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Aliases for EDDM3B Gene

Aliases for EDDM3B Gene

  • Epididymal Protein 3B 2 3 5
  • Family With Sequence Similarity 12, Member B (Epididymal) 2 3
  • Human Epididymis-Specific Protein 3-Beta 3 4
  • HE3-BETA 3 4
  • FAM12B 3 4
  • HE3B 3 4
  • Epididymal Secretory Protein E3-Beta 3
  • Human Epididymis-Specific 3 Beta 3
  • Ribonuclease A M2 3
  • RAM2 3
  • EP3B 3

External Ids for EDDM3B Gene

Previous HGNC Symbols for EDDM3B Gene

  • FAM12B

Previous GeneCards Identifiers for EDDM3B Gene

  • GC14P021236
  • GC14P001357

Summaries for EDDM3B Gene

Entrez Gene Summary for EDDM3B Gene

  • Testicular sperm are morphologically differentiated but are not progressively motile nor able to fertilize an egg. Post-testicular maturation requires exposure of spermatozoa to the microenvironment of the epididymal lumen. Spermatozoa undergo extensive changes in the epididymis, including enzymatic modifications, loss of pre-existing components and addition of new glycoproteins from epididymal secretions. These modifying proteins and enzymes are synthesized by epithelial cells lining the epididymal duct and secreted apically into the lumen, where they come into contact with, and may be absorbed onto, the sperm membranes. The proteins encoded by the genes in this cluster are synthesized and secreted by epididymal epithelial cells. [provided by RefSeq, Jul 2008]

GeneCards Summary for EDDM3B Gene

EDDM3B (Epididymal Protein 3B) is a Protein Coding gene. An important paralog of this gene is EDDM3A.

UniProtKB/Swiss-Prot for EDDM3B Gene

  • Possible function in sperm maturation.

Additional gene information for EDDM3B Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EDDM3B Gene

Genomics for EDDM3B Gene

GeneHancer (GH) Regulatory Elements for EDDM3B Gene

Promoters and enhancers for EDDM3B 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
GH14I020767 Promoter/Enhancer 1 EPDnew ENCODE 550.8 0.0 -14 0.9 SMARCA5 NBN EBF1 BATF EDDM3B EDDM3A
GH14I020819 Enhancer 1.3 Ensembl ENCODE dbSUPER 11.8 +52.8 52764 2.6 HDAC1 ATF1 TAF9B ARNT NFRKB SIN3A CHAMP1 ZNF280A TCF12 CBX5 HNRNPC EDDM3B RNASE6 ENSG00000178107 SUPT16H CHD8 APEX1 GC14P020814 ENSG00000259130
GH14I020848 Enhancer 1.1 FANTOM5 Ensembl ENCODE 11.6 +80.6 80586 1.3 MEIS2 PKNOX1 FOXA2 SIN3A ZIC2 FOSL1 ZNF335 FOSL2 FOS SMARCE1 PNP EDDM3B PIP4P1 ARHGEF40 RNASE6 TEP1 ENSG00000259130 GC14P020814
GH14I020714 Enhancer 1.1 FANTOM5 Ensembl ENCODE 11.5 -53.0 -53021 2.5 CTCF NFIB FEZF1 ZEB2 ZIC2 OSR2 ZNF335 RBAK POLR2A GLIS1 EDDM3A RNASE6 ENSG00000258515 METTL3 SUPT16H METTL17 EDDM3B RNASE1 ANG ARHGEF40
GH14I020705 Enhancer 0.8 Ensembl ENCODE 11 -61.3 -61296 2.6 SMARCE1 SOX6 ZNF507 TEAD3 SREBF1 SP1 ZNF217 ZNF766 CTBP1 ENSG00000258451 EDDM3A ANG EDDM3B RNASE1 METTL17 ZNF219 TPPP2 ENSG00000255472 RNASE13
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around EDDM3B on UCSC Golden Path with GeneCards custom track

Genomic Locations for EDDM3B Gene

Genomic Locations for EDDM3B Gene
chr14:20,768,427-20,770,948
(GRCh38/hg38)
Size:
2,522 bases
Orientation:
Plus strand
chr14:21,236,586-21,239,107
(GRCh37/hg19)

Genomic View for EDDM3B Gene

Genes around EDDM3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EDDM3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EDDM3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EDDM3B Gene

Proteins for EDDM3B Gene

  • Protein details for EDDM3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P56851-EP3B_HUMAN
    Recommended name:
    Epididymal secretory protein E3-beta
    Protein Accession:
    P56851
    Secondary Accessions:
    • A0PK89

    Protein attributes for EDDM3B Gene

    Size:
    147 amino acids
    Molecular mass:
    17584 Da
    Quaternary structure:
    No Data Available

neXtProt entry for EDDM3B Gene

Post-translational modifications for EDDM3B Gene

No Post-translational modifications

Other Protein References for EDDM3B Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for EDDM3B Gene

Domains & Families for EDDM3B Gene

Gene Families for EDDM3B Gene

Human Protein Atlas (HPA):
  • Predicted secreted proteins

Protein Domains for EDDM3B Gene

Suggested Antigen Peptide Sequences for EDDM3B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with EDDM3B: view

No data available for UniProtKB/Swiss-Prot for EDDM3B Gene

Function for EDDM3B Gene

Molecular function for EDDM3B Gene

UniProtKB/Swiss-Prot Function:
Possible function in sperm maturation.

Gene Ontology (GO) - Molecular Function for EDDM3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003674 molecular_function ND --
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with EDDM3B: view
genes like me logo Genes that share phenotypes with EDDM3B: view

Animal Models for EDDM3B Gene

MGI Knock Outs for EDDM3B:

Animal Model Products

miRNA for EDDM3B Gene

miRTarBase miRNAs that target EDDM3B

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for EDDM3B Gene

Localization for EDDM3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for EDDM3B Gene

Secreted.

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 EDDM3B gene
Compartment Confidence
extracellular 5

Gene Ontology (GO) - Cellular Components for EDDM3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005576 extracellular region IEA --
genes like me logo Genes that share ontologies with EDDM3B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for EDDM3B Gene

Pathways & Interactions for EDDM3B Gene

SuperPathways for EDDM3B Gene

No Data Available

Interacting Proteins for EDDM3B Gene

Gene Ontology (GO) - Biological Process for EDDM3B Gene

None

No data available for Pathways by source and SIGNOR curated interactions for EDDM3B Gene

Drugs & Compounds for EDDM3B Gene

No Compound Related Data Available

Transcripts for EDDM3B Gene

mRNA/cDNA for EDDM3B Gene

(1) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(6) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for EDDM3B Gene

Epididymal protein 3B:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for EDDM3B Gene

No ASD Table

Relevant External Links for EDDM3B Gene

GeneLoc Exon Structure for
EDDM3B
ECgene alternative splicing isoforms for
EDDM3B

Expression for EDDM3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for EDDM3B Gene

NURSA nuclear receptor signaling pathways regulating expression of EDDM3B Gene:

EDDM3B

SOURCE GeneReport for Unigene cluster for EDDM3B Gene:

Hs.525202

mRNA Expression by UniProt/SwissProt for EDDM3B Gene:

P56851-EP3B_HUMAN
Tissue specificity: Epididymis.
genes like me logo Genes that share expression patterns with EDDM3B: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for EDDM3B Gene

Orthologs for EDDM3B Gene

This gene was present in the common ancestor of mammals.

Orthologs for EDDM3B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia EDDM3B 33 34
  • 99.32 (n)
cow
(Bos Taurus)
Mammalia LOC100297646 33
  • 70.78 (n)
rat
(Rattus norvegicus)
Mammalia Eddm3b 33
  • 70.24 (n)
dog
(Canis familiaris)
Mammalia EDDM3B 33
  • 70.19 (n)
-- 34
  • 51 (a)
OneToMany
mouse
(Mus musculus)
Mammalia Eddm3b 33 16 34
  • 69.95 (n)
oppossum
(Monodelphis domestica)
Mammalia -- 34
  • 39 (a)
OneToMany
Species where no ortholog for EDDM3B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • chicken (Gallus gallus)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for EDDM3B Gene

ENSEMBL:
Gene Tree for EDDM3B (if available)
TreeFam:
Gene Tree for EDDM3B (if available)

Paralogs for EDDM3B Gene

Paralogs for EDDM3B Gene

(1) SIMAP similar genes for EDDM3B Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for EDDM3B Gene

genes like me logo Genes that share paralogs with EDDM3B: view

Variants for EDDM3B Gene

Sequence variations from dbSNP and Humsavar for EDDM3B Gene

SNP ID Clin Chr 14 pos Variation AA Info Type
rs1000038268 -- 20,768,283(+) T/C upstream_transcript_variant
rs1000177132 -- 20,767,829(+) G/T upstream_transcript_variant
rs1000991790 -- 20,769,742(+) C/A/T intron_variant
rs1001042803 -- 20,769,459(+) A/G intron_variant
rs1002499488 -- 20,770,836(+) A/G 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for EDDM3B Gene

Variant ID Type Subtype PubMed ID
esv23438 CNV gain+loss 19812545
esv2759972 CNV gain+loss 17122850
nsv428293 CNV gain+loss 18775914

Variation tolerance for EDDM3B Gene

Residual Variation Intolerance Score: 52% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.13; 22.89% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EDDM3B Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
EDDM3B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EDDM3B Gene

Disorders for EDDM3B Gene

Additional Disease Information for EDDM3B

No disorders were found for EDDM3B Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for EDDM3B Gene

Publications for EDDM3B Gene

  1. Major human epididymis-specific gene product, HE3, is the first representative of a novel gene family. (PMID: 7514008) Kirchhoff C … Ivell R (Molecular reproduction and development 1994) 2 3 4 58
  2. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark HF … Gray A (Genome research 2003) 3 4 58
  3. Comparative genomic analysis of eutherian ribonuclease A genes. (PMID: 24337645) Premzl M (Molecular genetics and genomics : MGG 2014) 3 58
  4. A proteome-scale map of the human interactome network. (PMID: 25416956) Rolland T … Vidal M (Cell 2014) 3 58
  5. Toward a confocal subcellular atlas of the human proteome. (PMID: 18029348) Barbe L … Andersson-Svahn H (Molecular & cellular proteomics : MCP 2008) 3 58

Products for EDDM3B Gene

Sources for EDDM3B Gene

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