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] See more...

Aliases for ODF3 Gene

Aliases for ODF3 Gene

  • Outer Dense Fiber Of Sperm Tails 3 2 3 5
  • SHIPPO1 2 3 4
  • Transcript Induced In Spermiogenesis Protein 50 3 4
  • Outer Dense Fiber Protein 3 3 4
  • Cancer/Testis Antigen 135 2 3
  • TISP50 3 4
  • CT135 2 3
  • Outer Dense Fiber Of Sperm Tails Protein 3 4
  • Sperm Tail Protein SHIPPO 1 4
  • Sperm Tail Protein SHIPPO1 3
  • HSHIPPO 2
  • ODF3 5

External Ids for ODF3 Gene

Previous GeneCards Identifiers for ODF3 Gene

  • GC11M000109
  • GC11M000998
  • GC11P000186
  • GC11P000016

Summaries for ODF3 Gene

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. Diseases associated with ODF3 include Salpingitis and Chronic Salpingitis. An important paralog of this gene is ODF3B.

UniProtKB/Swiss-Prot Summary for ODF3 Gene

  • 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.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for ODF3 Gene

Genomics for ODF3 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for ODF3 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J000196 Promoter 0.3 EPDnew 600.7 0.0 -10 0.1 ODF3 RIC8A piR-52171-001 SCGB1C1 BET1L
GH11J000197 Enhancer 0.2 Ensembl 600.7 -0.5 -460 0.6 ODF3 piR-52171-001 SCGB1C1 BET1L
GH11J000304 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 10.8 +116.9 116855 18.4 GATAD2A CTCF HNRNPL TEAD4 PRDM10 REST IKZF1 POLR2A BACH1 LARP7 IFITM2 IFITM3 IFITM1 HSALNG0081954 ENSG00000254910 PGGHG PIDD1 TMEM80 ENSG00000270030 ENSG00000251661
GH11J000266 Enhancer 1.4 FANTOM5 ENCODE dbSUPER 11.4 +73.3 73291 6.8 SP1 LEF1 POLR2A BACH1 JUND LARP7 STAT3 DDX20 ZNF143 MTA2 IFITM2 PSMD13 RIC8A SIRT3 PGGHG ENSG00000254559 ODF3 SCGB1C1 BET1L NLRP6
GH11J000222 Enhancer 1.1 Ensembl ENCODE dbSUPER 12.2 +25.0 24969 1.1 IKZF1 HDAC1 FOXJ2 GTF2E2 ZNF766 HMBOX1 MTA3 E2F5 NR2C2 ZBTB11 RIC8A PSMD13 SIRT3 ODF3 SCGB1C1 BET1L NLRP6 PGGHG ENSG00000255026 piR-43105-065
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around ODF3 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for ODF3

Top Transcription factor binding sites by QIAGEN in the ODF3 gene promoter:
  • E47
  • Elk-1
  • MRF-2
  • NF-1
  • NF-1/L
  • Nkx2-5
  • p53
  • Pax-4a
  • Roaz
  • Tal-1beta

Genomic Locations for ODF3 Gene

Genomic Locations for ODF3 Gene
chr11:196,761-200,261
(GRCh38/hg38)
Size:
3,501 bases
Orientation:
Plus strand
chr11:196,738-200,261
(GRCh37/hg19)
Size:
3,524 bases
Orientation:
Plus strand

Genomic View for ODF3 Gene

Genes around ODF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ODF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ODF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ODF3 Gene

Proteins for ODF3 Gene

  • Protein details for ODF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96PU9-ODF3A_HUMAN
    Recommended name:
    Outer dense fiber protein 3
    Protein Accession:
    Q96PU9
    Secondary Accessions:
    • B7ZLT0
    • Q69YX0

    Protein attributes for ODF3 Gene

    Size:
    254 amino acids
    Molecular mass:
    27710 Da
    Quaternary structure:
    No Data Available
    Miscellaneous:
    • 'Shippo' is a Japanese word for tail.

    Alternative splice isoforms for ODF3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for ODF3 Gene

Post-translational modifications for ODF3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for ODF3 Gene

No data available for DME Specific Peptides for ODF3 Gene

Domains & Families for ODF3 Gene

Gene Families for ODF3 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for ODF3 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for ODF3 Gene

GenScript: Design optimal peptide antigens:
  • Transcript induced in spermiogenesis protein 50 (ODF3A_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q96PU9

UniProtKB/Swiss-Prot:

ODF3A_HUMAN :
  • Belongs to the ODF3 family.
Family:
  • Belongs to the ODF3 family.
genes like me logo Genes that share domains with ODF3: view

Function for ODF3 Gene

Molecular function for ODF3 Gene

UniProtKB/Swiss-Prot 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.

Phenotypes From GWAS Catalog for ODF3 Gene

Gene Ontology (GO) - Molecular Function for ODF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 23355646
genes like me logo Genes that share ontologies with ODF3: view
genes like me logo Genes that share phenotypes with ODF3: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ODF3

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for ODF3 Gene

Localization for ODF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ODF3 Gene

Cytoplasm. Note=Expressed in the cytoplasmic lobe of spermatids. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ODF3 gene
Compartment Confidence
cytoskeleton 3
nucleus 2
cytosol 2
mitochondrion 1
golgi apparatus 1
peroxisome 0

Gene Ontology (GO) - Cellular Components for ODF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001520 outer dense fiber IEA,IBA 21873635
GO:0005737 cytoplasm IEA --
GO:0005856 cytoskeleton IBA 21873635
genes like me logo Genes that share ontologies with ODF3: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for ODF3 Gene

Pathways & Interactions for ODF3 Gene

PathCards logo

SuperPathways for ODF3 Gene

No Data Available

Interacting Proteins for ODF3 Gene

Gene Ontology (GO) - Biological Process for ODF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007275 multicellular organism development IEA --
GO:0007283 spermatogenesis IEA --
GO:0030154 cell differentiation IEA --
genes like me logo Genes that share ontologies with ODF3: view

No data available for Pathways by source and SIGNOR curated interactions for ODF3 Gene

Drugs & Compounds for ODF3 Gene

No Compound Related Data Available

Transcripts for ODF3 Gene

mRNA/cDNA for ODF3 Gene

2 REFSEQ mRNAs :
7 NCBI additional mRNA sequence :
4 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for ODF3

Alternative Splicing Database (ASD) splice patterns (SP) for ODF3 Gene

No ASD Table

Relevant External Links for ODF3 Gene

GeneLoc Exon Structure for
ODF3

Expression for ODF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for ODF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

  • Testis (Reproductive System)

mRNA differential expression in normal tissues according to GTEx for ODF3 Gene

This gene is overexpressed in Testis (x47.4).

Protein differential expression in normal tissues from HIPED for ODF3 Gene

This gene is overexpressed in Testis (54.6) and Ovary (14.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for ODF3 Gene



Protein tissue co-expression partners for ODF3 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for ODF3

SOURCE GeneReport for Unigene cluster for ODF3 Gene:

Hs.350949

mRNA Expression by UniProt/SwissProt for ODF3 Gene:

Q96PU9-ODF3A_HUMAN
Tissue specificity: Testis-specific.
genes like me logo Genes that share expression patterns with ODF3: view

No data available for Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for ODF3 Gene

Orthologs for ODF3 Gene

This gene was present in the common ancestor of animals.

Orthologs for ODF3 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia ODF3 30 31
  • 99.34 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia ODF3 30 31
  • 90.29 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia ODF3 30 31
  • 89.11 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Odf3 30 17 31
  • 88.98 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Odf3 30
  • 88.98 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia ODF3 31
  • 61 (a)
OneToOne
Chicken
(Gallus gallus)
Aves -- 31
  • 50 (a)
OneToMany
-- 31
  • 45 (a)
OneToMany
-- 31
  • 44 (a)
OneToMany
-- 31
  • 39 (a)
OneToMany
-- 31
  • 34 (a)
OneToMany
-- 31
  • 32 (a)
OneToMany
Lizard
(Anolis carolinensis)
Reptilia ODF3 31
  • 51 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia odf3 30
  • 56.52 (n)
Str.3041 30
African clawed frog
(Xenopus laevis)
Amphibia MGC52679 30
Zebrafish
(Danio rerio)
Actinopterygii odf3b 30
  • 56.97 (n)
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.5039 30
Fruit Fly
(Drosophila melanogaster)
Insecta CG8086 31
  • 5 (a)
ManyToMany
Species where no ortholog for ODF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Oppossum (Monodelphis domestica)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for ODF3 Gene

ENSEMBL:
Gene Tree for ODF3 (if available)
TreeFam:
Gene Tree for ODF3 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for ODF3: view image

Paralogs for ODF3 Gene

Paralogs for ODF3 Gene

(3) SIMAP similar genes for ODF3 Gene using alignment to 4 proteins:

  • ODF3A_HUMAN
  • B7ZLT0_HUMAN
  • C3U2T1_HUMAN
  • F8W6Z3_HUMAN
genes like me logo Genes that share paralogs with ODF3: view

Variants for ODF3 Gene

Additional dbSNP identifiers (rs#s) for ODF3 Gene

Structural Variations from Database of Genomic Variants (DGV) for ODF3 Gene

Variant ID Type Subtype PubMed ID
dgv1010n100 CNV gain 25217958
dgv1011n100 CNV gain 25217958
dgv1012n100 CNV gain 25217958
dgv1505n54 CNV gain 21841781
esv22231 CNV gain 19812545
esv3625060 CNV gain 21293372
esv3625061 CNV gain 21293372
esv3625062 CNV loss 21293372
nsv1052484 CNV gain 25217958
nsv1110190 CNV duplication 24896259
nsv1124633 CNV duplication 24896259
nsv1148110 CNV duplication 26484159
nsv467630 CNV gain 19166990
nsv467631 CNV gain 19166990
nsv522596 CNV gain 19592680
nsv552760 CNV gain 21841781
nsv552762 CNV gain 21841781
nsv552765 CNV gain 21841781
nsv951267 CNV deletion 24416366

Variation tolerance for ODF3 Gene

Residual Variation Intolerance Score: 80.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.44; 64.01% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for ODF3 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
ODF3

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for ODF3 Gene

Disorders for ODF3 Gene

MalaCards: The human disease database

(7) MalaCards diseases for ODF3 Gene - From: DISEASES

Disorder Aliases PubMed IDs
salpingitis
chronic salpingitis
lymphogranuloma venereum
  • climatic or tropical bubo
granuloma inguinale
  • donovanosis
inflammatory spondylopathy
  • inflammatory spondylopathies in disease classified elsewhere
- elite association - COSMIC cancer census association via MalaCards
Search ODF3 in MalaCards View complete list of genes associated with diseases
genes like me logo Genes that share disorders with ODF3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for ODF3 Gene

Publications for ODF3 Gene

  1. Molecular cloning and characterization of a complementary DNA encoding sperm tail protein SHIPPO 1. (PMID: 11870087) Egydio de Carvalho C … Nishimune Y (Biology of reproduction 2002) 2 3 4 23
  2. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  3. A genome- and phenome-wide association study to identify genetic variants influencing platelet count and volume and their pleiotropic effects. (PMID: 24026423) Shameer K … Kullo IJ (Human genetics 2014) 3
  4. Identification of sperm head proteins involved in zona pellucida binding. (PMID: 23355646) Petit FM … Auer J (Human reproduction (Oxford, England) 2013) 3
  5. Expression of splice variants of cancer-testis genes ODF3 and ODF4 in the testis of a prostate cancer patient. (PMID: 23096689) Ghafouri-Fard S … Modarressi MH (Genetics and molecular research : GMR 2012) 3

Products for ODF3 Gene

Sources for ODF3 Gene