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GIFtS

ODF4 Gene

protein-coding   GIFtS: 41
GCID: GC17P008243

outer dense fiber of sperm tails 4
  Search for ODF4
in
MalaCards
our new
 Human Malady Compendium 
Biological research products
for ODF4    

Aliases
for ODF4 gene

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section
Aliases
Outer Dense Fiber Of Sperm Tails 41 2     CT1342
OPPO11 2 3 5     Cancer/Testis Antigen 1342
CT1361 2     Cancer/Testis Antigen 1362
Outer Dense Fiber Of Sperm Tails Protein 42 3     Outer Dense Fiber 42
Testis-Specific Protein Oppo 12 3     Outer Dense Fiber Protein 42
HOPPO11     

External Ids:    HGNC: 190561   Entrez Gene: 1468522   Ensembl: ENSG000001846507   OMIM: 6100975   UniProtKB: Q2M2E33   

Export aliases for ODF4 gene to outside databases

Previous GC identifers: GC17P008978 GC17P008186 GC17P008443 GC17P008183


Summaries
for ODF4 gene

(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 ODF4:
This gene encodes a protein that is localized in the outer dense fibers of the tails of mature sperm. This protein is
thought to have some important role in the sperm tail. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: ODFP4_HUMAN, Q2M2E3
Function: Component of the outer dense fibers (ODF) of spermatozoa which could be involved in sperm tail structure,
sperm movement and general organization of cellular cytoskeleton (By similarity)




Genomic Views
for ODF4 gene

(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_000017.10  NC_018928.1  NT_010718.16  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the ODF4 gene promoter:
         AhR   AP-1   HTF   AP-4   Tal-1beta   E47   Evi-1   AREB6   c-Myb   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: ODF4 promoter sequence
   Search SABiosciences Chromatin IP Primers for ODF4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat ODF4


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

Entrez Gene cytogenetic band: 17p13.1   Ensembl cytogenetic band:  17p13.1   HGNC cytogenetic band: 17p13

ODF4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ODF4 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P008243:  view genomic region     (about GC identifiers)

Start:
 8,243,182 bp from pter      End:
 8,249,364 bp from pter
Size:
 6,183 bases      Orientation:
 plus strand

Proteins
for ODF4 gene

(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: ODFP4_HUMAN, Q2M2E3 (See protein sequence)
Recommended Name: Outer dense fiber protein 4  
Size: 257 amino acids; 29233 Da
Subcellular location: Membrane; Multi-pass membrane protein (Potential)
Secondary accessions: Q8J021

Explore the universe of human proteins at neXtProt for ODF4: NX_Q2M2E3

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q2M2E3

    • ODF4 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_694552.2  
    ENSEMBL proteins: 
     ENSP00000331086   ENSP00000461942  

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    Uscn Proteins for ODF4

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001520outer dense fiber IEA--
    GO:0016021integral to membrane IEA--


    ODF4 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for ODF4 gene

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

    ProtoNet protein and cluster: Q2M2E3


    Function
    for ODF4 gene

    (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: ODFP4_HUMAN, Q2M2E3
    Function: Component of the outer dense fibers (ODF) of spermatozoa which could be involved in sperm tail structure,
    sperm movement and general organization of cellular cytoskeleton (By similarity)

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    Pathways & Interactions
    for ODF4 gene

    (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 ODF4

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007275multicellular organismal development IEA--
    GO:0007283spermatogenesis IEA--
    GO:0030154cell differentiation IEA--


    ODF4 for ontologies           About GeneDecksing



    Drugs & Compounds
    for ODF4 gene

    (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 ODF4
    Search CenterWatch for drugs/clinical trials and news about ODF4 / ODFP4 

    Transcripts
    for ODF4 gene

    (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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    About This Section
    REFSEQ mRNAs for ODF4 gene: 
    NM_153007.4  

    Unigene Cluster for ODF4:

    Outer dense fiber of sperm tails 4
    Hs.186045  [show with all ESTs]
    Unigene Representative Sequence: AY237799
    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000328248(uc002gle.1) ENST00000584943

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    hsa-miR-3150b-3p hsa-miR-3692
    SwitchGear 3'UTR luciferase reporter plasmid: ODF4 3' UTR sequence
    Inhib. RNA
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    Clone
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    Primer
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat ODF4

    Additional cDNA sequence: 

    AB081120.1 AY237799.1 BC112010.1 BC112014.1 FJ235526.1 

    1 DOTS entry:

    DT.100016303 

    8 AceView cDNA sequences:

    AA583225 BX094858 AY237799 AB081120 AI862103 NM_153007 AI125365 AI968783 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for ODF4    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3a · 3b
    SP1:        -                     
    SP2:                              


    ECgene alternative splicing isoforms for ODF4

    Expression
    for ODF4 gene

    (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

    ODF4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TGTAATCTTT

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

    ODF4 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)
    TestisSeminiferous TubulesMature Sertoli CellsTestis
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See ODF4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for ODF4

    SOURCE GeneReport for Unigene cluster: Hs.186045

    UniProtKB/Swiss-Prot: ODFP4_HUMAN, Q2M2E3
    Tissue specificity: Expressed in testis and sperm; especially localized to sperm tail (at protein level)

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    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ODF4

    Orthologs
    for ODF4 gene

    (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 mouse.

    Orthologs for ODF4 gene from 1/5 species (see all 5)    About this table
    Organism Taxonomic
    classification    		 Gene Description Human
    Similarity    		 Orthology
    Type    		 Details
    mouse
    (Mus musculus)    		 Mammalia Odf41 , 5 outer dense fiber of sperm tails 41, 5 64.52(n)1
    54.46(a)1    		   11 (42.19 cM)5
    2528681  NM_145746.21  NP_665689.11 
     689218355 


    ENSEMBL Gene Tree for ODF4 (if available)
    TreeFam Gene Tree for ODF4 (if available) 

    Paralogs
    for ODF4 gene

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

    Genomic Variants
    for ODF4 gene

    (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

    10/193 NCBI SNPs in ODF4 are shown (see all 193)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 17 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs65031021,2
    		C,F,A,H,--8241190(+) AGTCAA/GAAGAA 1 -- us2k1 trp323Minor allele frequency- N:0.00NS EA NA WA CSA 2558
    rs620642921,2
    		F,--8241204(+) GGAAGG/AAACTG 1 -- us2k11Minor allele frequency- A:0.04NA 120
    rs1810959601,2
    		--8241370(+) ATCAGC/TGAGCA 1 -- us2k10--------
    rs1854089731,2
    		--8241380(+) ATTTGC/GGGTTG 1 -- us2k10--------
    rs1495008581,2
    		--8241548(+) GAGGAC/TGTCAG 1 -- us2k10--------
    rs1909073111,2
    		--8241549(+) AGGACA/GTCAGG 1 -- us2k10--------
    rs1825018781,2
    		--8241572(+) ATGGTA/GGAGGC 1 -- us2k10--------
    rs80696201,2
    		C,F,H,--8241651(+) AATAAA/GCCAGT 1 -- us2k115Minor allele frequency- G:0.09NS EA NA WA 1880
    rs80691581,2
    		C,F,H,--8241673(+) ATTTTC/TGAGTT 1 -- us2k120Minor allele frequency- T:0.35NS EA NA WA CSA 2346
    rs80679991,2
    		C,F,--8241702(+) AAACAG/ACTTGC 1 -- us2k17Minor allele frequency- A:0.35WA NA CSA EA 366

    HapMap Linkage Disequilibrium report for ODF4 (8243182 - 8249364 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for ODF4
         2 CNVs: 43957 102397

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    Disorders / Diseases
    for ODF4 gene

    (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
    ODF4 for disorders           About MalaCards

    ODF4 for disorders           About GeneDecksing

    OMIM gene information: 610097    OMIM disorders: --


    Export disorders for ODF4 gene to outside databases

    Publications
    for ODF4 gene

    (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 ODF4 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with ODF4)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning and characterization of the human orthologue of the oppo 1 gene encoding a sperm tail protein. (PubMed id 12728016)1, 2, 9 Kitamura K....Nishimune Y. (2003)
    2. Expression of splice variants of cancer-testis genes ODF3 and ODF4 in the testis of a prostate cancer patient. (PubMed id 23096689)1 Ghafouri-Fard S. and Modarressi M.H. (2012)
    3. Expression of testis-specific genes, TEX101 and ODF4, in chronic myeloid leukemia and evaluation of TEX101 immunogenicity. (PubMed id 22588436)1 Ghafouri-Fard S....Yazarloo F. (2012)
    4. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    5. Isolation and expression analysis of the testis-specific gene, human OPPO1. (PubMed id 15270212)1 Miyamoto T....Ishikawa M. (2004)
    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)

    External Searches for ODF4 gene

    (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)

    Genome Databases showing ODF4 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 146852 HGNC: 19056 AceView: ODF4 Ensembl:ENSG00000184650 euGenes: HUgn146852
    ECgene: ODF4 H-InvDB: ODF4

    Other Databases showing ODF4 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing ODF4 gene

    (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 ODF4 Pharmacogenomics, SNPs, Pathways

    Intellectual Property
    for ODF4 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for ODF4 gene:
    Search GeneIP for patents involving ODF4

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



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    About This Section

     
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