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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

YIPF4 Gene

protein-coding   GIFtS: 48
GCID: GC02P032502

Yip1 Domain Family, Member 4

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

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, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

GeneCards Summary for YIPF4 Gene: 
YIPF4 (Yip1 domain family, member 4) is a protein-coding gene. Diseases associated with YIPF4 include skin sarcoidosis, and denys-drash syndrome.

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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000002.11  NT_022184.15  NC_018913.2  
Regulatory elements:
   SABiosciences 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 SABiosciences Chromatin IP Primers for YIPF4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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:
32,537,002 bp from pter
Size:
34,045 bases      Orientation:
plus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: YIPF4_HUMAN, Q9BSR8 (See protein sequence)
Recommended Name: Protein YIPF4  
Size: 244 amino acids; 27083 Da
Subunit: Interacts with YIPF3
Subcellular location: Golgi apparatus, cis-Golgi network membrane; Multi-pass membrane protein

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

Explore proteomics data for YIPF4 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9BSR8

  • YIPF4 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    YIPF4 Protein Expression
    REFSEQ proteins: NP_115688.1  
    ENSEMBL proteins: 
     ENSP00000238831   ENSP00000394339   ENSP00000414267  

    Human Recombinant Protein Products for YIPF4: 
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    Browse Sino Biological Cell Lysates 
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    Cloud-Clone Corp. Proteins for YIPF4 

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005783endoplasmic reticulum IDA--
    GO:0005794Golgi apparatus IEA--
    GO:0016020membrane ----
    GO:0016021integral to membrane IEA--

    YIPF4 for ontologies           About GeneDecksing



    YIPF4 Antibody Products: 
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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    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


    YIPF4 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    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:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for YIPF4 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for YIPF4

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for YIPF4 
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    SwitchGear 3'UTR luciferase reporter plasmidYIPF4 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YIPF4


    (Pathways according to EMD Millipore, 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 SABiosciences, 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for YIPF4

    STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

    3 Interacting proteins for YIPF4 (Q9BSR82, 3 ENSP000002388314) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    YIPF3Q9GZM52, 3MINT-68058 I2D: score=5 
    UBCENSP000003448184STRING: ENSP00000344818
    --ENSP000002597374STRING: ENSP00000259737
    About this table

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for YIPF4

    Search CenterWatch for drugs/clinical trials and news about 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,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    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 QIAGEN miScript miRNA 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
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for YIPF4
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat YIPF4
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat YIPF4
    Sirion Biotech Customized lentivirus for stable overexpression of YIPF4 
                         Customized lentivirus expression plasmids for stable overexpression of YIPF4 
    Primer
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    OriGene qPCR primer pairs and template standards for YIPF4
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat YIPF4
      QIAGEN 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 

    24/144 AceView cDNA sequences (see all 144):

    BQ100815 AL709356 BP341511 CA942153 BM764320 BF594359 NM_032312 AK098486 
    CK823051 AW572456 AI554076 BM712551 AA287059 AI469999 CB123136 AI079278 
    BG829335 AA283121 BC004875 BE139521 CK823050 AI738476 CB148723 BG036183 

    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™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    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


    See YIPF4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for YIPF4

    SOURCE GeneReport for Unigene cluster: Hs.468099
        SABiosciences 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)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for YIPF4 gene from 6/16 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 93.31(n)1
    97.95(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 84.29(n)
    95.9(a)
      421464  NM_001031058.1  NP_001026229.1 
    lizard
    (Anolis carolinensis)
    Reptilia YIPF46
    Uncharacterized protein
    77(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 Protein Y60A3A.19 59.07(n)
    53.95(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)
    About This Section
      --

    (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) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/610 SNPs in YIPF4 are shown (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 - 32537002 bp)

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

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    5 diseases for YIPF4:    About MalaCards
    skin sarcoidosis    denys-drash syndrome    carpal tunnel syndrome    sarcoidosis
    neuroblastoma

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

    YIPF4 for disorders           About GeneDecksing


    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)
    About This Section

    PubMed articles for YIPF4 gene, integrated from 9 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 Locali zing Yip domain family proteins. (PubMed id 21757827)1, 2 Tanimoto K....Nakamura N. (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. (2004)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (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. (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. (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. (2012)
    7. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    8. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    9. Systematic and quantitative assessment of the ubiquiti n-modified proteome. (PubMed id 21906983)1 Kim W....Gygi S.P. (2011)
    10. Ubiquitin ligase substrate identification through qua ntitative proteomics at both the protein and peptide levels. (PubMed id 21987572)1 Lee K.A....Doedens J.R. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 84272 HGNC: 28145 AceView: MGC11061 Ensembl:ENSG00000119820 euGenes: HUgn84272
    ECgene: YIPF4 H-InvDB: YIPF4

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    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.)
    About This Section
    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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     ThermoFisher Antibodies for YIPF4
     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat YIPF4
     inGenious Targeting Laboratory - Custom generated mouse model solutions for YIPF4
     inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for YIPF4
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
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