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ODF3B Gene

protein-coding   GIFtS: 42
GCID: GC22M050968

Outer Dense Fiber Of Sperm Tails 3B

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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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Aliases
Outer Dense Fiber Of Sperm Tails 3B1 2
Outer Dense Fiber Protein 3-Like Protein 32 3
ODF3L32 3
Orf2 5' To PD-ECGF/TP2
Outer Dense Fiber Protein 3B2

External Ids:    HGNC: 343881   Entrez Gene: 4408362   Ensembl: ENSG000001779897   UniProtKB: A8MYP83   

Export aliases for ODF3B gene to outside databases

Previous GC identifers: GC22M049317 GC22M033859


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for ODF3B Gene:
ODF3B (outer dense fiber of sperm tails 3B) is a protein-coding gene. An important paralog of this gene is ODF3.


(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_000022.10  NT_011526.8  NC_018933.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the ODF3B gene promoter:
         Sp1   HTF   MIF-1   Pax-4a   Arnt   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for ODF3B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ODF3B


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

Entrez Gene cytogenetic band: 22q13.33   Ensembl cytogenetic band:  22q13.33   HGNC cytogenetic band: 22q13.33

ODF3B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ODF3B gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22M050968:  view genomic region     (about GC identifiers)

Start:
50,968,139 bp from pter      End:
50,971,009 bp from pter
Size:
2,871 bases      Orientation:
minus 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: ODF3B_HUMAN, A8MYP8 (See protein sequence)
Recommended Name: Outer dense fiber protein 3B  
Size: 253 amino acids; 27280 Da
Secondary accessions: A0PK18
Alternative splicing: 2 isoforms:  A8MYP8-1   A8MYP8-2   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for ODF3B: NX_A8MYP8

Explore proteomics data for ODF3B at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ODF3B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001014440.2  
    ENSEMBL proteins: 
     ENSP00000384310   ENSP00000385123   ENSP00000384012   ENSP00000390712   ENSP00000393668  
     ENSP00000382804  

    ODF3B Human Recombinant Protein Products:

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    Cloud-Clone Corp. Proteins for ODF3B

     
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    antibodies-online proteins for ODF3B (3 products) 

     
    antibodies-online peptides for ODF3B

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    antibodies-online antibodies for ODF3B (20 products) 

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    Cloud-Clone Corp. CLIAs for ODF3B
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    antibodies-online kits for ODF3B (4 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 A8MYP8

    ProtoNet protein and cluster: A8MYP8

    UniProtKB/Swiss-Prot: ODF3B_HUMAN, A8MYP8
    Similarity: Belongs to the ODF3 family
    Similarity: Contains 1 STPGR (Sperm-tail PG-rich) repeat


    Find genes that share domains with ODF3B           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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    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for ODF3B

    miRNA
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    miRTarBase miRNAs that target ODF3B:
    hsa-mir-335-5p (MIRT018217)

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    (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 COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2
    mitochondrion1

    (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 ODF3B
    Interactions:

        Search GeneGlobe Interaction Network for ODF3B

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

    Selected Interacting proteins for ODF3B (ENSP000003828044) 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

    (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 ODF3B



    (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 ODF3B gene: 
    NM_001014440.3  

    Unigene Cluster for ODF3B:

    Outer dense fiber of sperm tails 3B
    Hs.531314  [show with all ESTs]
    Unigene Representative Sequence: S72487
    9 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000468249 ENST00000401779(uc003bmg.2) ENST00000403326 ENST00000405135
    ENST00000428989 ENST00000463472 ENST00000469660 ENST00000437588 ENST00000329363(uc003bmh.2)

    miRNA
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat ODF3B
    Primer
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      QuantiTect SYBR Green Assays in human, mouse, rat ODF3B
      QuantiFast Probe-based Assays in human, mouse, rat ODF3B

    Additional mRNA sequence: 

    BC127934.1 BC127935.1 S72487.1 

    12 DOTS entries:

    DT.92455500  DT.446158  DT.100879983  DT.95259846  DT.85105232  DT.97834969  DT.120637975  DT.86857045 
    DT.120638065  DT.92326825  DT.100879980  DT.40198457 

    Selected AceView cDNA sequences (see all 481):

    CA308094 CA306381 BF514999 BM127080 CR604852 CR619786 BM727471 BE857125 
    BQ225451 CB216979 BM127130 CR608324 BG120390 BX348084 AI268720 AI151089 
    BE502258 CB851017 BI962661 BU734727 AW014906 BQ447931 AI765458 BF436372 

    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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    ODF3B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: ACCGTGCGCG
    ODF3B Expression
    About this image

    ODF3B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ODF3B Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.531314
        Custom PCR Arrays for ODF3B
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for ODF3B

    (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 ODF3B gene from Selected species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Odf3b1 , 5 outer dense fiber of sperm tails 3B1, 5 78.68(n)1
    73.82(a)1
      15 (44.86 cM)5
    701131  NM_001013022.11  NP_001013040.11 
     893774505 
    lizard
    (Anolis carolinensis)
    Reptilia ODF3B6
    outer dense fiber of sperm tails 3B
    54(a)
    1 ↔ 1
    GL343682.1(129620-132646)
    zebrafish
    (Danio rerio)
    Actinopterygii odf3b6
    outer dense fiber of sperm tails 3B
    51(a)
    1 ↔ 1
    18(7074673-7083233) ENSDARG00000042391
    fruit fly
    (Drosophila melanogaster)
    Insecta CG80866
    --
    4(a)
    many ↔ many
    2L(8244160-8257502)


    ENSEMBL Gene Tree for ODF3B (if available)
    TreeFam Gene Tree for ODF3B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ODF3B gene
    ODF32  ODF3L22  ODF3L12  
    4 SIMAP similar genes for ODF3B using alignment to 6 protein entries:     ODF3B_HUMAN (see all proteins):
    orf2 5' to PD-ECGF/TP    ODF3    ODF3L2    orf3 5' of PD-ECGF/TP

    Find genes that share paralogs with ODF3B           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 ODF3B (see all 66)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 22 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs121698891,2
    C,F--50970516(+) CGGGTG/AGGGGG 1 -- ut511Minor allele frequency- A:0.14WA 118
    rs1171883001,2
    F--50970714(+) GAGCGG/TATCCA 1 -- int11Minor allele frequency- T:0.03NA 120
    rs72927351,2
    C,F--50970803(+) AGGGAA/GTCACC 1 -- int12Minor allele frequency- G:0.30CSA WA 120
    rs1393547141,2
    --50970808(+) ATCACC/TTGGGG 1 -- int10--------
    rs1819735881,2
    --50970937(+) AAACAA/GAGCGA 1 -- ut510--------
    rs747951691,2
    C,F--50970996(+) GTGGCC/TCTTTC 1 -- ut512Minor allele frequency- T:0.11CSA WA 120
    rs762847751,2
    F--50971037(+) CCCCCC/TCAACC 1 -- us2k11Minor allele frequency- T:0.01WA 118
    rs3617251,2
    C,F,A--50971047(-) GGCGGA/GCCCAG 1 -- us2k15Minor allele frequency- G:0.43NA WA 244
    rs1873333591,2
    --50971197(+) AATCTA/GCAGAC 1 -- us2k10--------
    rs1432759931,2
    --50971204(+) AGACAA/GAAGCA 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for ODF3B (50968139 - 50971009 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for ODF3B (see all 16):    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv915495CNV Loss21882294
    dgv5065n71CNV Loss21882294
    nsv834238CNV Loss17160897
    dgv5064n71CNV Loss21882294
    nsv834239CNV Loss17160897
    dgv5066n71CNV Loss21882294
    nsv471224CNV Loss18288195
    dgv5067n71CNV Loss21882294
    nsv914556CNV Loss21882294
    dgv5062n71CNV Loss21882294

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing ODF3B
    DNA2.0 Custom Variant and Variant Library Synthesis for ODF3B

    (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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    Find genes that share disorders with ODF3B           About GenesLikeMe

    Genetic Association Database (GAD): ODF3B
    Human Genome Epidemiology (HuGE) Navigator: ODF3B (3 documents)

    Export disorders for ODF3B 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 ODF3B gene, integrated from 10 sources (see all 12):
    (articles sorted by number of sources associating them with ODF3B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. (PubMed id 21833088)1, 4  ....Compston A. (Nature 2011)
    2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PubMed id 20628086)1, 4 Bailey S.D....Anand S. (Diabetes Care 2010)
    3. Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. (PubMed id 19862010)1, 4 Ganesh S.K....Lin J.P. (Nat. Genet. 2009)
    4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    5. The DNA sequence of human chromosome 22. (PubMed id 10591208)1, 2 Dunham I.... Wright H. (Nature 1999)
    6. Seventy-five genetic loci influencing the human red blood cell. (PubMed id 23222517)1 van der Harst P....Chambers J.C. (Nature 2012)
    7. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. (PubMed id 23251661)1 Comuzzie A.G....Butte N.F. (PLoS ONE 2012)
    8. Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip. (PubMed id 19913121)1 Talmud P.J.... . (Am. J. Hum. Genet. 2009)
    9. Expressed sequence tag analysis of adult human lens for the NEIBank project: over 2000 non-redundant transcripts, novel genes and splice variants. (PubMed id 12107413)1 Wistow G.... Peterson K. (Mol. Vis. 2002)
    10. 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: 440836 HGNC: 34388 AceView: ECGF1andSCO2andLOC440836 Ensembl:ENSG00000177989 euGenes: HUgn440836
    ECgene: ODF3B H-InvDB: ODF3B

    (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 ODF3B 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 ODF3B gene:
    Search GeneIP for patents involving ODF3B

    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, 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
    Advanced Cell Diagnostics, Animal models from genOway)
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