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

Gene ID: 286451, updated on 7-Apr-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 act upstream of or within intestinal epithelial cell development. Located in Golgi apparatus subcompartment and endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
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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Location:
Xq12-q13.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (68499051..68537282)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (66932508..66970741)
105.20220307 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: 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 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 (30) 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)

Genotypes

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_2023_10

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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