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YIPF7 Gene

protein-coding   GIFtS: 39
GCID: GC04M044624

Yip1 Domain Family, Member 7

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(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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This gene clusters with an RNA gene
Subcategory (RNA class): antisense

Quality score for the ORGUL clustered with this gene is 3

Aliases
Yip1 Domain Family, Member 71 2     Protein YIPF72
Five-Pass Transmembrane Protein Localizing In The Golgi Apparatus And The
Endoplasmic Reticulum 92 3
     FINGER93
YIP1 Family Member 72 3     YIP1B3
FinGER92     

External Ids:    HGNC: 268251   Entrez Gene: 2855252   Ensembl: ENSG000001777527   UniProtKB: Q8N8F63   
ORGUL members:         

Export aliases for YIPF7 gene to outside databases

Previous GC identifers: GC04M044466 GC04M044325 GC04M043946


(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 YIPF7 Gene:
YIPF7 (Yip1 domain family, member 7) is a protein-coding gene. An important paralog of this gene is YIPF5.


(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_000004.11  NT_006238.12  NC_018915.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the YIPF7 gene promoter:
         GR   Pbx1a   AML1a   AP-1   GR-beta   POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   LCR-F1   POU3F2   GR-alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidYIPF7 promoter sequence
   Search Chromatin IP Primers for YIPF7

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat YIPF7


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

Entrez Gene cytogenetic band: 4p12   Ensembl cytogenetic band:  4p12   HGNC cytogenetic band: 4p13

YIPF7 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
YIPF7 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04M044624:  view genomic region     (about GC identifiers)

Start:
44,624,086 bp from pter      End:
44,680,573 bp from pter
Size:
56,488 bases      Orientation:
minus 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: YIPF7_HUMAN, Q8N8F6 (See protein sequence)
Recommended Name: Protein YIPF7  
Size: 280 amino acids; 30632 Da
Caution: It is uncertain whether Met-1 or Met-25 is the initiator
Secondary accessions: Q3SY21 Q3SY22
Alternative splicing: 4 isoforms:  Q8N8F6-1   Q8N8F6-2   Q8N8F6-3   Q8N8F6-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for YIPF7: NX_Q8N8F6

Post-translational modifications: 

  • Glycosylation2 at Asn39
  • REFSEQ proteins: NP_872398.2  
    ENSEMBL proteins: 
     ENSP00000412696   ENSP00000477355   ENSP00000332772  

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    (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 Q8N8F6

    ProtoNet protein and cluster: Q8N8F6

    UniProtKB/Swiss-Prot: YIPF7_HUMAN, Q8N8F6
    Similarity: Belongs to the YIP1 family


    Find genes that share domains with YIPF7           About GenesLikeMe


    (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,
    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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    Phenotypes:
         1 GenomeRNAi human phenotype for YIPF7:
     Decreased POU5F1-GFP protein e 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for YIPF7
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    (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
    YIPF7_HUMAN, Q8N8F6: Endoplasmic reticulum membrane; Multi-pass membrane protein (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    endoplasmic reticulum5
    plasma membrane3

    Gene Ontology (GO): 3 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005789endoplasmic reticulum membrane IEA--
    GO:0016020membrane ----
    GO:0016021integral component of membrane IEA--

    Find genes that share ontologies with YIPF7           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 YIPF7
    Interactions:

        Search GeneGlobe Interaction Network for YIPF7

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

    Selected Interacting proteins for YIPF7 (ENSP000004126964) via UniProtKB, MINT, STRING, and/or I2D (see all 68)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    RABAC1ENSP000002220084STRING: ENSP00000222008
    IER3IP1ENSP000002564334STRING: ENSP00000256433
    SEC13ENSP000003121224STRING: ENSP00000312122
    YIPF6ENSP000004175734STRING: ENSP00000417573
    RAB1AENSP000003872864STRING: ENSP00000387286
    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 YIPF7



    (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 YIPF7 gene: 
    NM_182592.2  

    Unigene Cluster for YIPF7:

    Yip1 domain family, member 7
    Hs.596000  [show with all ESTs]
    Unigene Representative Sequence: AK096895
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000415895 ENST00000510035(uc010ify.2) ENST00000502794 ENST00000508947
    ENST00000332990(uc021xnx.1)
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      QuantiTect SYBR Green Assays in human, mouse, rat YIPF7
      QuantiFast Probe-based Assays in human, mouse, rat YIPF7

    Additional mRNA sequence: 

    AK096895.1 BC103995.1 BC103996.1 

    2 DOTS entries:

    DT.99930440  DT.65287862 

    6 AceView cDNA sequences:

    AI672261 AI480122 BX279752 NM_182592 AK096895 R88629 

    GeneLoc Exon Structure


    (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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    YIPF7 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    YIPF7 Expression
    About this image

    YIPF7 Protein expression data from MOPED1, PaxDb2 and MaxQB3 --

    SOURCE GeneReport for Unigene cluster: Hs.596000
        Custom PCR Arrays for YIPF7
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YIPF7

    (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 and fungi.

    Orthologs for YIPF7 gene from Selected species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Yipf71 , 5 Yip1 domain family, member 71, 5 83.6(n)1
    81.5(a)1
      5 (37.13 cM)5
    755811  NM_023784.51  NP_076273.11 
     695166755 
    chicken
    (Gallus gallus)
    Aves YIPF71 Yip1 domain family, member 7 71.76(n)
    69.8(a)
      422774  NM_001277822.1  NP_001264751.1 
    lizard
    (Anolis carolinensis)
    Reptilia YIPF76
    Yip1 domain family, member 7
    62(a)
    1 ↔ 1
    5(102140270-102197447)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia yipf71 Yip1 domain family, member 7 66.53(n)
    64.61(a)
      100492489  XM_002933464.2  XP_002933510.2 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1233211 zgc:123321 62.62(n)
    59.92(a)
      559912  NM_001037233.1  NP_001032310.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG124046
    --
    41(a)
    1 → many
    2L(12993748-13000631)
    worm
    (Caenorhabditis elegans)
    Secernentea F32D8.146
    Protein F32D8.14, isoform b (F32D8.14) mRNA, compl...
    37(a)
    1 → many
    V(10893649-10894767) WBGene00009336
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes YIP16
    Integral membrane protein required for the biogene...
    33(a)
    1 → many
    VII(842845-843591) YGR172C


    ENSEMBL Gene Tree for YIPF7 (if available)
    TreeFam Gene Tree for YIPF7 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for YIPF7 gene
    YIPF52  
    1 SIMAP similar gene for YIPF7 using alignment to 3 protein entries:     YIPF7_HUMAN (see all proteins):
    YIPF5

    Find genes that share paralogs with YIPF7           About GenesLikeMe



    (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 YIPF7 (see all 712)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 4 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs68443101,2
    C,F--44623876(+) TAAGAA/CGGAAG 1 -- ds50011Minor allele frequency- C:0.04WA 118
    rs1900241901,2
    --44623902(+) GTGGTA/GAGTCA 1 -- ds50010--------
    rs359629071,2
    C--44623946(+) TAAAGT/-AAGTG 1 -- ds50011Minor allele frequency- -:0.50CSA 2
    rs680873341,2
    C--44623947(+) AAAGA-/TAGTGA 1 -- ds50010--------
    rs1811000071,2
    --44623957(+) AATTGA/TAAGGC 1 -- ds50010--------
    rs68195331,2
    C,H--44624009(+) ACATAC/TCCCTG 1 -- ds50014Minor allele frequency- T:0.00NS EA 408
    rs748628821,2
    C,F--44624076(+) TGTCAT/CGAAAG 1 -- ds50011Minor allele frequency- C:0.02NA 120
    rs793798761,2
    C,F--44624101(+) TACTAG/CAGATT 1 -- ds50012Minor allele frequency- C:0.17WA 120
    rs9903561,2
    C,F,A,H--44624156(+) AATACA/CTCTAT 1 -- ds500136Minor allele frequency- C:0.44MN EA NA NS WA CSA 4823
    rs32138981,2
    C,F,H--44624177(+) AGGGTT/CGATCA 1 -- ds500113Minor allele frequency- C:0.09EA NS NA 2574

    HapMap Linkage Disequilibrium report for YIPF7 (44624086 - 44680573 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for YIPF7:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv509893CNV Loss20534489

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing YIPF7
    DNA2.0 Custom Variant and Variant Library Synthesis for YIPF7

    (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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      --

    (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 YIPF7 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with YIPF7)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    2. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    3. Generation and annotation of the DNA sequences of human chromosomes 2 and 4. (PubMed id 15815621)2 Hillier L.W.... Wilson R.K. (Nature 2005)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    6. Toward a complete human genome sequence. (PubMed id 9847074)1 Sulston J.E. and Waterston R. (Genome Res. 1998)

    (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: 285525 HGNC: 26825 AceView: FLJ39576 Ensembl:ENSG00000177752 euGenes: HUgn285525
    ECgene: YIPF7 H-InvDB: YIPF7

    (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 YIPF7 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 YIPF7 gene:
    Search GeneIP for patents involving YIPF7

    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, LSBio, eBioscience, 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
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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