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    PTPDC1 protein tyrosine phosphatase domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 138639, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PTPDC1provided by HGNC
    Official Full Name
    protein tyrosine phosphatase domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:30184
    See related
    Ensembl:ENSG00000158079 AllianceGenome:HGNC:30184
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PTP9Q22
    Summary
    The protein encoded by this gene contains a characteristic motif of protein tyrosine phosphatases (PTPs). PTPs regulate activities of phosphoproteins through dephosphorylation. They are signaling molecules involved in the regulation of a wide variety of biological processes. The specific function of this protein has not yet been determined. Alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in testis (RPKM 3.6), adrenal (RPKM 2.2) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    9q22.32
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (94030813..94109856)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (106198554..106277594)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (96793095..96872138)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96715091-96715655 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96715656-96716219 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96717631-96718162 Neighboring gene uncharacterized LOC124902216 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96718163-96718693 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110021 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96730989-96731521 Neighboring gene BARX1 divergent transcript Neighboring gene BARX homeobox 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:96741809-96742308 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:96748340-96749539 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:96767229-96768428 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28627 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20051 Neighboring gene CYCS pseudogene 24 Neighboring gene Sharpr-MPRA regulatory region 768 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:96856496-96857248 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:96880956-96881652 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110048 Neighboring gene tripartite motif-containing protein 54-like Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110072 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_110085 Neighboring gene PTPDC1-MIRLET7DHG intergenic CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20053 Neighboring gene miRlet-7a-1/let-7f-1/let-7d cluster host gene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20054 Neighboring gene microRNA let-7a-1

    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. A genome-wide association study identifies new susceptibility loci for esophageal adenocarcinoma and Barrett's esophagus. Levine DM, et al. Nat Genet, 2013 Dec. PMID 24121790, Free PMC Article
    2. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Lango Allen H, et al. Nature, 2010 Oct 14. PMID 20881960, Free PMC Article
    3. A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome. Yao Z, et al. Mol Cell, 2017 Jan 19. PMID 28065597, Free PMC Article
    4. Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism. Antoniali G, et al. Nat Commun, 2017 Oct 6. PMID 28986522, Free PMC Article
    5. Defining the Protein-Protein Interaction Network of the Human Protein Tyrosine Phosphatase Family. Li X, et al. Mol Cell Proteomics, 2016 Sep. PMID 27432908, Free PMC Article

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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
    A genome-wide association study identifies new susceptibility loci for esophageal adenocarcinoma and Barrett's esophagus.
    EBI GWAS Catalog
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ42922

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein tyrosine phosphatase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein tyrosine/serine/threonine phosphatase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cilium assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in dephosphorylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    protein tyrosine phosphatase domain-containing protein 1
    Names
    protein tyrosine phosphatase PTP9Q22
    NP_001240758.1
    NP_001240759.1
    NP_689635.3
    NP_818931.1

    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_001253829.2 → NP_001240758.1  protein tyrosine phosphatase domain-containing protein 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (3) is longer than isoform 1.
      Source sequence(s)
      AK289692, AW052114, BC067120, DA218576, DA312531
      Consensus CDS
      CCDS75860.1
      UniProtKB/TrEMBL
      A0A087WTF0, A8K0X7
      Related
      ENSP00000477817.1, ENST00000620992.5
      Conserved Domains (1) summary
      smart00404
      Location:208 → 289
      PTPc_motif; Protein tyrosine phosphatase, catalytic domain motif

    2. NM_001253830.2 → NP_001240759.1  protein tyrosine phosphatase domain-containing protein 1 isoform 4

      See identical proteins and their annotated locations for NP_001240759.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, uses an alternate splice site in the coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (4) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK094631, AW052114, BC051654, BC067120
      UniProtKB/TrEMBL
      A8K0X7
      Conserved Domains (1) summary
      smart00404
      Location:154 → 235
      PTPc_motif; Protein tyrosine phosphatase, catalytic domain motif

    3. NM_152422.4 → NP_689635.3  protein tyrosine phosphatase domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_689635.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform (1).
      Source sequence(s)
      AK094631, AK124912, AW052114, BC031279, BC067120, DA218576
      Consensus CDS
      CCDS6708.1
      UniProtKB/TrEMBL
      A8K0X7
      Related
      ENSP00000288976.3, ENST00000288976.3
      Conserved Domains (1) summary
      smart00404
      Location:206 → 287
      PTPc_motif; Protein tyrosine phosphatase, catalytic domain motif

    4. NM_177995.3 → NP_818931.1  protein tyrosine phosphatase domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_818931.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK094631, AW052114, BC067120
      Consensus CDS
      CCDS6707.1
      UniProtKB/Swiss-Prot
      A2A3K4, Q5T3M4, Q6NXE8, Q8IWM1, Q8N1X4, Q8N9F5
      UniProtKB/TrEMBL
      A8K0X7
      Related
      ENSP00000364509.3, ENST00000375360.7
      Conserved Domains (1) summary
      smart00404
      Location:154 → 235
      PTPc_motif; Protein tyrosine phosphatase, catalytic domain motif

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      94030813..94109856
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      106198554..106277594
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2A3K4.1 GenPept UniProtKB/Swiss-Prot:A2A3K4

    Gene LinkOut

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

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