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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

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