conserved Domains (3) summary
      cd01851
      Location:174 → 410
      GBP; Guanylate-binding protein (GBP) family (N-terminal domain)
      cd15734
      Location:711 → 771
      FYVE_ZFYV1; FYVE domains found in zinc finger FYVE domain-containing protein 1 (ZFYV1) and similar proteins
      cl28890
      Location:594 → 655
      FYVE_like_SF; FYVE domain like superfamily

    4. NM_178441.2 → NP_848535.1  zinc finger FYVE domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_848535.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate 5' exon structure, and thus differs in the 5' UTR and 5' coding region, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1. Both variants 2 and 4 encode the same isoform (2).
      Source sequence(s)
      AF311602, AI073571, AW070816, BX339655, CK005173, HY248287
      Consensus CDS
      CCDS41969.1
      UniProtKB/Swiss-Prot
      Q9HBF4
      Related
      ENSP00000452232.1, ENST00000555072.1
      Conserved Domains (2) summary
      cd15734
      Location:296 → 356
      FYVE_ZFYV1; FYVE domains found in zinc finger FYVE domain-containing protein 1 (ZFYV1) and similar proteins
      cl22851
      Location:179 → 240
      PHD_SF; PHD finger superfamily

    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_000014.9 Reference GRCh38.p14 Primary Assembly

      Range
      72969445..73027106 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047431482.1 → XP_047287438.1  zinc finger FYVE domain-containing protein 1 isoform X2

    2. XM_017021373.2 → XP_016876862.1  zinc finger FYVE domain-containing protein 1 isoform X2

      UniProtKB/Swiss-Prot
      Q9HBF4
      Conserved Domains (2) summary
      cd15734
      Location:296 → 356
      FYVE_ZFYV1; FYVE domains found in zinc finger FYVE domain-containing protein 1 (ZFYV1) and similar proteins
      cl22851
      Location:179 → 240
      PHD_SF; PHD finger superfamily

    3. XM_047431481.1 → XP_047287437.1  zinc finger FYVE domain-containing protein 1 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060938.1 Alternate T2T-CHM13v2.0

      Range
      67175059..67232660 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054376226.1 → XP_054232201.1  zinc finger FYVE domain-containing protein 1 isoform X2

    2. XM_054376227.1 → XP_054232202.1  zinc finger FYVE domain-containing protein 1 isoform X2

    3. XM_054376225.1 → XP_054232200.1  zinc finger FYVE domain-containing protein 1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9HBF4.1 GenPept UniProtKB/Swiss-Prot:Q9HBF4

    Gene LinkOut

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

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