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

FAM109A Gene

protein-coding   GIFtS: 46
GCID: GC12M111798

family with sequence similarity 109, member A

  Search for FAM109A
in our new
 Human Malady Compendium 
Biological research products
for FAM109A
    

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

Aliases
Family With Sequence Similarity 109, Member A1 2     SES12
27 KDa Inositol Polyphosphate Phosphatase-Interacting Protein A2 3     Protein FAM109A2
IPIP27A2 3     Sesquipedalian-11
FLJ323561     Ses13

External Ids:    HGNC: 265091   Entrez Gene: 1447172   Ensembl: ENSG000001983247   OMIM: 6142395   UniProtKB: Q8N4B13   

Export aliases for FAM109A gene to outside databases

Previous GC identifers: GC12M110262 GC12M108813


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

Entrez Gene summary for FAM109A:
This gene encodes a protein that localizes to the endosome and interacts with the enzyme, inositol polyphosphate
5-phosphatase OCRL-1. Alternate splicing results in multiple transcript variants. (provided by RefSeq, May 2010)

UniProtKB/Swiss-Prot: SESQ1_HUMAN, Q8N4B1
Function: Plays a role in endocytic trafficking. Required for receptor recycling from endosomes, both to the
trans-Golgi network and the plasma membrane




(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_000012.11  NC_018923.1  NT_009775.17  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the FAM109A gene promoter:
         p53   AML1a   Egr-1   HSF1 (long)   CREB   deltaCREB   FOXO4   HSF1short   c-Myb   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFAM109A promoter sequence
   Search SABiosciences Chromatin IP Primers for FAM109A

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat FAM109A


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

Entrez Gene cytogenetic band: 12q24.12   Ensembl cytogenetic band:  12q24.12   HGNC cytogenetic band: 12q24.12

FAM109A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM109A gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M111798:  view genomic region     (about GC identifiers)

Start:
111,798,339 bp from pter      End:
111,806,925 bp from pter
Size:
8,587 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: SESQ1_HUMAN, Q8N4B1 (See protein sequence)
Recommended Name: Sesquipedalian-1  
Size: 249 amino acids; 27215 Da
Subunit: Forms homodimers and heterodimers with FAM109B. Interacts with OCRL and INPP5B
Subcellular location: Early endosome. Recycling endosome. Golgi apparatus, trans-Golgi network. Cytoplasmic vesicle,
clathrin-coated vesicle. Note=Interaction with OCRL may be crucial for targeting to endosome and to the trans-Golgi
network. Also found on macropinosomes. Not detected in late endosomes, nor in lysosomes
Miscellaneous: Was named after 'sesquipedalian', an unnecessarily long description of a simple thing (PubMed:20133602)
1 PDB 3D structure from and Proteopedia for FAM109A:
3QIS (3D)    
Secondary accessions: J3KP50 Q6PJL9 Q96MH8
Alternative splicing: 4 isoforms:  Q8N4B1-1   Q8N4B1-2   Q8N4B1-3   Q8N4B1-4   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for FAM109A: NX_Q8N4B1

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q8N4B1

  • FAM109A Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (3 alternative transcripts): 
    NP_001171467.1  NP_001171468.1  NP_653272.2  

    ENSEMBL proteins: 
     ENSP00000447353   ENSP00000376426   ENSP00000449994   ENSP00000447349   ENSP00000448625  
     ENSP00000447539   ENSP00000390552   ENSP00000354461  

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    Uscn Proteins for FAM109A

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005769early endosome IDA--
    GO:0005794Golgi apparatus IEA--
    GO:0005802trans-Golgi network IDA--
    GO:0030136clathrin-coated vesicle IDA--
    GO:0055037recycling endosome IDA--


    FAM109A 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

    FAM109A for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR001849 Pleckstrin_homology
     IPR011993 PH_like_dom

    Graphical View of Domain Structure for InterPro Entry Q8N4B1

    ProtoNet protein and cluster: Q8N4B1

    1 Blocks protein family: IPB001849 Pleckstrin-like

    UniProtKB/Swiss-Prot: SESQ1_HUMAN, Q8N4B1
    Domain: The F&H motif, an approximately 12-13 amino-acid sequence centered around Phe and His residues, is essential
    for binding to OCRL and INPP5B (PubMed:21666675)
    Similarity: Belongs to the sesquipedalian family
    Similarity: Contains 1 PH domain


    (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: SESQ1_HUMAN, Q8N4B1
    Function: Plays a role in endocytic trafficking. Required for receptor recycling from endosomes, both to the
    trans-Golgi network and the plasma membrane

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    hsa-miR-30c hsa-miR-3607-3p hsa-miR-4318 hsa-miR-3065-3p hsa-miR-30d hsa-miR-218 hsa-miR-1224-5p hsa-miR-30a
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    Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI--
    GO:0005543phospholipid binding IEA--
    GO:0042803protein homodimerization activity IPI--


    FAM109A for ontologies           About GeneDecksing



    (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 FAM109A

    STRING Interaction Network Preview (showing 3 interactants - click image to see more details)

    3 Interacting proteins for FAM109A (Q8N4B12, 3 ENSP000003544614) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PLEKHJ1Q9NW612, 3, ENSP000003180754MINT-8266755 I2D: score=2 STRING: ENSP00000318075
    OCRLQ019683, ENSP000003601544I2D: score=1 STRING: ENSP00000360154
    INPP5BENSP000003621154STRING: ENSP00000362115
    About this table

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001881receptor recycling IMP--
    GO:0007032endosome organization IMP--
    GO:0042147retrograde transport, endosome to Golgi IMP--


    FAM109A 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
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for FAM109A
    Search CenterWatch for drugs/clinical trials and news about FAM109A / SESQ1 

    (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,
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    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 FAM109A gene (3 alternative transcripts): 
    NM_001177996.1  NM_001177997.1  NM_144671.4  

    Unigene Cluster for FAM109A:

    Family with sequence similarity 109, member A
    Hs.173088  [show with all ESTs]
    Unigene Representative Sequence: NM_001177996
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000547838(uc001tsc.3) ENST00000392658 ENST00000548163 ENST00000547710
    ENST00000551863 ENST00000549321 ENST00000450786 ENST00000361483(uc021rdy.1 uc001tsd.4 uc009zvu.3)


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    8/13 QIAGEN miScript miRNA Assays for microRNAs that regulate FAM109A (see all 13):
    hsa-miR-30c hsa-miR-3607-3p hsa-miR-4318 hsa-miR-3065-3p hsa-miR-30d hsa-miR-218 hsa-miR-1224-5p hsa-miR-30a
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    Additional cDNA sequence: 

    AK056918.1 AK093052.1 AK299344.1 BC014091.2 BC018996.2 BC034809.1 

    9 DOTS entries:

    DT.101980216  DT.100021898  DT.208220  DT.121142082  DT.121142093  DT.121142083  DT.121142088  DT.121142092 
    DT.95157198 

    24/53 AceView cDNA sequences (see all 53):

    BF873344 AK056918 NM_144671 CB306616 BU507932 AW016521 BU741613 BF224390 
    BC034809 AA007367 BM558909 BU501318 BF869986 BM558949 AK093052 BX435432 
    BF514876 BF436293 BF971961 BX442117 CD671724 BF435061 AX747887 BC014091 

    GeneLoc Exon Structure

    5/8 Alternative Splicing Database (ASD) splice patterns (SP) for FAM109A (see all 8)    About this scheme

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


    ECgene alternative splicing isoforms for FAM109A

    (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

    FAM109A expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GGAGGGGTTC

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

    About this image
    See FAM109A Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for FAM109A

    SOURCE GeneReport for Unigene cluster: Hs.173088
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    In Situ
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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 FAM109A gene from 6/19 species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Fam109a1 , 5 family with sequence similarity 109, member A1, 5 75.48(n)1
    75(a)1
      5 (62.01 cM)5
    2317171  NM_175474.31  NP_780683.11 
     1218490285 
    chicken
    (Gallus gallus)
    Aves FAM109A6
    Uncharacterized protein
    61(a)
    1 ↔ 1
    15(6149959-6150675)
    lizard
    (Anolis carolinensis)
    Reptilia FAM109A6
    --
    53(a)
    1 ↔ 1
    GL343423.1(665191-665979)
    zebrafish
    (Danio rerio)
    Actinopterygii si:ch211-193c2.21 si:ch211-193c2.2 54.97(n)
    50.2(a)
      565272  XM_688552.3  XP_693644.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG123936
    --
    22(a)
    1 → many
    2L(6047999-6050474)
    worm
    (Caenorhabditis elegans)
    Secernentea Y37D8A.256
    --
    26(a)
    1 → many
    III(12818357-12820151)


    ENSEMBL Gene Tree for FAM109A (if available)
    TreeFam Gene Tree for FAM109A (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for FAM109A gene
    FAM109B2  
    18 SIMAP similar genes for FAM109A using alignment to 5 protein entries:     SESQ1_HUMAN (see all proteins):
    CYTH4    CYTH3    CYTH1    CYTH2    PLEKHH2    FAM109B
    PLEKHH1    SWAP70    ARHGAP24    PLEK2    ARHGAP22    RASGRF1
    RASGRF2    ANLN    ARHGAP25    DAPP1    PLEKHA5    PLEKHJ1

    FAM109A for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for FAM109A
    PGOHUM00000261222


    (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

    10/163 NCBI SNPs in FAM109A are shown (see all 163    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs747941261,2
    C,--108812949(+) GAACTT/CTGGGC 3 -- ds50012Minor allele frequency- C:0.10CSA WA 120
    rs1114728211,2
    --108813128(+) AGAACG/ATGCCT 3 -- ds50012Minor allele frequency- A:0.10CSA WA 120
    rs10587061,2
    C,F,H,--108813613(-) CAAGCC/TCTGCT 3 -- ut3112Minor allele frequency- T:0.03MN NS NA WA 1760
    rs619443671,2
    --108814030(+) GGTGTC/TCTCAG 3 -- ut312Minor allele frequency- T:0.03NA 122
    rs1809776081,2
    C--108814296(+) TGCGGC/TTTTTT 3 -- ut310--------
    rs38092721,2
    C,F,A,H,--108815030(+) GTGACG/ATTCCC 3 -- ut31 ese328Minor allele frequency- A:0.17EA NA NS WA 4050
    rs734123521,2
    C,--108816953(+) GTCCCT/CGCCCT 3 -- int13Minor allele frequency- C:0.17WA EA 240
    rs125816561,2
    C,H--108818695(+) TCTCAG/AGCCAC 3 -- ut51 int1 ese35Minor allele frequency- A:0.00NS EA NA 300
    rs791915841,2
    C,F,--108818860(+) GTGCCT/CAAGTC 3 -- int11Minor allele frequency- C:0.09WA 118
    rs169414451,2
    C,F,--108819001(+) CTTCCG/AATCTC 3 -- int15Minor allele frequency- A:0.03NA WA 260

    HapMap Linkage Disequilibrium report for FAM109A (111798339 - 111806925 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for FAM109A
         1 CNV: 48942

    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, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section

    FAM109A for disorders           About MalaCards

    FAM109A for disorders           About GeneDecksing

    OMIM gene information: 614239    OMIM disorders: --


    Export disorders for FAM109A 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 FAM109A gene integrated from 9 sources:
    (articles sorted by number of sources associating them with FAM109A)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The PH domain proteins IPIP27A and B link OCRL1 to receptor recycling in the endocytic pathway. (PubMed id 21233288)1, 2 Noakes C.J.... Lowe M. (2011)
    2. Two closely related endocytic proteins that share a c ommon OCRL-binding motif with APPL1. (PubMed id 20133602)1, 2 Swan L.E....De Camilli P. (2010)
    3. 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)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    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. Recognition of the F&H motif by the Lowe syndrome protein OCRL. (PubMed id 21666675)2 Pirruccello M....De Camilli P. (2011)
    7. A directed protein interaction network for investigat ing intracellular signal transduction. (PubMed id 21900206)1 Vinayagam A....Wanker E.E. (2011)
    8. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (2006)
    9. The finished DNA sequence of human chromosome 12. (PubMed id 16541075)2 Scherer S.E.... Gibbs R.A. (2006)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 144717 HGNC: 26509 AceView: FLJ32356 Ensembl:ENSG00000198324 euGenes: HUgn144717
    ECgene: FAM109A H-InvDB: FAM109A

    (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 FAM109A 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 FAM109A gene:
    Search GeneIP for patents involving FAM109A

    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: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013

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