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    YIPF1 Yip1 domain family member 1 [ Homo sapiens (human) ]

    Gene ID: 54432, updated on 28-Oct-2024

    Summary

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    Official Symbol
    YIPF1provided by HGNC
    Official Full Name
    Yip1 domain family member 1provided by HGNC
    Primary source
    HGNC:HGNC:25231
    See related
    Ensembl:ENSG00000058799 MIM:617521; AllianceGenome:HGNC:25231
    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
    Yip5a; FinGER1; DJ167A19.1; YIPFbeta3A
    Summary
    Predicted to enable small GTPase binding activity. Predicted to be involved in vesicle-mediated transport. Located in several cellular components, including Golgi apparatus subcompartment; nucleoplasm; and transport vesicle. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 28.9), prostate (RPKM 18.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See YIPF1 in Genome Data Viewer
    Location:
    1p32.3
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (53851733..53889797, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (53734613..53772679, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (54317406..54355470, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene NDC1 transmembrane nucleoporin Neighboring gene uncharacterized LOC124904725 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:54277212-54277746 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 912 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1050 Neighboring gene ribosomal protein L37 pseudogene 7 Neighboring gene Sharpr-MPRA regulatory region 6831 Neighboring gene Sharpr-MPRA regulatory region 3939 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54359446-54359946 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:54359947-54360447 Neighboring gene uncharacterized LOC124904180 Neighboring gene iodothyronine deiodinase 1 Neighboring gene uncharacterized LOC124904181 Neighboring gene intraflagellar transport 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. High-content screening microscopy identifies novel proteins with a putative role in secretory membrane traffic. Starkuviene V, et al. Genome Res, 2004 Oct. PMID 15466293, Free PMC Article
    2. Genetic polymorphisms of the human PNPLA3 gene are strongly associated with severity of non-alcoholic fatty liver disease in Japanese. Kawaguchi T, et al. PLoS One, 2012. PMID 22719876, Free PMC Article
    3. YIPF1, YIPF2, and YIPF6 are medial-/trans-Golgi and trans-Golgi network-localized Yip domain family proteins, which play a role in the Golgi reassembly and glycan synthesis. Soonthornsit J, et al. Exp Cell Res, 2017 Apr 15. PMID 28286305
    4. Image-based genome-wide siRNA screen identifies selective autophagy factors. Orvedahl A, et al. Nature, 2011 Dec 1. PMID 22020285, Free PMC Article
    5. LncRNAs-directed PTEN enzymatic switch governs epithelial-mesenchymal transition. Hu Q, et al. Cell Res, 2019 Apr. PMID 30631154, Free PMC Article

    See all (26) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Knockdown of YIPF1 and YIPF2, but not that of YIPF6, also reduced intracellular glycans in HT-29 cells. Thus, we confirmed that YIPF1, YIPF2, and YIPF6 play a significant role in supporting normal glycan synthesis
      Title: YIPF1, YIPF2, and YIPF6 are medial-/trans-Golgi and trans-Golgi network-localized Yip domain family proteins, which play a role in the Golgi reassembly and glycan synthesis.
    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
    Genetic polymorphisms of the human PNPLA3 gene are strongly associated with severity of non-alcoholic fatty liver disease in Japanese.
    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

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables small GTPase binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in Golgi apparatus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi apparatus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in Golgi medial cisterna IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi trans cisterna IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    		  
    located_in trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in transport vesicle IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    protein YIPF1
    Names
    YIP1 family member 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_018982.5 → NP_061855.1  protein YIPF1

      See identical proteins and their annotated locations for NP_061855.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) is the protein-coding transcript.
      Source sequence(s)
      AL031427, AL391003, AL596480, BI757212
      Consensus CDS
      CCDS584.1
      UniProtKB/Swiss-Prot
      B2RCM7, D3DQ40, Q9NWJ1, Q9Y548
      UniProtKB/TrEMBL
      B7Z6F5
      Related
      ENSP00000072644.1, ENST00000072644.7
      Conserved Domains (1) summary
      pfam04893
      Location:86 → 268
      Yip1; Yip1 domain

    RNA

    1. NR_036639.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) contains an alternate exon in the 3' end, compared to variant 1, which renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL031427, AL391003, AL596480

    2. NR_036640.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon in the 5' end and contains an alternate exon in the 3' end, compared to variant 1, which renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL031427, AL391003, AL596480

    3. NR_135075.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks two consecutive internal exons, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AA405430, AK000823, BI561906, BX405963
      Related
      ENST00000371399.5

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      53851733..53889797 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      53734613..53772679 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y548.1 GenPept UniProtKB/Swiss-Prot:Q9Y548

    Gene LinkOut

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

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