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

YIPF3 Gene

protein-coding   GIFtS: 48
GCID: GC06M043479

Yip1 domain family, member 3

(Previous name: chromosome 6 open reading frame 109 )
(Previous symbol: C6orf109)
 Explore 5 diseases affiliated with
YIPF3 via our new
 Human Malady Compendium 
Biological research products
for YIPF3
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
Yip1 Domain Family, Member 31 2     Natural Killer Cell-Specific Antigen KLIP12 3
KLIP11 2 3 5     DKFZp566C2431
C6orf1091 2 3     Chromosome 6 Open Reading Frame 1091
FinGER31 2     Protein YIPF32
DJ337H4.31     YIP1 Family Member 33
Killer Lineage Protein 12 3     

External Ids:    HGNC: 210231   Entrez Gene: 258442   Ensembl: ENSG000001372077   OMIM: 6097755   UniProtKB: Q9GZM53   

Export aliases for YIPF3 gene to outside databases

Previous GC identifers: GC06M043588 GC06M043197


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

UniProtKB/Swiss-Prot: YIPF3_HUMAN, Q9GZM5
Function: Involved in the maintenance of the Golgi structure. May play a role in hematopoiesis

Gene Wiki entry for YIPF3


(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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.1  NT_007592.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the YIPF3 gene promoter:
         GR   SRF   RP58   SRF (504 AA)   FOXD1   CUTL1   E2F-1   E2F   STAT3   GR-alpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidYIPF3 promoter sequence
   Search SABiosciences Chromatin IP Primers for YIPF3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat YIPF3


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

Entrez Gene cytogenetic band: 6p21.1   Ensembl cytogenetic band:  6p21.1   HGNC cytogenetic band: 6p21.1

YIPF3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
YIPF3 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M043479:  view genomic region     (about GC identifiers)

Start:
43,479,565 bp from pter      End:
43,484,728 bp from pter
Size:
5,164 bases      Orientation:
minus strand

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

UniProtKB/Swiss-Prot: YIPF3_HUMAN, Q9GZM5 (See protein sequence)
Recommended Name: Protein YIPF3  
Size: 350 amino acids; 38248 Da
Subunit: Interacts with YIPF4
Subcellular location: Cell membrane; Multi-pass membrane protein. Cytoplasm. Golgi apparatus, cis-Golgi network
membrane; Multi-pass membrane protein. Note=Localization to the cytoplasm or to the cell membrane is developmentally
and ontogenetically regulated
Developmental stage: Expressed in fetal liver (at protein level). Expressed in embryonic hematopoiesis sites
Sequence caution: Sequence=CAI42626.1; Type=Erroneous gene model prediction;
Secondary accessions: Q5JTD2 Q6FI85 Q8NI57 Q9NWE3 Q9Y3U9

Explore the universe of human proteins at neXtProt for YIPF3: NX_Q9GZM5

Post-translational modifications:

  • N-glycosylated in the ER (40 kDa form I), then O-glycosylated in the Golgi apparatus (46 kDa form II), the C-terminal
  • lumenal region is later removed in the Golgi apparatus to produce a 36 kDa form III. O-glycosylated with core 1-like
    and core 2-like glycans. O-glycan heterogeneity at Thr-346: HexNAc (minor), HexHexNAc (major), Hex1HexNAc2 (minor),
    Hex2HexNAc2 (minor) and dHex1Hex2HexNAc2 (minor)1
  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9GZM5

  • YIPF3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_056203.2  
    ENSEMBL proteins: 
     ENSP00000361499   ENSP00000427207   ENSP00000259737   ENSP00000425023   ENSP00000425494  
     ENSP00000426339   ENSP00000424629   ENSP00000421461   ENSP00000421053   ENSP00000392699  
     ENSP00000390056   ENSP00000423544   ENSP00000421094  

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    Uscn Proteins for YIPF3

    Gene Ontology (GO): 5 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005794Golgi apparatus IEA--
    GO:0005886plasma membrane IEA--
    GO:0016021integral to membrane IEA--
    GO:0030133transport vesicle IDA--
    GO:0043231intracellular membrane-bounded organelle ----


    YIPF3 for ontologies           About GeneDecksing



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    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    YIPF3 for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR026637 YIPF3

    Graphical View of Domain Structure for InterPro Entry Q9GZM5

    ProtoNet protein and cluster: Q9GZM5

    UniProtKB/Swiss-Prot: YIPF3_HUMAN, Q9GZM5
    Similarity: Belongs to the YIP1 family


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: YIPF3_HUMAN, Q9GZM5
    Function: Involved in the maintenance of the Golgi structure. May play a role in hematopoiesis

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for YIPF3

    1 GenomeRNAi human phenotype for YIPF3:
     Decreased nuclei size in G2M 


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for YIPF3

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    4 Interacting proteins for YIPF3 (Q9GZM52, 3 ENSP000002597374) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    YIPF4Q9BSR82, 3, ENSP000002388314MINT-68058 I2D: score=5 STRING: ENSP00000238831
    PLSCR1O151622, 3, ENSP000003454944MINT-66387 I2D: score=5 STRING: ENSP00000345494
    UNC93B1Q9H1C43, ENSP000002274714I2D: score=1 STRING: ENSP00000227471
    UBCENSP000003448184STRING: ENSP00000344818
    About this table

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0030154cell differentiation IEA--


    YIPF3 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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
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    Browse Tocris compounds for YIPF3
    Search CenterWatch for drugs/clinical trials and news about YIPF3 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for YIPF3 gene: 
    NM_015388.3  

    Unigene Cluster for YIPF3:

    Yip1 domain family, member 3
    Hs.440950  [show with all ESTs]
    Unigene Representative Sequence: AK021433
    18/20 Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 20):
    ENST00000372422(uc003ovl.2) ENST00000510102(uc011dvk.2) ENST00000259737
    ENST00000504851 ENST00000506469 ENST00000509315 ENST00000490447 ENST00000503147
    ENST00000503972 ENST00000514627 ENST00000460547 ENST00000512713 ENST00000455768
    ENST00000416380 ENST00000372417 ENST00000500090 ENST00000488966 ENST00000502714


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    hsa-miR-3678-3p hsa-miR-544 hsa-miR-1910 hsa-miR-3160-3p
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    Additional cDNA sequence: 

    AF162672.1 AK000946.1 AK021433.1 AK021655.1 AK022757.1 AK298150.1 AK308961.1 AL050274.1 
    BC019297.1 CR533541.1 

    24/27 DOTS entries (see all 27):

    DT.75111219  DT.100757794  DT.100883220  DT.121405535  DT.99995562  DT.121405526  DT.97860216  DT.100883226 
    DT.121405815  DT.121405354  DT.121405362  DT.100031673  DT.95134767  DT.100638435  DT.100883230  DT.100883241 
    DT.100883243  DT.121405547  DT.121405548  DT.121405802  DT.86846320  DT.87016652  DT.95134790  DT.95134846 

    24/560 AceView cDNA sequences (see all 560):

    BM698074 CR602267 CR611260 BX354877 AA463938 AW401849 AU126250 CR611748 
    BQ937554 CR618212 BQ672942 CR590349 BQ924682 CB216823 CR607768 BQ898475 
    BQ681901 AV702588 CR621993 NM_015388 BI758153 CR615118 CR615153 BQ582249 

    GeneLoc Exon Structure

    5/15 Alternative Splicing Database (ASD) splice patterns (SP) for YIPF3 (see all 15)    About this scheme

    ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g ^ 2a · 2b · 2c · 2d ^ 3 ^ 4 ^ 5a · 5b · 5c · 5d ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^
    SP1:                                      -     -     -     -                                   -     -     -           -                                       
    SP2:                                                                                            -     -     -           -                                       
    SP3:                                      -     -                                               -     -     -           -                                       
    SP4:                                      -     -     -     -     -                             -     -     -           -                                       
    SP5:                                      -     -                                               -     -     -           -                                       

    ExUns: 11a · 11b ^ 12
    SP1:                  
    SP2:                  
    SP3:                  
    SP4:                  
    SP5:                  


    ECgene alternative splicing isoforms for YIPF3

    (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

    YIPF3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TTTCGTAGAT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image
    See YIPF3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for YIPF3

    SOURCE GeneReport for Unigene cluster: Hs.440950

    UniProtKB/Swiss-Prot: YIPF3_HUMAN, Q9GZM5
    Tissue specificity: Expressed by nucleated hematopoietic cells (at protein level)

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    In Situ
    Assay Products:
     

     
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    (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 YIPF3 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 Yipf31 , 5 Yip1 domain family, member 31, 5 89.63(n)1
    97.12(a)1
      17 (22.90 cM)5
    280641  NM_145353.21  NP_663328.21 
     462480805 
    chicken
    (Gallus gallus)
    Aves YIPF31 Yip1 domain family, member 3 78.21(n)
    84.94(a)
      421453  NM_001012566.1  NP_001012584.1 
    lizard
    (Anolis carolinensis)
    Reptilia YIPF36
    --
    83(a)
    1 ↔ 1
    1(231033146-231050760)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.154512 Xenopus laevis transcribed sequence with moderate similarity more 79.18(n)    BX843138.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wufj97f062 wufj97f06 75.52(n)   334511  BC044136.1 
    worm
    (Caenorhabditis elegans)
    Secernentea Y53C12A.31 Protein Y53C12A.3 47.93(n)
    39.76(a)
      174528  NM_063692.2  NP_496093.1 


    ENSEMBL Gene Tree for YIPF3 (if available)
    TreeFam Gene Tree for YIPF3 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for YIPF3 gene

    YIPF3 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for YIPF3
    PGOHUM00000250731


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    10/88 NCBI SNPs in YIPF3 are shown (see all 88    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 6 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs77432441,2
    C,F,A,H,--43479067(+) GAGCAT/GATTAA 2 -- us2k1 int120Minor allele frequency- G:0.24NS EA NA WA CSA 2343
    rs1484743671,2
    C,--43479097(+) GGTGC-/TATGTTA 2 -- us2k1 int10--------
    rs1423343841,2
    --43479151(+) AGGAGC/TTGGCC 2 -- us2k1 int10--------
    rs779781991,2
    --43479160(+) CCCCAG/CTACCA 2 -- us2k1 int11Minor allele frequency- C:0.01EA 120
    rs581610941,2
    C,--43479170(+) ACCAAG/AGCAAA 2 -- us2k1 int11Minor allele frequency- A:0.50WA 2
    rs1149651981,2
    --43479354(+) TCCATC/GAGGCT 2 -- us2k1 int11Minor allele frequency- G:0.01WA 118
    rs1115556251,2
    --43479384(+) GCCTCG/CCTGCC 2 -- us2k1 int11Minor allele frequency- C:0.50CSA 2
    rs1894708511,2
    --43479516(+) AGTAGG/TAAAGT 2 -- us2k1 int10--------
    rs1913085061,2
    --43479543(+) GACAGG/TGAGGA 2 -- us2k1 int10--------
    rs1838586381,2
    --43479562(+) TCAGCC/TGCTGC 2 -- int1 us2k10--------

    HapMap Linkage Disequilibrium report for YIPF3 (43479565 - 43484728 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for YIPF3
         1 CNV: 9530

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    (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.)
    About This Section

    YIPF3 for disorders           About GeneDecksing

    OMIM gene information: 609775    OMIM disorders: --

    5 diseases for YIPF3:    About MalaCards
    denys-drash syndrome    nephroblastoma    choroiditis    choroid cancer
    hematopoiesis


    Export disorders for YIPF3 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 YIPF3 gene, integrated from 9 sources (see all 22):
    (articles sorted by number of sources associating them with YIPF3)
        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. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (2003)
    5. Characterization of a novel hematopoietic marker expressed from early embryonic hematopoietic stem cells to adult mature lineages. (PubMed id 12490290)1, 2 Prost S....Kirszenbaum M. (2002)
    6. Towards a catalog of human genes and proteins: sequencing and analysis of 500 novel complete protein coding human cDNAs. (PubMed id 11230166)1, 2 Wiemann S.... Poustka A. (2001)
    7. LC-MS/MS characterization of O-glycosylation sites and glycan structures of human cerebrospinal fluid glycoproteins. (PubMed id 23234360)2 Halim A.... Nilsson J. (2013)
    8. Methods for quantification of in vivo changes in prote in ubiquitination following proteasome and deubiquitinase inhibition. (PubMed id 22505724)1 Udeshi N.D....Carr S.A. (2012)
    9. Mapping a dynamic innate immunity protein interaction network regulating type I interferon production. (PubMed id 21903422)1 Li S....Dorf M.E. (2011)
    10. Human urinary glycoproteomics; attachment site specific analysis of N-and O-linked glycosylations by CID and ECD. (PubMed id 22171320)2 Halim A.... Larson G. (2011)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 25844 HGNC: 21023 AceView: C6orf109 Ensembl:ENSG00000137207 euGenes: HUgn25844
    ECgene: YIPF3 H-InvDB: YIPF3

    (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 YIPF3 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 YIPF3 gene:
    Search GeneIP for patents involving YIPF3

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



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    GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013

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