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

Gene ID: 54432, updated on 7-Apr-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, Apr 2022]
Expression
Ubiquitous expression in thyroid (RPKM 28.9), prostate (RPKM 18.8) and 25 other tissues See more
Orthologs
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (53851733..53889797, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (53734613..53772679, complement)
105.20220307 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
  • 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 (25) 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_2023_10

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

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