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

SPANXD Gene

protein-coding   GIFtS: 39
GCID: GC0XM140786

SPANX Family, Member D

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
SPANX Family, Member D1 2     SPANX-C2
Cancer/Testis Antigen 11.42 3     Cancer/Testis Antigen Family 11, Member 42
Nuclear-Associated Protein SPAN-Xd2 3     dJ171K16.12
CT11.42 3     SPAN-Xd Protein2
SPANX-D2 3     Sperm Protein Associated With The Nucleus On The X Chromosome D2
Cancer/Testis Antigen Family 111     Sperm Protein Associated With The Nucleus, X Chromosome, Family Member D2
Member 41     SPANX Family Member D3

External Ids:    HGNC: 143321   Entrez Gene: 646482   Ensembl: ENSG000001964067   OMIM: 3006705   UniProtKB: Q9BXN63   

Export aliases for SPANXD gene to outside databases

Previous GC identifers: GC0XU990341 GC0XM137643 GC0XM138718 GC0XM139479 GC0XM140511 GC0XM140613


(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 SPANXD Gene:
Temporally regulated transcription and translation of several testis-specific genes is required to initiate the
series of molecular and morphological changes in the male germ cell lineage necessary for the formation of mature
spermatozoa. This gene is a member of the SPANX family of cancer/testis-associated genes, which are located in a
cluster on chromosome X. The SPANX genes encode differentially expressed testis-specific proteins that localize
to various subcellular compartments. This particular gene encodes a sperm protein that is associated with the
nucleus but, although a role in spermatogenesis is suggested, the specific function of this family member has not
yet been determined. (provided by RefSeq, Jul 2008)

GeneCards Summary for SPANXD Gene: 
SPANXD (SPANX family, member D) is a protein-coding gene. Diseases associated with SPANXD include germ cell tumors, and infertility. An important paralog of this gene is SPANXA2.




(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 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000023.10  NC_018934.2  NT_011786.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the SPANXD gene promoter:
         Max1   POU3F2   Evi-1   MEF-2A   S8   CBF-A   CBF-B   CP1A   aMEF-2   c-Myc   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for SPANXD

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


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

Entrez Gene cytogenetic band: Xq27.1   Ensembl cytogenetic band:  Xq27.2   HGNC cytogenetic band: Xq27.2

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

GeneLoc information about chromosome X         GeneLoc Exon Structure

GeneLoc location for GC0XM140786:  view genomic region     (about GC identifiers)

Start:
140,785,568 bp from pter      End:
140,786,896 bp from pter
Size:
1,329 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB 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 Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: SPNXD_HUMAN, Q9BXN6 (See protein sequence)
Recommended Name: Sperm protein associated with the nucleus on the X chromosome D  
Size: 97 amino acids; 11029 Da
Subcellular location: Cytoplasm (By similarity). Nucleus (By similarity). Note=Associated with nuclear craters (By
similarity)
Developmental stage: Detected in round and elongating spermatids
Secondary accessions: Q5JWI1

Explore the universe of human proteins at neXtProt for SPANXD: NX_Q9BXN6

Explore proteomics data for SPANXD at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9BXN6

  • SPANXD Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    SPANXD Protein Expression
    REFSEQ proteins: NP_115793.1  
    ENSEMBL proteins: 
     ENSP00000359546  

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    Gene Ontology (GO): 2 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--
    GO:0005737cytoplasm IEA--

    SPANXD for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR010007 SPANX_prot

    Graphical View of Domain Structure for InterPro Entry Q9BXN6

    ProtoNet protein and cluster: Q9BXN6

    UniProtKB/Swiss-Prot: SPNXD_HUMAN, Q9BXN6
    Similarity: Belongs to the SPAN-X family


    SPANXD for domains           About GeneDecksing


    (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,
    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, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Animal Models:
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    (Pathways according to EMD Millipore, 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 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 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

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

    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, 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 SPANXD (SPNXD)

    Search CenterWatch for drugs/clinical trials and news about SPANXD / SPNXD

    (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,
    Conferences by KenesGroup, 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, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for SPANXD gene: 
    NM_032417.2  

    Unigene Cluster for SPANXD:

    SPANX family, member D
    Hs.375036  [show with all ESTs]
    Unigene Representative Sequence: BM554791
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000370515(uc004fbq.3)
    miRNA
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    Additional mRNA sequence: 

    AF312765.1 AJ457795.1 BC005382.1 BC062672.1 BC103960.1 BC103961.1 BC121070.2 BC134418.1 

    2 DOTS entries:

    DT.101961078  DT.100036177 

    12 AceView cDNA sequences:

    BM554791 AF312765 NM_032417 CB119085 CB106942 NM_145665 BC005382 AI808260 
    AI143898 AJ457795 BC062672 BF212177 

    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

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


    See SPANXD Protein Expression from SPIRE MOPED and PaxDB
    SOURCE GeneReport for Unigene cluster: Hs.375036

    UniProtKB/Swiss-Prot: SPNXD_HUMAN, Q9BXN6
    Tissue specificity: Detected in testis, sperm and a melanoma cell line

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for SPANXD

    (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 human and chimp.

    Orthologs for SPANXD gene from 1 species (see representative species )    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chimpanzee
    (Pan troglodytes)
    Mammalia LOC4939811 SPANX A/D member 1 89(n)
    77.32(a)
      493981  NM_001009153.1  NP_001009153.1 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for SPANXD gene
    SPANXA21 2  SPANXA11 2  SPANXC1 2  SPANXB21 2  SPANXB11 2  
    11 SIMAP similar genes for SPANXD using alignment to 5 protein entries:     SPNXD_HUMAN (see all proteins):
    SPANXA2    SPANXE    SPANXA1    SPANXC    SPANXB1    SPANXB2
    SPANXF1    SPANXN5    SPANXN2    SPANXN1    SPANXN3

    SPANXD for paralogs           About GeneDecksing



    (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) 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

    9 SNPs in SPANXD are shown    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr X posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs29835921,2
    C--140785696(-) CCCGAA/GAGAAC 2 K E mis11Minor allele frequency- G:0.00NA 2
    rs59536181,2,4
    C--140785714(+) ATTCAG/CCAGTT 2 /L /V mis12Minor allele frequency- C:0.41NA MN 186
    rs1393639031,2
    C,F--140785790(+) GTTTTT/CAGTTT 2 /L syn11Minor allele frequency- C:0.02NA 4476
    rs1496694801,2
    C--140785792(+) TTTTAG/TTTTTT 2 I L mis10--------
    rs1490902061,2
    C,F--140785822(+) TGAGTA/CCCCAC 2 D Y mis11Minor allele frequency- C:0.00NA 4472
    rs3731494781,2
    ----140785829(+) CCACTC/TGAGGT 2 S syn10--------
    rs3690002401,2
    ----140785827(+) ACCCAC/GTCGAG 2 T S mis10--------
    rs3768788091,2
    ----140785831(+) ACTCGA/GGGTCT 2 P S mis10--------

    HapMap Linkage Disequilibrium report for SPANXD (140785568 - 140786896 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for SPANXD:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv471606CNV Gain15918152
    nsv9984CNV Gain18304495
    esv25564CNV Gain+Loss19812545
    essv9625CNV CNV17122850
    dgv2483e1CNV Complex17122850

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 300670    OMIM disorders: --

    5 diseases for SPANXD:    About MalaCards
    germ cell tumors    infertility    prostate cancer    melanoma
    prostatitis


    SPANXD for disorders           About GeneDecksing

    Genetic Association Database (GAD): SPANXD
    Human Genome Epidemiology (HuGE) Navigator: SPANXD (1 document)

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

    1. SPANX gene variation in fertile and infertile males. (PubMed id 20073942)1, 4 Hansen S....Carrell D. (2010)
    2. Dynamic structure of the SPANX gene cluster mapped to the prostate cancer susceptibility locus HPCX at Xq27. (PubMed id 16251457)1, 2 Kouprina N.... Larionov V. (2005)
    3. The human SPANX multigene family: genomic organization, alignment and expression in male germ cells and tumor cell lines. (PubMed id 12758128)1, 2 Zendman A.J.... van Muijen G.N.P. (2003)
    4. A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study. (PubMed id 17903299)4 Kathiresan S....Cupples L.A. (2007)
    5. The DNA sequence of the human X chromosome. (PubMed id 15772651)2 Ross M.T.... Bentley D.R. (2005)
    6. 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. (2004)
    7. 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)
    8. Differential nuclear localization of the cancer/testis-associated protein, SPAN-X/CTp11, in transfected cells and in 50% of human spermatozoa. (PubMed id 11133693)1 Westbrook V.A....Herr J.C. (2001)
    9. Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )2 Aoki H.... Hino O. (2000)

    (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: 64648 HGNC: 14332 AceView: SPANXD Ensembl:ENSG00000196406 euGenes: HUgn64648
    ECgene: SPANXD H-InvDB: SPANXD

    (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 SPANXD Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for SPANXD Genetics and Cytogenetics in Oncology and Haematology

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for SPANXD gene:
    Search GeneIP for patents involving SPANXD

    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, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, 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, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 3 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    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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