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    DPY19L3 dpy-19 like C-mannosyltransferase 3 [ Homo sapiens (human) ]

    Gene ID: 147991, updated on 14-Apr-2024

    Summary

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    Official Symbol
    DPY19L3provided by HGNC
    Official Full Name
    dpy-19 like C-mannosyltransferase 3provided by HGNC
    Primary source
    HGNC:HGNC:27120
    See related
    Ensembl:ENSG00000178904 MIM:613894; AllianceGenome:HGNC:27120
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to enable mannosyltransferase activity. Predicted to be involved in protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan. Predicted to be integral component of membrane. Predicted to be active in nuclear inner membrane. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in testis (RPKM 5.7), prostate (RPKM 5.6) and 25 other tissues See more
    Orthologs
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    Genomic context

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    Location:
    19q13.11
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (32405770..32485890)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (34924425..35004566)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (32896676..32976796)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904689 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:32845640-32845808 Neighboring gene Sharpr-MPRA regulatory region 4314 Neighboring gene zinc finger protein 507 Neighboring gene DPY19L3 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10480 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10481 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:32911836-32912044 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14429 Neighboring gene Sharpr-MPRA regulatory region 12835 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:33051335-33051521 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14430 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:33071921-33072097 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr19:33083895-33085094 Neighboring gene programmed cell death 5 Neighboring gene ankyrin repeat domain 27 Neighboring gene small nucleolar RNA, H/ACA box 68B

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Topological analysis of DPY19L3, a human C-mannosyltransferase. Niwa Y, et al. FEBS J, 2018 Mar. PMID 29405629
    2. Identification of DPY19L3 as the C-mannosyltransferase of R-spondin1 in human cells. Niwa Y, et al. Mol Biol Cell, 2016 Mar 1. PMID 26764097, Free PMC Article
    3. Genome-wide association study of bipolar disorder in European American and African American individuals. Smith EN, et al. Mol Psychiatry, 2009 Aug. PMID 19488044, Free PMC Article
    4. Global landscape of HIV-human protein complexes. Jäger S, et al. Nature, 2011 Dec 21. PMID 22190034, Free PMC Article
    5. Global mapping of herpesvirus-host protein complexes reveals a transcription strategy for late genes. Davis ZH, et al. Mol Cell, 2015 Jan 22. PMID 25544563, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DPY19L3 promotes vasculogenic mimicry by its C-mannosyltransferase activity.
      Title: DPY19L3 promotes vasculogenic mimicry by its C-mannosyltransferase activity.
    2. Data indicate that N-glycosylations of C-mannosyltransferase DPY19L3 (DPY19L3) do not have any roles for its enzymatic activity.
      Title: Topological analysis of DPY19L3, a human C-mannosyltransferase.
    3. DPY19L3 is the C-mannosyltransferase of Rspo1 at tryptophan(156).
      Title: Identification of DPY19L3 as the C-mannosyltransferase of R-spondin1 in human cells.
    4. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association study of bipolar disorder in European American and African American individuals.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Genome-wide association study of bipolar disorder in European American and African American individuals.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpr vpr HIV-1 Vpr is identified to have a physical interaction with dpy-19-like 3 (DPY19L3) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC35440, DKFZp686J17135

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables mannosyltransferase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mannosyltransferase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in protein C-linked glycosylation via 2'-alpha-mannosyl-L-tryptophan IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein glycosylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nuclear inner membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    protein C-mannosyl-transferase DPY19L3; probable C-mannosyltransferase DPY19L3
    Names
    dpy-19 like 3
    dpy-19-like 3
    dpy-19-like protein 3
    protein dpy-19 homolog 3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001172774.2 → NP_001166245.1  protein C-mannosyl-transferase DPY19L3

      See identical proteins and their annotated locations for NP_001166245.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) represents use of an alternate promoter and 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AK126757, AK129497, AL833713, DA852420
      Consensus CDS
      CCDS12422.1
      UniProtKB/Swiss-Prot
      Q68DC7, Q6ZPD9, Q6ZTB7, Q6ZTS2
      UniProtKB/TrEMBL
      K7ELH8
      Related
      ENSP00000376081.2, ENST00000392250.7
      Conserved Domains (1) summary
      pfam10034
      Location:56 → 712
      Dpy19; Q-cell neuroblast polarisation

    2. NM_207325.3 → NP_997208.2  protein C-mannosyl-transferase DPY19L3

      See identical proteins and their annotated locations for NP_997208.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AK126757, AL833713, BC131725, DR005952
      Consensus CDS
      CCDS12422.1
      UniProtKB/Swiss-Prot
      Q68DC7, Q6ZPD9, Q6ZTB7, Q6ZTS2
      UniProtKB/TrEMBL
      K7ELH8
      Related
      ENSP00000344937.4, ENST00000342179.9
      Conserved Domains (1) summary
      pfam10034
      Location:56 → 712
      Dpy19; Q-cell neuroblast polarisation

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      32405770..32485890
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047438247.1 → XP_047294203.1  probable C-mannosyltransferase DPY19L3 isoform X2

    2. XM_047438252.1 → XP_047294208.1  probable C-mannosyltransferase DPY19L3 isoform X4

    3. XM_047438249.1 → XP_047294205.1  probable C-mannosyltransferase DPY19L3 isoform X3

    4. XM_047438253.1 → XP_047294209.1  probable C-mannosyltransferase DPY19L3 isoform X6

    5. XM_017026366.1 → XP_016881855.1  probable C-mannosyltransferase DPY19L3 isoform X2

      UniProtKB/TrEMBL
      K7ELH8
      Conserved Domains (1) summary
      pfam10034
      Location:56 → 677
      Dpy19; Q-cell neuroblast polarisation

    6. XM_011526526.3 → XP_011524828.1  probable C-mannosyltransferase DPY19L3 isoform X1

      See identical proteins and their annotated locations for XP_011524828.1

      UniProtKB/Swiss-Prot
      Q68DC7, Q6ZPD9, Q6ZTB7, Q6ZTS2
      UniProtKB/TrEMBL
      K7ELH8
      Conserved Domains (1) summary
      pfam10034
      Location:56 → 712
      Dpy19; Q-cell neuroblast polarisation

    7. XM_047438248.1 → XP_047294204.1  probable C-mannosyltransferase DPY19L3 isoform X2

    8. XM_047438251.1 → XP_047294207.1  probable C-mannosyltransferase DPY19L3 isoform X3

    9. XM_047438250.1 → XP_047294206.1  probable C-mannosyltransferase DPY19L3 isoform X3

    10. XM_006723045.2 → XP_006723108.1  probable C-mannosyltransferase DPY19L3 isoform X5

      Conserved Domains (1) summary
      pfam10034
      Location:1 → 515
      Dpy19; Q-cell neuroblast polarization

    11. XM_017026367.3 → XP_016881856.1  probable C-mannosyltransferase DPY19L3 isoform X7

    RNA

    1. XR_007066627.1 RNA Sequence

    2. XR_007066628.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      34924425..35004566
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319954.1 → XP_054175929.1  probable C-mannosyltransferase DPY19L3 isoform X2

    2. XM_054319959.1 → XP_054175934.1  probable C-mannosyltransferase DPY19L3 isoform X4

    3. XM_054319961.1 → XP_054175936.1  probable C-mannosyltransferase DPY19L3 isoform X6

    4. XM_054319953.1 → XP_054175928.1  probable C-mannosyltransferase DPY19L3 isoform X1

      UniProtKB/Swiss-Prot
      Q68DC7, Q6ZPD9, Q6ZTB7, Q6ZTS2

    5. XM_054319956.1 → XP_054175931.1  probable C-mannosyltransferase DPY19L3 isoform X2

    6. XM_054319955.1 → XP_054175930.1  probable C-mannosyltransferase DPY19L3 isoform X2

    7. XM_054319958.1 → XP_054175933.1  probable C-mannosyltransferase DPY19L3 isoform X3

    8. XM_054319957.1 → XP_054175932.1  probable C-mannosyltransferase DPY19L3 isoform X3

    9. XM_054319960.1 → XP_054175935.1  probable C-mannosyltransferase DPY19L3 isoform X5

    10. XM_054319962.1 → XP_054175937.1  probable C-mannosyltransferase DPY19L3 isoform X7

    RNA

    1. XR_008485108.1 RNA Sequence

    2. XR_008485109.1 RNA Sequence

    3. XR_008485110.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6ZPD9.1 GenPept UniProtKB/Swiss-Prot:Q6ZPD9

    Gene LinkOut

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