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YIPF4 Gene

protein-coding   GIFtS: 50
GCID: GC02P032502

Yip1 Domain Family, Member 4

  See YIPF4-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Yip1 Domain Family, Member 41 2
YIP1 Family Member 42 3
FinGER42
Protein YIPF42
Putative Protein Product Of Nbla111892

External Ids:    HGNC: 281451   Entrez Gene: 842722   Ensembl: ENSG000001198207   UniProtKB: Q9BSR83   

Export aliases for YIPF4 gene to outside databases

Previous GC identifers: GC02P032416 GC02P032356 GC02P032242


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for YIPF4 Gene:
YIPF4 (Yip1 domain family, member 4) is a protein-coding gene. Diseases associated with YIPF4 include skin sarcoidosis.

UniProtKB/Swiss-Prot: YIPF4_HUMAN, Q9BSR8
Function: Involved in the maintenance of the Golgi structure

Gene Wiki entry for YIPF4 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000002.11  NT_022184.16  NC_018913.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the YIPF4 gene promoter:
         MAZR   RelA   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   NF-kappaB   POU3F2   HNF-4alpha1   c-Ets-1   CP2   NF-kappaB1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidYIPF4 promoter sequence
   Search Chromatin IP Primers for YIPF4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat YIPF4


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 2p22.3   Ensembl cytogenetic band:  2p22.3   HGNC cytogenetic band: 2p22.3

YIPF4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
YIPF4 gene location

GeneLoc information about chromosome 2         GeneLoc Exon Structure

GeneLoc location for GC02P032502:  view genomic region     (about GC identifiers)

Start:
32,502,958 bp from pter      End:
32,541,663 bp from pter
Size:
38,706 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: YIPF4_HUMAN, Q9BSR8 (See protein sequence)
Recommended Name: Protein YIPF4  
Size: 244 amino acids; 27083 Da
Subunit: Interacts with YIPF3

Explore the universe of human proteins at neXtProt for YIPF4: NX_Q9BSR8

Explore proteomics data for YIPF4 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys47
  • Modification sites at PhosphoSitePlus

  • See YIPF4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_115688.1  
    ENSEMBL proteins: 
     ENSP00000238831   ENSP00000394339   ENSP00000414267  

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    Cloud-Clone Corp. Proteins for YIPF4

     
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    antibodies-online peptides for YIPF4

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    antibodies-online antibodies for YIPF4 (10 products) 

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    antibodies-online kits for YIPF4 (8 products) 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    YIPF: Yip1 domain family

    1 InterPro protein domain:
     IPR006977 Yip1

    Graphical View of Domain Structure for InterPro Entry Q9BSR8

    ProtoNet protein and cluster: Q9BSR8

    UniProtKB/Swiss-Prot: YIPF4_HUMAN, Q9BSR8
    Similarity: Belongs to the YIP1 family


    Find genes that share domains with YIPF4           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: YIPF4_HUMAN, Q9BSR8
    Function: Involved in the maintenance of the Golgi structure

    Phenotypes:
         2 GenomeRNAi human phenotypes for YIPF4:

     Cell division defect  Increased S DNA content 

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for YIPF4

    miRNA
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    miRTarBase miRNAs that target YIPF4:
    hsa-mir-125a-5p (MIRT045777), hsa-mir-16-5p (MIRT031780)

    Block miRNA regulation of human, mouse, rat YIPF4 using miScript Target Protectors
    5 qRT-PCR Assays for microRNAs that regulate YIPF4:
    hsa-miR-3926 hsa-miR-3140-3p hsa-miR-4325 hsa-miR-1271 hsa-miR-96
    SwitchGear 3'UTR luciferase reporter plasmidYIPF4 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat YIPF4

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    Clone
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    GenScript: all cDNA clones in your preferred vector: YIPF4 (NM_032312)
    Sino Biological Human cDNA Clone for YIPF4
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat YIPF4

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YIPF4


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    YIPF4_HUMAN, Q9BSR8: Golgi apparatus, cis-Golgi network membrane; Multi-pass membrane protein
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum4
    golgi apparatus3
    plasma membrane3

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005783endoplasmic reticulum IDA--
    GO:0005794Golgi apparatus IDA--
    GO:0005886plasma membrane IDA--
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with YIPF4           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for YIPF4
    Interactions:

        Search GeneGlobe Interaction Network for YIPF4

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for YIPF4 (Q9BSR82, 3 ENSP000002388314) via UniProtKB, MINT, STRING, and/or I2D (see all 66)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    YIPF3Q9GZM52, 3MINT-68058 I2D: score=5 
    RABAC1ENSP000002220084STRING: ENSP00000222008
    UBCENSP000003448184STRING: ENSP00000344818
    IER3IP1ENSP000002564334STRING: ENSP00000256433
    SEC13ENSP000003121224STRING: ENSP00000312122
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for YIPF4



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for YIPF4 gene: 
    NM_032312.3  

    Unigene Cluster for YIPF4:

    Yip1 domain family, member 4
    Hs.468099  [show with all ESTs]
    Unigene Representative Sequence: NM_032312
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000238831(uc002rok.3) ENST00000495355 ENST00000437765 ENST00000441084

    miRNA
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    5 qRT-PCR Assays for microRNAs that regulate YIPF4:
    hsa-miR-3926 hsa-miR-3140-3p hsa-miR-4325 hsa-miR-1271 hsa-miR-96
    SwitchGear 3'UTR luciferase reporter plasmidYIPF4 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat YIPF4
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    GenScript: all cDNA clones in your preferred vector: YIPF4 (NM_032312)
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    Primer
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    OriGene qPCR primer pairs and template standards for YIPF4
    OriGene qSTAR qPCR primer pairs in human, mouse for YIPF4
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      QuantiTect SYBR Green Assays in human, mouse, rat YIPF4
      QuantiFast Probe-based Assays in human, mouse, rat YIPF4

    Additional mRNA sequence: 

    AB072898.1 AK098486.1 BC004875.2 

    10 DOTS entries:

    DT.445375  DT.100786410  DT.95278781  DT.121019647  DT.86853571  DT.100786408  DT.121019649  DT.95278780 
    DT.95278782  DT.86995158 

    Selected AceView cDNA sequences (see all 144):

    AI554076 BP341511 AU279440 BM764320 BQ100815 AW572456 AI911943 AL709356 
    BQ101107 BP338222 CK823051 BQ100705 BU607528 BQ100982 AA223546 BG682213 
    AA287059 BM760364 BE139521 CB243252 BG829335 CA942153 AK098486 BM712551 

    GeneLoc Exon Structure

    5 Alternative Splicing Database (ASD) splice patterns (SP) for YIPF4    About this scheme

    ExUns: 1a · 1b · 1c ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b · 6c
    SP1:                                                                        
    SP2:                                      -                                 
    SP3:                    -     -     -                                       
    SP4:                                      -                                 
    SP5:                          -     -                                       


    ECgene alternative splicing isoforms for YIPF4

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    YIPF4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTTCGATACT
    YIPF4 Expression
    About this image

    YIPF4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    YIPF4 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.468099
        Custom PCR Arrays for YIPF4
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YIPF4

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for YIPF4 gene from Selected species (see all 16)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Yipf41 , 5 Yip1 domain family, member 41, 5 93.25(n)1
    97.84(a)1
      17 (45.64 cM)5
    678641  NM_026417.41  NP_080693.21 
     744894935 
    chicken
    (Gallus gallus)
    Aves YIPF41 Yip1 domain family, member 4 85.06(n)
    96.98(a)
      421464  NM_001031058.1  NP_001026229.1 
    lizard
    (Anolis carolinensis)
    Reptilia YIPF46
    Yip1 domain family, member 4
    76(a)
    1 ↔ 1
    1(232077871-232090391)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.165522 Xenopus laevis transcribed sequence with strong similarity more 74.74(n)    CF289991.1 
    zebrafish
    (Danio rerio)
    Actinopterygii Dr.61342 Transcribed sequence with moderate similarity to protein more 77.09(n)    CK028284.1 
    worm
    (Caenorhabditis elegans)
    Secernentea CELE_Y60A3A.191 CELE_Y60A3A.19 59.01(n)
    53.15(a)
      180305  NM_001129584.1  NP_001123056.1 


    ENSEMBL Gene Tree for YIPF4 (if available)
    TreeFam Gene Tree for YIPF4 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for YIPF4 (see all 610)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 2 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1475857961,2
    --32500991(+) TCAATA/GCCTTA 1 -- us2k10--------
    rs1840694021,2
    --32501070(+) GGAACA/GTACAA 1 -- us2k10--------
    rs1422008021,2
    C--32501161(+) GCATGC/TCTTCC 1 -- us2k10--------
    rs1459212851,2
    C--32501164(+) TGCCTA/TCCTCT 1 -- us2k10--------
    rs602662021,2
    C--32501369(+) GTGATG/TACTCT 1 -- us2k10--------
    rs1414056571,2
    --32501423(+) CTAGCA/GCAGCC 1 -- us2k10--------
    rs8058301,2
    C,F,H--32501475(+) gagagC/Ttcggg 1 -- us2k17Minor allele frequency- T:0.43MN NA WA EA 432
    rs1867874821,2
    --32501523(+) CAGAAG/TAATTT 1 -- us2k10--------
    rs1501960801,2
    --32501810(+) TGGTGA/GCAGGC 1 -- us2k10--------
    rs1915436521,2
    --32501846(+) GCTGAA/GGCAGG 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for YIPF4 (32502958 - 32541663 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for YIPF4:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2422335CNV Duplication17116639
    nsv819851CNV Loss19587683

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing YIPF4
    DNA2.0 Custom Variant and Variant Library Synthesis for YIPF4

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    1 disease for YIPF4:    
    About MalaCards
    skin sarcoidosis

    1 disease from the University of Copenhagen DISEASES database for YIPF4:
    Skin sarcoidosis

    Find genes that share disorders with YIPF4           About GenesLikeMe


    Export disorders for YIPF4 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for YIPF4 gene, integrated from 10 sources (see all 20):
    (articles sorted by number of sources associating them with YIPF4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Characterization of YIPF3 and YIPF4, cis-Golgi localizing Yip domain family proteins. (PubMed id 21757827)1, 2 Tanimoto K.... Nakamura N. (Cell Struct. Funct. 2011)
    2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    4. Neuroblastoma oligo-capping cDNA project: toward the understanding of the genesis and biology of neuroblastoma. (PubMed id 12880961)1, 2 Ohira M.... Nakagawara A. (Cancer Lett. 2003)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    6. Systems-wide analysis of ubiquitylation dynamics reveals a key role for PAF15 ubiquitylation in DNA-damage bypass. (PubMed id 23000965)1 Povlsen L.K....Choudhary C. (Nat. Cell Biol. 2012)
    7. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (BMC Syst. Biol. 2011)
    8. A proteome-wide, quantitative survey of in vivo ubiquitylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (amp 2011)
    9. Systematic and quantitative assessment of the ubiquitin-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (Mol. Cell 2011)
    10. Ubiquitin ligase substrate identification through quantitative proteomics at both the protein and peptide levels. (PubMed id 21987572)1 Lee K.A....Doedens J.R. (J. Biol. Chem. 2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 84272 HGNC: 28145 AceView: MGC11061 Ensembl:ENSG00000119820 euGenes: HUgn84272
    ECgene: YIPF4 H-InvDB: YIPF4

    (According to HUGE)
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for YIPF4 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for YIPF4 gene:
    Search GeneIP for patents involving YIPF4

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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