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    YIPF6 Yip1 domain family member 6 [ Homo sapiens (human) ]

    Gene ID: 286451, updated on 10-Dec-2024

    Summary

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    Official Symbol
    YIPF6provided by HGNC
    Official Full Name
    Yip1 domain family member 6provided by HGNC
    Primary source
    HGNC:HGNC:28304
    See related
    Ensembl:ENSG00000181704 MIM:300996; AllianceGenome:HGNC:28304
    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
    Yip4; FinGER6; YIPFalpha3
    Summary
    Predicted to enable identical protein binding activity. Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport. Predicted to act upstream of or within intestinal epithelial cell development. Located in Golgi apparatus subcompartment and endoplasmic reticulum. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in thyroid (RPKM 11.2), prostate (RPKM 8.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See YIPF6 in Genome Data Viewer
    Location:
    Xq12-q13.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (68499051..68537282)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (66932508..66970741)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (67718893..67757124)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene oligophrenin 1 Neighboring gene akirin 1 pseudogene 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:67575188-67575688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:67575689-67576189 Neighboring gene Sharpr-MPRA regulatory region 7273 Neighboring gene nuclear distribution protein nudE-like 1-like Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:67718059-67718733 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chrX:67767078-67767642 Neighboring gene RNA, U6 small nuclear 245, pseudogene Neighboring gene Sharpr-MPRA regulatory region 12156 Neighboring gene ribosomal protein L31 pseudogene 63

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. High levels of the AR-V7 Splice Variant and Co-Amplification of the Golgi Protein Coding YIPF6 in AR Amplified Prostate Cancer Bone Metastases. Djusberg E, et al. Prostate, 2017 May. PMID 28144969
    2. YIPF6 controls sorting of FGF21 into COPII vesicles and promotes obesity. Wang L, et al. Proc Natl Acad Sci U S A, 2019 Jul 23. PMID 31289229, 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. Identifying protein partners of CLN8, an ER-resident protein involved in neuronal ceroid lipofuscinosis. Passantino R, et al. Biochim Biophys Acta, 2013 Mar. PMID 23142642
    5. Stasimon/Tmem41b localizes to mitochondria-associated ER membranes and is essential for mouse embryonic development. Van Alstyne M, et al. Biochem Biophys Res Commun, 2018 Nov 30. PMID 30352685, Free PMC Article

    See all (31) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Levels of YIPF6 protein in human liver correlate with hepatic steatosis and correlate inversely with levels of FGF21 in serum from patients with nonalcoholic fatty liver disease.
      Title: YIPF6 controls sorting of FGF21 into COPII vesicles and promotes obesity.
    2. YIPF6 overexpression in prostate cancer tumor cell lines resulted in reduced cell proliferation and colony formation.
      Title: High levels of the AR-V7 Splice Variant and Co-Amplification of the Golgi Protein Coding YIPF6 in AR Amplified Prostate Cancer Bone Metastases.
    3. 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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC21416

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in intestinal epithelial cell development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in COPII-coated ER to Golgi transport vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi medial cisterna IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in Golgi membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in Golgi trans cisterna IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cis-Golgi network IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in trans-Golgi network IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    protein YIPF6
    Names
    YIP1 family member 6

    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_001195214.2 → NP_001182143.1  protein YIPF6 isoform B

      See identical proteins and their annotated locations for NP_001182143.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (B) lacks an in-frame exon in the 5' coding region, compared to variant A. The resulting protein (isoform B) is shorter than isoform A.
      Source sequence(s)
      AK303992, AL928603, CN311465
      Consensus CDS
      CCDS56604.1
      UniProtKB/TrEMBL
      B1AV70
      Related
      ENSP00000363751.2, ENST00000374622.3
      Conserved Domains (1) summary
      cl21557
      Location:22 → 188
      Yip1; Yip1 domain

    2. NM_173834.4 → NP_776195.2  protein YIPF6 isoform A

      See identical proteins and their annotated locations for NP_776195.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (A) represents the longer transcript and encodes the longer isoform (A).
      Source sequence(s)
      AL928603, BC012469
      Consensus CDS
      CCDS14389.1
      UniProtKB/Swiss-Prot
      B4E1U7, G5E997, Q5JP08, Q96EC8
      UniProtKB/TrEMBL
      A8K9X0
      Related
      ENSP00000417573.1, ENST00000462683.6
      Conserved Domains (1) summary
      cl21557
      Location:54 → 231
      Yip1; Yip1 domain

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      68499051..68537282
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      66932508..66970741
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96EC8.2 GenPept UniProtKB/Swiss-Prot:Q96EC8

    Gene LinkOut

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

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