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DYDC1 Gene

protein-coding   GIFtS: 49
GCID: GC10M082086

DPY30 Domain Containing 1

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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
DPY30 Domain Containing 11 2
DPY30D12 3
DPY30 Domain-Containing Protein 12

External Ids:    HGNC: 234601   Entrez Gene: 1432412   Ensembl: ENSG000001707887   OMIM: 6151545   UniProtKB: Q8WWB33   

Export aliases for DYDC1 gene to outside databases

Previous GC identifers: GC10U900476 GC10M075939


(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 DYDC1 Gene:
This gene encodes a member of a family of proteins that contains a DPY30 domain. The encoded protein is involved
in acrosome formation during spermatid development. This gene locus overlaps with a closely related gene on the
opposite strand. Alternative splicing results in multiple transcript variants. (provided by RefSeq, Jun 2012)

GeneCards Summary for DYDC1 Gene:
DYDC1 (DPY30 domain containing 1) is a protein-coding gene. An important paralog of this gene is DYDC2.

UniProtKB/Swiss-Prot: DYDC1_HUMAN, Q8WWB3
Function: Plays a crucial role during acrosome biogenesis




(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_000010.10  NT_030059.14  NC_018921.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the DYDC1 gene promoter:
         Nkx5-1   E47   NF-AT   NF-AT4   NF-AT2   HFH-1   NF-AT3   Hand1   Chx10   NF-AT1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidDYDC1 promoter sequence
   Search Chromatin IP Primers for DYDC1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DYDC1


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

Entrez Gene cytogenetic band: 10q23.1   Ensembl cytogenetic band:  10q23.1   HGNC cytogenetic band: 10q22.3

DYDC1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DYDC1 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10M082086:  view genomic region     (about GC identifiers)

Start:
82,095,861 bp from pter      End:
82,116,511 bp from pter
Size:
20,651 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: DYDC1_HUMAN, Q8WWB3 (See protein sequence)
Recommended Name: DPY30 domain-containing protein 1  
Size: 177 amino acids; 20893 Da
Subunit: Interacts with SH3GL3
Caution: Sequence AAQ84766 was incorrectly indicated as originating from mouse
Sequence caution: Sequence=BAC86339.1; Type=Miscellaneous discrepancy; Note=Intron retention;
Secondary accessions: Q5QP03 Q5QP04 Q6WNP4 Q6ZU87

Explore the universe of human proteins at neXtProt for DYDC1: NX_Q8WWB3

Explore proteomics data for DYDC1 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See DYDC1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_001255982.1  NP_620167.1  

    ENSEMBL proteins: 
     ENSP00000361278   ENSP00000361276   ENSP00000414798   ENSP00000388160   ENSP00000402890  

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    (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:
     IPR007858 Dpy-30_motif

    Graphical View of Domain Structure for InterPro Entry Q8WWB3

    ProtoNet protein and cluster: Q8WWB3

    UniProtKB/Swiss-Prot: DYDC1_HUMAN, Q8WWB3
    Similarity: Belongs to the dpy-30 family


    Find genes that share domains with DYDC1           About GenesLikeMe


    (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,
    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: DYDC1_HUMAN, Q8WWB3
    Function: Plays a crucial role during acrosome biogenesis

    Animal Models:

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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
    cytosol2
    nucleus2
    cytoskeleton1

    (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 DYDC1
    Interactions:

        Search GeneGlobe Interaction Network for DYDC1

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    4 Interacting proteins for DYDC1 (Q8WWB32, 3 ENSP000003612764) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MID2Q9UJV32, 3, ENSP000002628434MINT-68349 I2D: score=4 STRING: ENSP00000262843
    NME5P565972, 3, ENSP000002651914MINT-66095 I2D: score=4 STRING: ENSP00000265191
    DPY30Q9C0052, 3, ENSP000002950664MINT-67906 I2D: score=4 STRING: ENSP00000295066
    USHBP1Q8N6Y03, ENSP000002525974I2D: score=3 STRING: ENSP00000252597
    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 Tocris compounds for DYDC1



    (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 DYDC1 gene (2 alternative transcripts): 
    NM_001269053.1  NM_138812.3  

    Unigene Cluster for DYDC1:

    DPY30 domain containing 1
    Hs.407751  [show with all ESTs]
    Unigene Representative Sequence: AK125908
    5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000372204(uc001kbx.3) ENST00000372202 ENST00000454362 ENST00000453477
    ENST00000421924(uc001kby.1 uc009xsr.1)
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      QuantiFast Probe-based Assays in human, mouse, rat DYDC1

    Additional mRNA sequence: 

    AK125908.1 AK292542.1 BC019250.1 

    4 DOTS entries:

    DT.97808345  DT.40127509  DT.100740807  DT.95363590 

    11 AceView cDNA sequences:

    BI829226 AL040530 BC019250 BI546816 BG718556 BI559804 AK125908 BX102394 
    AA906283 NM_138812 BI828082 

    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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    DYDC1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GAACAACTGA
    DYDC1 Expression
    About this image

    DYDC1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    DYDC1 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.407751

    UniProtKB/Swiss-Prot: DYDC1_HUMAN, Q8WWB3
    Tissue specificity: Brain and testis. Accumulates during late stage of spermiogenesis

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    In Situ
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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 chordates.

    Orthologs for DYDC1 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Dydc11 , 5 DPY30 domain containing 11, 5 73.53(n)1
    68.82(a)1
      14 (22.36 cM)5
    694961  NM_027094.11  NP_081370.11 
     410729115 
    chicken
    (Gallus gallus)
    Aves DYDC11 DPY30 domain containing 1 57.56(n)
    51.33(a)
      423627  NM_001199517.1  NP_001186446.1 
    lizard
    (Anolis carolinensis)
    Reptilia DYDC16
    DPY30 domain containing 1
    43(a)
    1 ↔ 1
    GL343233.1(1771379-1791521)
    tropical clawed frog
    (Xenopus tropicalis)
    Amphibia dydc21 DPY30 domain containing 2 58.95(n)
    52.89(a)
      100496524  XM_002933899.2  XP_002933945.2 
    zebrafish
    (Danio rerio)
    Actinopterygii DYDC26
    DPY30 domain containing 2
    20(a)
    1 → many
    12(49041230-49046526) ENSDARG00000091663


    ENSEMBL Gene Tree for DYDC1 (if available)
    TreeFam Gene Tree for DYDC1 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for DYDC1 gene
    DYDC22  
    1 SIMAP similar gene for DYDC1 using alignment to 2 protein entries:     DYDC1_HUMAN (see all proteins):
    DYDC2

    Find genes that share paralogs with DYDC1           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 DYDC1 (see all 151)    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1871772631,2
    --82095404(+) CAGTGA/GTTCTC 2 -- ds50010--------
    rs751880241,2
    C--82095456(+) ACCAC-/GGCCCG 2 -- ds50010--------
    rs350541301,2
    C,F--82095457(+) ACCAC-/GCCCGG 2 -- ds50013Minor allele frequency- G:0.25NA CSA 8
    rs1914806231,2
    --82095518(+) ACACTA/GGTCTC 2 -- ds50010--------
    rs728153211,2
    C,F--82095804(+) AGAGGA/GAAAAA 2 -- ds50011Minor allele frequency- G:0.03NA 120
    rs1454239451,2
    C--82095885(+) AAAAAC/TATTTA 2 -- ut310--------
    rs13403831,2
    C,F,O,A,H--82095968(-) TAAGGC/AATATT 2 -- int126Minor allele frequency- A:0.21MN NS EA WA NA CSA EU 3736
    rs1845020791,2
    --82096053(+) AAACTC/TTTTGG 2 -- int10--------
    rs1426559941,2
    --82096080(+) CAAATA/GATACT 2 -- int10--------
    rs1468955521,2
    --82096135(+) TTCCAC/TCCTTT 2 -- int10--------

    HapMap Linkage Disequilibrium report for DYDC1 (82095861 - 82116511 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for DYDC1:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv831923CNV Loss17160897
    nsv520763CNV Gain19592680

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing DYDC1
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    (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: 615154    OMIM disorders: --


    Find genes that share disorders with DYDC1           About GenesLikeMe

    Genetic Association Database (GAD): DYDC1
    Human Genome Epidemiology (HuGE) Navigator: DYDC1 (1 document)

    Export disorders for DYDC1 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 DYDC1 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with DYDC1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Interaction of SH3P13 and DYDC1 protein: a germ cell component that regulates acrosome biogenesis during spermiogenesis. (PubMed id 19545932)1, 2 Li S.... Wang L. (Eur. J. Cell Biol. 2009)
    2. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PubMed id 16385451)1, 4 Grupe A....Goate A. (Am. J. Hum. Genet. 2006)
    3. 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)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    5. The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)1, 2 Deloukas P.... Rogers J. (Nature 2004)
    6. Myofibrillar myopathy with arrhythmogenic right ventricular cardiomyopathy 7: corroboration and narrowing of the critical region on 10q22.3. (PubMed id 18197198)1 Kuhl A....Jenne D.E. (Eur. J. Hum. Genet. 2008)
    7. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (Nature 2005)
    8. 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)
    9. (PubMed id )2 

    (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: 143241 HGNC: 23460 AceView: LOC143241 Ensembl:ENSG00000170788 euGenes: HUgn143241
    ECgene: DYDC1 H-InvDB: DYDC1

    (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 DYDC1 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 DYDC1 gene:
    Search GeneIP for patents involving DYDC1

    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, LSBio, eBioscience, 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 inGenious Targeting Laboratory, genOway)
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