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FAM9A Gene

protein-coding   GIFtS: 41
GCID: GC0XM008759

Family With Sequence Similarity 9, Member A

  See FAM9A-related disease
at  

(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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Aliases
Family With Sequence Similarity 9, Member A1 2
Testis Expressed 39A1 2
TEX39A2
Protein FAM9A2

External Ids:    HGNC: 184031   Entrez Gene: 1714822   Ensembl: ENSG000001833047   OMIM: 3004775   UniProtKB: Q8IZU13   

Export aliases for FAM9A gene to outside databases

Previous GC identifers: GC0XU990384 GC0XM008105 GC0XM008170 GC0XM008568 GC0XM008718 GC0XM006586


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for FAM9A Gene:
This gene is a member of a gene family which arose through duplication on the X chromosome. The encoded protein
may be a nuclear protein that is localized to the nucleolus, and has some similarity to a synaptonemal complex
protein. Multiple alternatively spliced variants, encoding the same protein, have been identified. (provided by
RefSeq, Aug 2011)

GeneCards Summary for FAM9A Gene:
FAM9A (family with sequence similarity 9, member A) is a protein-coding gene. Diseases associated with FAM9A include uterine fibroid. An important paralog of this gene is FAM9B.




(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:
NC_000023.11  NC_018934.2  NT_167197.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the FAM9A gene promoter:
         S8   ATF-2   HSF2   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidFAM9A promoter sequence
   Search Chromatin IP Primers for FAM9A

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat FAM9A


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

Entrez Gene cytogenetic band: Xp22.32   Ensembl cytogenetic band:  Xp22.31   HGNC cytogenetic band: Xp22.32

FAM9A Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
FAM9A gene location

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM008759:  view genomic region     (about GC identifiers)

Start:
8,758,836 bp from pter      End:
8,769,424 bp from pter
Size:
10,589 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: FAM9A_HUMAN, Q8IZU1 (See protein sequence)
Recommended Name: Protein FAM9A  
Size: 332 amino acids; 37339 Da
Secondary accessions: B7ZLH5 Q2M2D1

Explore the universe of human proteins at neXtProt for FAM9A: NX_Q8IZU1

Explore proteomics data for FAM9A at MOPED


See FAM9A Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001164657.1  NP_777611.1  

ENSEMBL proteins: 
 ENSP00000370391   ENSP00000440163  

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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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1 InterPro protein domain:
 IPR006888 Cor1/Xlr/Xmr

Graphical View of Domain Structure for InterPro Entry Q8IZU1

ProtoNet protein and cluster: Q8IZU1

UniProtKB/Swiss-Prot: FAM9A_HUMAN, Q8IZU1
Similarity: Belongs to the FAM9 family


Find genes that share domains with FAM9A           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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     Gene Ontology (GO): 1 molecular function term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005515protein binding IPI--
     
Find genes that share ontologies with FAM9A           About GenesLikeMe


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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
FAM9A_HUMAN, Q8IZU1: Nucleus, nucleolus
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
nucleus5
cytosol2

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005730nucleolus IEA--

Find genes that share ontologies with FAM9A           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 FAM9A
Interactions:

    Search GeneGlobe Interaction Network for FAM9A

2 Interacting proteins for FAM9A (Q8IZU11) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
KDM1AO603411EBI-8468186,EBI-710124
PRMT1Q998731EBI-8468186,EBI-78738
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(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
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Browse Tocris compounds for FAM9A



(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 FAM9A gene (2 alternative transcripts): 
NM_001171186.1  NM_174951.3  

Unigene Cluster for FAM9A:

Family with sequence similarity 9, member A
Hs.382062
Unigene Representative Sequence: NM_001171186
2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000381003(uc004csg.3) ENST00000543214(uc022bsk.1)
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Additional mRNA sequence: 

AF494343.1 BC112022.1 BC113449.1 BC143805.1 

1 DOTS entry:

DT.75140127 

3 AceView cDNA sequences:

NM_174951 AF494343 AI743444 

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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FAM9A expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GTCAATTAAA
FAM9A Expression
About this image

FAM9A Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

FAM9A Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.382062

UniProtKB/Swiss-Prot: FAM9A_HUMAN, Q8IZU1
Tissue specificity: Expressed exclusively in testis

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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)
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  --

ENSEMBL Gene Tree for FAM9A (if available)
TreeFam Gene Tree for FAM9A (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for FAM9A gene
FAM9B2  FAM9C2  
1 SIMAP similar gene for FAM9A using alignment to 1 protein entry:     FAM9A_HUMAN:
FAM9C

Find genes that share paralogs with FAM9A           About GenesLikeMe


1 Pseudogenes.org Pseudogene for FAM9A
PGOHUM00000249310


(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 FAM9A (see all 237)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr X posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs59344841,2
C--8758380(+) CAAGAA/TCACAG 2 -- ds50010--------
rs1900854561,2
--8758580(+) CAGTGG/TCACAA 2 -- ds50010--------
rs1511431191,2
--8758705(+) TAGTAA/GAGATG 2 -- ds50010--------
rs1391164951,2
--8758711(+) AGATGA/GGGTTT 2 -- ds50010--------
rs1823396961,2
--8758878(+) TTCTAC/TGTTTT 2 -- ut310--------
rs1865124121,2
--8759276(+) CAGTGC/GTTACA 2 -- int10--------
rs617325701,2
C,F--8759332(+) GACACG/AATTCT 2 -- ut313Minor allele frequency- A:0.09NS CSA 54
rs617325711,2
C,F--8759342(+) TTTTTA/GAAAAC 2 -- ut311Minor allele frequency- G:0.03NS 70
rs1919826881,2
C--8759349(+) AAACAC/TGGCTA 2 -- ut310--------
rs1510835431,2
C,F--8759414(+) GTCCTT/CGGCAG 4 /K /E mis11Minor allele frequency- C:0.00NA 4496

HapMap Linkage Disequilibrium report for FAM9A (8758836 - 8769424 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for FAM9A:    About this table    
Variant IDTypeSubtypePubMed ID
esv2752339CNV Gain17911159

Locus Specific Mutation Databases (LSDB): FAM9A

Site Specific Mutation Identification with 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.)
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OMIM gene information: 300477    OMIM disorders: --

1 disease for FAM9A:    
About MalaCards
uterine fibroid

1 disease from the University of Copenhagen DISEASES database for FAM9A:
Uterine fibroid

Find genes that share disorders with FAM9A           About GenesLikeMe


Export disorders for FAM9A 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)
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PubMed articles for FAM9A gene integrated from 10 sources:
(articles sorted by number of sources associating them with FAM9A)
    Utopia: connect your pdf to the dynamic
world of online information

  1. A new gene family (FAM9) of low-copy repeats in Xp22.3 expressed exclusively in testis: implications for recombinations in this region. (PubMed id 12213195)1, 2, 9 Martinez-Garay I....Kutsche K. (Genomics 2002)
  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. (Genome Res. 2004)
  3. A Y2H-seq approach defines the human protein methyltransferase interactome. (PubMed id 23455924)1 Weimann M.... Stelzl U. (Nat. Methods 2013)
  4. 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)

(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: 171482 HGNC: 18403 AceView: FAM9A Ensembl:ENSG00000183304 euGenes: HUgn171482
ECgene: FAM9A H-InvDB: FAM9A

(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 FAM9A 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 FAM9A gene:
Search GeneIP for patents involving FAM9A

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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Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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