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ODF3 Gene

protein-coding   GIFtS: 44
GCID: GC11P000196

Outer Dense Fiber Of Sperm Tails 3

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(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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Outer Dense Fiber Of Sperm Tails 31 2     CT1352
SHIPPO12 3 5     Outer Dense Fiber Protein 32
Cancer/Testis Antigen 1351 2     Sperm Tail Protein SHIPPO12
Transcript Induced In Spermiogenesis Protein 502 3     Outer Dense Fiber Of Sperm Tails Protein 33
TISP502 3     Sperm Tail Protein SHIPPO 13

External Ids:    HGNC: 199051   Entrez Gene: 1137462   Ensembl: ENSG000001779477   OMIM: 6083565   UniProtKB: Q96PU93   
ORGUL members:         

Export aliases for ODF3 gene to outside databases

Previous GC identifers: GC11M000109 GC11M000998 GC11P000186 GC11P000016


(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 ODF3 Gene:
ODF3 is a component of sperm flagella outer dense fibers, which add stiffness, elastic recoil, and protection
against shearing forces during sperm movement.(supplied by OMIM, Apr 2004)

GeneCards Summary for ODF3 Gene:
ODF3 (outer dense fiber of sperm tails 3) is a protein-coding gene. An important paralog of this gene is ODF3B.

UniProtKB/Swiss-Prot: ODF3A_HUMAN, Q96PU9
Function: Outer dense fibers are filamentous structures located on the outside of the axoneme in the midpiece and
principal piece of the mammalian sperm tail. May help to maintain the passive elastic structures and elastic
recoil of the sperm tail




(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 at NCBI GenBank:
NC_000011.9  NC_018922.2  NT_009237.19  
Regulatory elements:
   Regulatory transcription factor binding sites in the ODF3 gene promoter:
         Elk-1   NF-1   NF-1/L   p53   Nkx2-5   Tal-1beta   E47   Roaz   Pax-4a   MRF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidODF3 promoter sequence
   Search Chromatin IP Primers for ODF3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ODF3


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

Entrez Gene cytogenetic band: 11p15.5   Ensembl cytogenetic band:  11p15.5   HGNC cytogenetic band: 11p15.5

ODF3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ODF3 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P000196:  view genomic region     (about GC identifiers)

Start:
196,738 bp from pter      End:
200,261 bp from pter
Size:
3,524 bases      Orientation:
plus 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., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: ODF3A_HUMAN, Q96PU9 (See protein sequence)
Recommended Name: Outer dense fiber protein 3  
Size: 254 amino acids; 27710 Da
Miscellaneous: 'Shippo' is a Japanese word for tail
Secondary accessions: Q69YX0
Alternative splicing: 2 isoforms:  Q96PU9-1   Q96PU9-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ODF3: NX_Q96PU9

Explore proteomics data for ODF3 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ODF3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001273065.1  NP_444510.2  

    ENSEMBL proteins: 
     ENSP00000325868   ENSP00000436588   ENSP00000339623  

    ODF3 Human Recombinant Protein Products:

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    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for ODF3

     
    Search eBioscience for Proteins for ODF3 

     
    antibodies-online proteins for ODF3 (3 products) 

     
    antibodies-online peptides for ODF3

    ODF3 Antibody Products:

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    antibodies-online antibodies for ODF3 (24 products) 

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    Cloud-Clone Corp. CLIAs for ODF3
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    antibodies-online kits for ODF3 (6 products) 


    (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:
     IPR010736 SHIPPO-rpt

    Graphical View of Domain Structure for InterPro Entry Q96PU9

    ProtoNet protein and cluster: Q96PU9

    UniProtKB/Swiss-Prot: ODF3A_HUMAN, Q96PU9
    Similarity: Belongs to the ODF3 family
    Similarity: Contains 2 STPGR (Sperm-tail PG-rich) repeats


    Find genes that share domains with ODF3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: ODF3A_HUMAN, Q96PU9
    Function: Outer dense fibers are filamentous structures located on the outside of the axoneme in the midpiece and
    principal piece of the mammalian sperm tail. May help to maintain the passive elastic structures and elastic
    recoil of the sperm tail

    Animal Models:

       genOway: Develop your customized and physiologically relevant rodent model for ODF3

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    1 qRT-PCR Assays for microRNA that regulate ODF3:
    hsa-miR-29a*
    SwitchGear 3'UTR luciferase reporter plasmidODF3 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for ODF3
    Predesigned siRNA for gene silencing in human, mouse, rat ODF3

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    Browse Sino Biological Human cDNA Clones
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for ODF3
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat ODF3

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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ODF3


    (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
    ODF3A_HUMAN, Q96PU9: Cytoplasm (By similarity). Note=Expressed in the cytoplasmic lobe of spermatids (By
    similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    cytosol2
    nucleus2
    mitochondrion1
    peroxisome1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001520outer dense fiber IEA--

    Find genes that share ontologies with ODF3           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 ODF3
    Interactions:

        Search GeneGlobe Interaction Network for ODF3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 10)

    Selected Interacting proteins for ODF3 (ENSP000003258684) via UniProtKB, MINT, STRING, and/or I2D (see all 10)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PFDN2ENSP000003569894STRING: ENSP00000356989
    VBP1ENSP000002864284STRING: ENSP00000286428
    ENSG00000206283ENSP000003726944STRING: ENSP00000372694
    ENSG00000235692ENSP000004156784STRING: ENSP00000415678
    ENSG00000237335ENSP000004123194STRING: ENSP00000412319
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

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

    Find genes that share ontologies with ODF3           About GenesLikeMe



    (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
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for ODF3 (ODF3A)



    (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 ODF3 gene (2 alternative transcripts): 
    NM_001286136.1  NM_053280.4  

    Unigene Cluster for ODF3:

    Outer dense fiber of sperm tails 3
    Hs.350949  [show with all ESTs]
    Unigene Representative Sequence: AL133658
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000325113(uc001lob.3 uc010qvk.2) ENST00000531679(uc001loc.3)
    ENST00000525282 ENST00000342593
    miRNA
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    1 qRT-PCR Assays for microRNA that regulate ODF3:
    hsa-miR-29a*
    SwitchGear 3'UTR luciferase reporter plasmidODF3 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat ODF3
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      QuantiTect SYBR Green Assays in human, mouse, rat ODF3
      QuantiFast Probe-based Assays in human, mouse, rat ODF3

    Additional mRNA sequence: 

    AB067774.1 AL133658.1 AY713299.1 BC126222.1 BC126248.1 BC144022.1 FJ436414.1 

    1 DOTS entry:

    DT.40127582 

    6 AceView cDNA sequences:

    NM_053280 BX093806 AL133658 AB067774 AI126587 AA977621 

    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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    ODF3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GCTGCCCGTG
    ODF3 Expression
    About this image

    ODF3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ODF3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.350949

    UniProtKB/Swiss-Prot: ODF3A_HUMAN, Q96PU9
    Tissue specificity: Testis-specific

        Custom PCR Arrays for ODF3
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    In Situ
    Assay Products:
     

     
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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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    This gene was present in the common ancestor of animals.

    Orthologs for ODF3 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Odf31 , 5 outer dense fiber of sperm tails 31, 5 88.98(n)1
    93.7(a)1
      7 (86.05 cM)5
    692871  NM_027019.31  NP_081295.21 
     1408478055 
    chicken
    (Gallus gallus)
    Aves --
    --
    (see all 6)
    Uncharacterized protein
    (see all 6)
    50(a)
    45(a)
    (see all 6)
    1 ↔ many
    1 ↔ many
    (see all 6)
    19(174704-176366) ENSGALG00000028649
    AADN03012277.1(21-1570) ENSGALG00000027892
    lizard
    (Anolis carolinensis)
    Reptilia ODF36
    outer dense fiber of sperm tails 3
    51(a)
    1 ↔ 1
    1(77245880-77254130)
    African clawed frog
    (Xenopus laevis)
    Amphibia MGC526792 hypothetical protein MGC52679 73.51(n)    BC041210.1 
    zebrafish
    (Danio rerio)
    Actinopterygii odf3b1 outer dense fiber of sperm tails 3B 56.97(n)
    52.59(a)
      335524  NM_199958.1  NP_956252.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG80866
    --
    5(a)
    many ↔ many
    2L(8244160-8257502)


    ENSEMBL Gene Tree for ODF3 (if available)
    TreeFam Gene Tree for ODF3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ODF3 gene
    ODF3B2  ODF3L22  ODF3L12  
    3 SIMAP similar genes for ODF3 using alignment to 4 protein entries:     ODF3A_HUMAN (see all proteins):
    ODF3B    ODF3L1    ODF3L2

    Find genes that share paralogs with ODF3           About GenesLikeMe



    (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 ODF3 (see all 231)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs3744181711,2
    C--15926(+) GTGAG-/AGGACC 1 -- us2k10--------
    rs29794271,2
    C,F--15993(-) CAAGGC/TCCCCC 1 -- us2k12Minor allele frequency- T:0.50NA CSA 4
    rs665027791,2
    C,F--16004(+) GTGAGC/GGGACC 1 -- us2k17Minor allele frequency- G:0.18NA CSA WA EA 368
    rs1116067091,2
    C--16019(+) GAGGGA/GACATG 1 -- us2k10--------
    rs1476370291,2
    C--16024(+) GACAT-/GGGGGG 1 -- us2k10--------
    rs1847650211,2
    C--16124(+) GGGACA/CTGGTG 1 -- us2k10--------
    rs2013332011,2
    --16172(+) AGGGG-/AACATG 1 -- us2k10--------
    rs1126057671,2
    C--16332(+) ATGGGG/TGGGAC 1 -- us2k10--------
    rs287061631,2
    C--16573(+) TGAGGG/AGGACC 1 -- us2k11Minor allele frequency- A:0.50CSA 2
    rs2016883981,2
    C--16573(+) TGAGG-/AGGACC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for ODF3 (196738 - 200261 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 9 variations for ODF3:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv896437CNV Loss21882294
    nsv896439CNV Loss21882294
    nsv467630CNV Gain19166990
    nsv467631CNV Gain19166990
    nsv522596CNV Gain19592680
    esv22231CNV Gain19812545
    nsv896436CNV Gain21882294
    dgv911n71CNV Gain21882294
    dgv910n71CNV Gain21882294

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing ODF3
    DNA2.0 Custom Variant and Variant Library Synthesis for ODF3

    (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: 608356    OMIM disorders: --


    Find genes that share disorders with ODF3           About GenesLikeMe


    Export disorders for ODF3 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 ODF3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with ODF3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Molecular cloning and characterization of a complementary DNA encoding sperm tail protein SHIPPO 1. (PubMed id 11870087)1, 2, 3, 9 Egydio de Carvalho C....Nishimune Y. (Biol. Reprod. 2002)
    2. A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects. (PubMed id 24026423)1 Shameer K....Kullo I.J. (Hum. Genet. 2014)
    3. Localization and identification of sumoylated proteins in human sperm: excessive sumoylation is a marker of defective spermatozoa. (PubMed id 23077236)1 Vigodner M....Callaway M. (Hum. Reprod. 2013)
    4. 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. (Genet. Mol. Res. 2012)
    5. A genome-wide association study identifies three loci associated with susceptibility to uterine fibroids. (PubMed id 21460842)1 Cha P.C....Nakamura Y. (Nat. Genet. 2011)
    6. Genome-scale RNAi screen for host factors required for HIV replication. (PubMed id 18976975)1 Zhou H....Espeseth A.S. (amp 2008)
    7. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (BMC Genomics 2007)
    8. 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. (Genome Res. 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. (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: 113746 HGNC: 19905 AceView: ODF3 Ensembl:ENSG00000177947 euGenes: HUgn113746
    ECgene: ODF3 H-InvDB: ODF3

    (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 ODF3 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 ODF3 gene:
    Search GeneIP for patents involving ODF3

    GeneCards and IP:
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    (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, eBioscience, antibodies-online, 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
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