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

EDDM3B Gene

protein-coding   GIFtS: 45
GCID: GC14P021236

Epididymal Protein 3B

(Previous names: family with sequence similarity 12, member B (epididymal))
(Previous symbol: FAM12B)
  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
Epididymal Protein 3B1 2     HE3-BETA2
FAM12B1 2 3 5     Epididymal Secretory Protein E3 Beta2
HE3B2 3 5     Epididymal Secretory Protein E3-Beta2
Family With Sequence Similarity 12, Member B (Epididymal)1 2     Human Epididymis-Specific 3 Beta2
Human Epididymis-Specific Protein 3-Beta2 3     HE3-beta3
EP3B2     

External Ids:    HGNC: 192231   Entrez Gene: 641842   Ensembl: ENSG000001815527   OMIM: 6115825   UniProtKB: P568513   

Export aliases for EDDM3B gene to outside databases

Previous GC identifer: GC14P001357


(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 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. Diseases associated with EDDM3B include epididymitis, and pancreatitis. GO annotations related to this gene include molecular_function. An important paralog of this gene is EDDM3A.

UniProtKB/Swiss-Prot: EP3B_HUMAN, P56851
Function: Possible function in sperm maturation




(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_000014.8  NC_018925.2  NT_026437.12  
Regulatory elements:
   Search SABiosciences Regulatory transcription factor binding sites for EDDM3B
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidEDDM3B promoter sequence
   Search SABiosciences Chromatin IP Primers for EDDM3B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat EDDM3B


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

Entrez Gene cytogenetic band: 14q11.2   Ensembl cytogenetic band:  14q11.2   HGNC cytogenetic band: 14q11.1

EDDM3B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
EDDM3B gene location

GeneLoc information about chromosome 14         GeneLoc Exon Structure

GeneLoc location for GC14P021236:  view genomic region     (about GC identifiers)

Start:
21,236,586 bp from pter      End:
21,239,107 bp from pter
Size:
2,522 bases      Orientation:
plus 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.,
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About This Section

UniProtKB/Swiss-Prot: EP3B_HUMAN, P56851 (See protein sequence)
Recommended Name: Epididymal secretory protein E3-beta precursor  
Size: 147 amino acids; 17584 Da
Subcellular location: Secreted (Potential)
Secondary accessions: A0PK89

Explore the universe of human proteins at neXtProt for EDDM3B: NX_P56851

Explore proteomics data for EDDM3B at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P56851

  • EDDM3B Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    EDDM3B Protein Expression
    REFSEQ proteins: NP_071755.1  
    ENSEMBL proteins: 
     ENSP00000314810  

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    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region NAS--

    EDDM3B 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:
     IPR023412 RNaseA_domain

    Graphical View of Domain Structure for InterPro Entry P56851

    ProtoNet protein and cluster: P56851

    1 Blocks protein domain: IPB001427 Pancreatic ribonuclease


    EDDM3B 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

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: EP3B_HUMAN, P56851
    Function: Possible function in sperm maturation

         Gene Ontology (GO): 1 molecular function term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
         
    EDDM3B for ontologies           About GeneDecksing


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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 EDDM3B

    Gene Ontology (GO): 1 biological process term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0007286spermatid development NAS--

    EDDM3B for ontologies           About GeneDecksing



    (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
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    Browse Tocris compounds for EDDM3B (EP3B)

    Search CenterWatch for drugs/clinical trials and news about EDDM3B / EP3B

    (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,
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    About This Section

    REFSEQ mRNAs for EDDM3B gene: 
    NM_022360.4  

    Unigene Cluster for EDDM3B:

    Epididymal protein 3B
    Hs.525202  [show with all ESTs]
    Unigene Representative Sequence: AY358865
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000326783(uc001vyd.3)
    miRNA
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    Additional mRNA sequence: 

    AY358865.1 BC128030.1 X76386.2 

    1 DOTS entry:

    DT.99986749 

    6 AceView cDNA sequences:

    NM_022360 AA621216 AI075915 AY358865 BX112699 X76386 

    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

    EDDM3B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTACAAAATC
    EDDM3B Expression
    About this image


    See EDDM3B Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for EDDM3B

    SOURCE GeneReport for Unigene cluster: Hs.525202

    UniProtKB/Swiss-Prot: EP3B_HUMAN, P56851
    Tissue specificity: Epididymis

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for EDDM3B

    (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 EDDM3B gene from 1/6 species (see all 6)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Eddm3b1 , 5 epididymal protein 3B1, 5 70.19(n)1
    57.75(a)1
      14 (26.38 cM)5
    2190261  NM_203508.11  NP_987104.11 
     511145655 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for EDDM3B gene
    EDDM3A2  
    1 SIMAP similar gene for EDDM3B using alignment to 1 protein entry:     EP3B_HUMAN:
    EDDM3A

    EDDM3B for paralogs           About GeneDecksing


    2 Pseudogenes.org Pseudogenes for EDDM3B
    PGOHUM00000240352 PGOHUM00000249760


    (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

    10/149 SNPs in EDDM3B are shown (see all 149)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 14 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1146342491,2
    F--21234669(+) ACATTC/GAAGTA 1 -- us2k11Minor allele frequency- G:0.02WA 118
    rs1881812781,2
    --21234683(+) TACATC/TATCCA 1 -- us2k10--------
    rs7620381,2
    C,F,O,H--21234768(+) ACGTGG/CTGGAA 1 -- us2k1 tfbs339Minor allele frequency- C:0.15MN NS EA NA WA CSA 3528
    rs1442135831,2
    C--21234779(+) ATTCCA/GGATGT 1 -- us2k10--------
    rs28739801,2
    C,F,O,H--21234794(+) TGGAAA/GGGTCA 1 -- us2k112Minor allele frequency- G:0.07NA NS EA WA 806
    rs1932605121,2
    --21234829(+) AGTTTA/GAGGGC 1 -- us2k10--------
    rs7620391,2
    C,F,A,H--21234851(+) ACCAGA/CGTGAG 1 -- us2k120Minor allele frequency- C:0.31MN NS EA NA WA 2528
    rs20090211,2
    C,F,O,A,H--21234998(+) GTAAGG/CACTAC 1 -- us2k1 tfbs334Minor allele frequency- C:0.44MN NS EA NA WA CSA 3366
    rs783206281,2
    F--21235007(+) ACAGCG/ATCAGC 1 -- us2k11Minor allele frequency- A:0.02EA 120
    rs1847649741,2
    --21235021(+) GGTTAC/TTGTTA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for EDDM3B (21236586 - 21239107 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for EDDM3B:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv901470CNV Gain21882294
    nsv428293CNV Gain+Loss18775914
    esv23438CNV Gain+Loss19812545
    dgv607e1CNV 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: 611582    OMIM disorders: --

    2 diseases for EDDM3B:    About MalaCards
    epididymitis    pancreatitis


    EDDM3B for disorders           About GeneDecksing


    Export disorders for EDDM3B 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 EDDM3B gene integrated from 9 sources:
    (articles sorted by number of sources associating them with EDDM3B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Major human epididymis-specific gene product, HE3, is the first representative of a novel gene family. (PubMed id 7514008)1, 2, 3 Kirchhoff C.... Ivell R. (1994)
    2. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PubMed id 12975309)1, 2 Clark H.F.... Gray A.M. (2003)
    3. Toward a confocal subcellular atlas of the human proteome. (PubMed id 18029348)1 Barbe L....Andersson-Svahn H. (2008)
    4. 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)
    5. 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)
    6. Human epididymal proteins and sperm function during fertilization: un update. (PubMed id 11715855)1 Lasserre A....Vazquez-Levin M.H. (2001)
    7. Molecular characterization of epididymal proteins. (PubMed id 9685187)1 Kirchhoff C. (1998)
    8. Function of human epididymal proteins in sperm maturation. (PubMed id 9739419)1 Kirchhoff C....Schroter S. (1998)
    9. Alterations in gene expression in the caput epididymides of nonobstructive azoospermic men. (PubMed id 17928628)9 Dube E....Cyr D.G. (2008)

    (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: 64184 HGNC: 19223 AceView: FAM12B Ensembl:ENSG00000181552 euGenes: HUgn64184
    ECgene: EDDM3B H-InvDB: EDDM3B

    (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 EDDM3B Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for EDDM3B gene:
    Search GeneIP for patents involving EDDM3B

    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: 4 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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