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    CTDNEP1 CTD nuclear envelope phosphatase 1 [ Homo sapiens (human) ]

    Gene ID: 23399, updated on 28-Oct-2024

    Summary

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    Official Symbol
    CTDNEP1provided by HGNC
    Official Full Name
    CTD nuclear envelope phosphatase 1provided by HGNC
    Primary source
    HGNC:HGNC:19085
    See related
    Ensembl:ENSG00000175826 MIM:610684; AllianceGenome:HGNC:19085
    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
    Also known as
    NET56; DULLARD; HSA011916
    Summary
    Enables protein serine/threonine phosphatase activity. Involved in several processes, including positive regulation of triglyceride biosynthetic process; protein dephosphorylation; and protein localization to nucleus. Located in endoplasmic reticulum membrane; lipid droplet; and nuclear membrane. Part of Nem1-Spo7 phosphatase complex. [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in spleen (RPKM 30.6), appendix (RPKM 29.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CTDNEP1 in Genome Data Viewer
    Location:
    17p13.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (7243591..7251978, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (7144513..7152901, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (7146910..7155297, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7128275-7128774 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:7132793-7133992 Neighboring gene dishevelled segment polarity protein 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8089 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8090 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:7142377-7143026 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11605 Neighboring gene PHD finger protein 23 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:7144925-7145476 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:7145477-7146028 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8094 Neighboring gene GABA type A receptor-associated protein Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:7154656-7155243 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:7155244-7155832 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8097 Neighboring gene elongator acetyltransferase complex subunit 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11607 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8098 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:7164637-7165600 Neighboring gene Sharpr-MPRA regulatory region 7888 Neighboring gene claudin 7 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8100 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:7185283-7186270 Neighboring gene solute carrier family 2 member 4

    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 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. Dullard promotes degradation and dephosphorylation of BMP receptors and is required for neural induction. Satow R, et al. Dev Cell, 2006 Dec. PMID 17141153
    2. Determinants for dephosphorylation of the RNA polymerase II C-terminal domain by Scp1. Zhang Y, et al. Mol Cell, 2006 Dec 8. PMID 17157258, Free PMC Article
    3. Structure and mechanism of the human CTDNEP1-NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology. Gao S, et al. Proc Natl Acad Sci U S A, 2024 May 28. PMID 38776370,
    4. Homo sapiens dullard protein phosphatase shows a preference for the insulin-dependent phosphorylation site of lipin1. Wu R, et al. Biochemistry, 2011 Apr 19. PMID 21413788, Free PMC Article
    5. Molecular cloning and characterization of dullard: a novel gene required for neural development. Satow R, et al. Biochem Biophys Res Commun, 2002 Jul 5. PMID 12083771

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Structure and mechanism of the human CTDNEP1-NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology.
      Title: Structure and mechanism of the human CTDNEP1-NEP1R1 membrane protein phosphatase complex necessary to maintain ER membrane morphology.
    2. Loss of phosphatase CTDNEP1 potentiates aggressive medulloblastoma by triggering MYC amplification and genomic instability.
      Title: Loss of phosphatase CTDNEP1 potentiates aggressive medulloblastoma by triggering MYC amplification and genomic instability.
    3. Regulated lipid synthesis and LEM2/CHMP7 jointly control nuclear envelope closure.
      Title: Regulated lipid synthesis and LEM2/CHMP7 jointly control nuclear envelope closure.
    4. CTDNEP1 is upregulated in non-alcoholic fatty liver disease. Up-regulation of miR-122 can trigger the compensatory response of LPIN1 and CTDNEP1 in hepatosteatosis.
      Title: Two Triacylglycerol Pathway Genes, CTDNEP1 and LPIN1, are Down-Regulated by hsa-miR-122-5p in Hepatocytes.
    5. dullard shows specificity for the peptide corresponding to the insulin-dependent phosphorylation site (Ser106) of lipin
      Title: Homo sapiens dullard protein phosphatase shows a preference for the insulin-dependent phosphorylation site of lipin1.
    6. Dullard participates in a unique phosphatase cascade regulating nuclear membrane biogenesis, a cascade that is conserved from yeast to mammals.
      Title: A conserved phosphatase cascade that regulates nuclear membrane biogenesis.
    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

    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

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables myosin phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein serine/threonine phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein serine/threonine phosphatase activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables protein serine/threonine phosphatase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in canonical Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in gamete generation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mesoderm development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mitotic nuclear membrane disassembly TAS
    Traceable Author Statement
    more info
    		  
    involved_in nuclear envelope organization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of canonical Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of triglyceride biosynthetic process IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in protein dephosphorylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein localization to nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of Nem1-Spo7 phosphatase complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in endoplasmic reticulum membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lipid droplet IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nuclear envelope IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nuclear envelope TAS
    Traceable Author Statement
    more info
    		  
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    CTD nuclear envelope phosphatase 1
    Names
    C-terminal domain nuclear envelope phosphatase 1
    dullard homolog
    serine/threonine-protein phosphatase dullard
    NP_001137247.1
    NP_056158.2

    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_001143775.2 → NP_001137247.1  CTD nuclear envelope phosphatase 1

      See identical proteins and their annotated locations for NP_001137247.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC003688, AC120057, BC009295
      Consensus CDS
      CCDS11093.1
      UniProtKB/Swiss-Prot
      D3DTN7, O95476, Q96GQ9
      UniProtKB/TrEMBL
      I3L4B2
      Related
      ENSP00000460683.1, ENST00000574322.6
      Conserved Domains (1) summary
      TIGR02251
      Location:61 → 229
      HIF-SF_euk; Dullard-like phosphatase domain

    2. NM_015343.5 → NP_056158.2  CTD nuclear envelope phosphatase 1

      See identical proteins and their annotated locations for NP_056158.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript.
      Source sequence(s)
      AC003688, AC120057, BC009295
      Consensus CDS
      CCDS11093.1
      UniProtKB/Swiss-Prot
      D3DTN7, O95476, Q96GQ9
      UniProtKB/TrEMBL
      I3L4B2
      Related
      ENSP00000321732.6, ENST00000318988.10
      Conserved Domains (1) summary
      TIGR02251
      Location:61 → 229
      HIF-SF_euk; Dullard-like phosphatase domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      7243591..7251978 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_021160020.1 Reference GRCh38.p14 PATCHES

      Range
      1354..7306 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      7144513..7152901 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O95476.2 GenPept UniProtKB/Swiss-Prot:O95476

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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