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

FAM3D Gene

protein-coding   GIFtS: 49
GCID: GC03M058619

family with sequence similarity 3, member D

 Explore 4 diseases affiliated with
FAM3D via our new
 Human Malady Compendium 
Biological research products
for FAM3D
    

(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 3, Member D1 2
EF71 2
OIT11 2
Cytokine-Like Protein EF-72
Protein FAM3D2

External Ids:    HGNC: 186651   Entrez Gene: 1311772   Ensembl: ENSG000001986437   OMIM: 6086195   UniProtKB: Q96BQ13   

Export aliases for FAM3D gene to outside databases

Previous GC identifers: GC03M057483 GC03M057988 GC03M058474 GC03M058577 GC03M058594


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

  --

(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_000003.11  NC_018914.1  NT_022517.18  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the FAM3D gene promoter:
         POU3F2 (N-Oct-5a)   POU3F2 (N-Oct-5b)   STAT5A   POU3F2   LCR-F1   c-Rel   HOXA5   MRF-2   Pax-4a   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFAM3D promoter sequence
   Search SABiosciences Chromatin IP Primers for FAM3D

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat FAM3D


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

Entrez Gene cytogenetic band: 3p14.2   Ensembl cytogenetic band:  3p14.2   HGNC cytogenetic band: 3p21.1

FAM3D Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM3D gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M058619:  view genomic region     (about GC identifiers)

Start:
58,619,670 bp from pter      End:
58,652,575 bp from pter
Size:
32,906 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: FAM3D_HUMAN, Q96BQ1 (See protein sequence)
Recommended Name: Protein FAM3D precursor  
Size: 224 amino acids; 24963 Da
Subcellular location: Secreted (Potential)
Secondary accessions: Q547G2

Explore the universe of human proteins at neXtProt for FAM3D: NX_Q96BQ1

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q96BQ1

  • FAM3D Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_620160.1  
    ENSEMBL proteins: 
     ENSP00000351632   ENSP00000417099   ENSP00000417453   ENSP00000418414   ENSP00000418982  

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    Uscn Proteins for FAM3D

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region NAS12160727


    FAM3D 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

    FAM3D for domains           About GeneDecksing

    1 InterPro domain/family:
     IPR026101 FAM3

    Graphical View of Domain Structure for InterPro Entry Q96BQ1

    ProtoNet protein and cluster: Q96BQ1

    UniProtKB/Swiss-Prot: FAM3D_HUMAN, Q96BQ1
    Similarity: Belongs to the FAM3 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

    miRNA
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    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM3D

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005125cytokine activity NAS12160727


    FAM3D for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for FAM3D:
     Increased G1 DNA content 

    Animal Models:
         Mouse knock-out Oit1tm1Lex for FAM3D
         1 MGI mutant phenotype (inferred from 1 allele(MGI details for Oit1):
     behavior/neurological 

    FAM3D for phenotypes           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 FAM3D

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0046676negative regulation of insulin secretion IDA12160727


    FAM3D 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 FAM3D
    Search CenterWatch for drugs/clinical trials and news about FAM3D 

    (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 FAM3D gene: 
    NM_138805.2  

    Unigene Cluster for FAM3D:

    Family with sequence similarity 3, member D
    Hs.61265  [show with all ESTs]
    Unigene Representative Sequence: AY358677
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000358781(uc003dkq.3) ENST00000483787 ENST00000489857 ENST00000482623
    ENST00000498347

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    hsa-miR-548p hsa-miR-545 hsa-miR-4282 hsa-miR-3667-3p
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    Inhib. RNA
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    Clone
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat FAM3D 
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat FAM3D
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat FAM3D

    Additional cDNA sequence: 

    AF494381.1 AK127546.1 AY358677.1 BC015359.1 

    7 DOTS entries:

    DT.99988086  DT.412932  DT.97846649  DT.120887453  DT.100737621  DT.95368904  DT.91690432 

    24/109 AceView cDNA sequences (see all 109):

    AI732367 AA563933 AY358677 BM848881 AA025434 BM987269 AI673534 CB145558 
    BM850007 AF494381 CK823244 AA514424 AA297176 BC015359 BM851081 NM_138805 
    BM848852 AA297147 AA470683 BM851193 BM851303 BM848978 BM848962 BM848979 

    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™, 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

    FAM3D expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CCCCCGAAGC

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

    About this image

    FAM3D expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    KidneyRenal Collecting Duct SystemKidney
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See FAM3D Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for FAM3D

    SOURCE GeneReport for Unigene cluster: Hs.61265

    UniProtKB/Swiss-Prot: FAM3D_HUMAN, Q96BQ1
    Tissue specificity: Abundantly expressed in placenta and weakly expressed in small intestine

        SABiosciences Custom PCR Arrays for FAM3D
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for FAM3D

    (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 FAM3D gene from 6/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Oit11 , 5 oncoprotein induced transcript 11, 5 77.98(n)1
    72.4(a)1
      14 (4.83 cM)5
    183001  NM_146050.21  NP_666162.11 
     83489485 
    chicken
    (Gallus gallus)
    Aves FAM3D1 family with sequence similarity 3, member D 63.81(n)
    59.01(a)
      416069  XM_414407.3  XP_414407.1 
    lizard
    (Anolis carolinensis)
    Reptilia FAM3D6
    --
    64(a)
    1 ↔ 1
    2(187019115-187028529)
    African clawed frog
    (Xenopus laevis)
    Amphibia BC056012.12   -- 74.68(n)    BC056012.1 
    zebrafish
    (Danio rerio)
    Actinopterygii im:71601596
    im:7160159
    28(a)
    1 ↔ 1
    6(46258029-46273326)
    worm
    (Caenorhabditis elegans)
    Secernentea Y73B3A.36
    M70.46
    Protein M70.4
    7(a)
    7(a)
    many ↔ many
    many ↔ many
    X(84043-93664)
    IV(2253004-2263662)


    ENSEMBL Gene Tree for FAM3D (if available)
    TreeFam Gene Tree for FAM3D (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for FAM3D gene
    FAM3C2  FAM3A2  FAM3B2  
    3 SIMAP similar genes for FAM3D using alignment to 5 protein entries:     FAM3D_HUMAN (see all proteins):
    FAM3A    FAM3C    FAM3B

    FAM3D for paralogs           About GeneDecksing



    (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

    10/703 NCBI SNPs in FAM3D are shown (see all 703    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs111306631,2
    C,F,A,H,--58619173(+) TACCCT/GTCACT 1 -- int116Minor allele frequency- G:0.12NS EA NA WA 1896
    rs1465561521,2
    --58619223(+) TACTTC/TTCTAT 1 -- int10--------
    rs1841603941,2
    --58619224(+) ACTTCC/TCTATT 1 -- int10--------
    rs46818861,2
    C,F,A,H,--58619263(+) TACTGG/ACTGCC 1 -- int121Minor allele frequency- A:0.34NS EA NA WA 2254
    rs1412029781,2
    --58619302(+) TGGGGC/TGGAGA 1 -- int10--------
    rs1179475241,2
    F,--58619349(+) CTGGCG/AGCTCC 1 -- int11Minor allele frequency- A:0.07EA 120
    rs1449012681,2
    --58619384(+) CTCCTC/TTCCCA 1 -- int10--------
    rs1147896241,2
    F,--58619422(+) CCTTCA/TGACAG 1 -- int11Minor allele frequency- T:0.02WA 118
    rs1482656551,2
    --58619425(+) TCAGAC/TAGAGG 1 -- int10--------
    rs38605621,2
    C,F,H,--58619522(+) AGGCCC/TATGGG 1 -- int121Minor allele frequency- T:0.11NA NS EA CSA WA 2484

    HapMap Linkage Disequilibrium report for FAM3D (58619670 - 58652575 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for FAM3D
         1 CNV: 68382

    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

    FAM3D for disorders           About GeneDecksing

    OMIM gene information: 608619    OMIM disorders: --

    4 diseases for FAM3D:    About MalaCards
    muscle-eye-brain disease    hearing loss    brain disease    schizophrenia

    1 disease from the University of Copenhagen DISEASES database for FAM3D:
    Sleep disorder
    Human Genome Epidemiology (HuGE) Navigator: FAM3D (1 document)

    Export disorders for FAM3D 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 FAM3D gene, integrated from 9 sources (see all 11):
    (articles sorted by number of sources associating them with FAM3D)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Cloning, expression, and initial characterization of a novel cytokine-like gene family. (PubMed id 12160727)1, 2, 3, 9 Zhu Y.... Young P.R. (2002)
    2. Identification of N-linked glycoproteins in human saliva by glycoprotein capture and mass spectrometry. (PubMed id 16740002)1, 2 Ramachandran P....Loo J.A. (2006)
    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. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (2003)
    5. Exome sequencing supports a de novo mutational paradi gm for schizophrenia. (PubMed id 21822266)1 Xu B....Karayiorgou M. (2011)
    6. An approach based on a genome-wide association study reveals candidate loci for narcolepsy. (PubMed id 20677014)1 Shimada M....Tokunaga K. (2010)
    7. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. (PubMed id 17207965)1 Lamesch P.... Vidal M. (2007)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    9. 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. (2002)
    10. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (1996)

    (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: 131177 HGNC: 18665 AceView: FAM3D Ensembl:ENSG00000198643 euGenes: HUgn131177
    ECgene: FAM3D H-InvDB: FAM3D

    (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 FAM3D 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 FAM3D gene:
    Search GeneIP for patents involving FAM3D

    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, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, 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
    About This Section

     
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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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    VWF
    (GIFTS: 73)
    von Willebrand factor
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    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


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