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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
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Genomic context

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See PTPDC1 in Genome Data Viewer
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

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