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    PTP4A1 protein tyrosine phosphatase 4A1 [ Homo sapiens (human) ]

    Gene ID: 7803, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PTP4A1provided by HGNC
    Official Full Name
    protein tyrosine phosphatase 4A1provided by HGNC
    Primary source
    HGNC:HGNC:9634
    See related
    Ensembl:ENSG00000112245 MIM:601585; AllianceGenome:HGNC:9634
    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
    HH72; PRL1; PRL-1; PTPCAAX1; PTP(CAAX1)
    Summary
    This gene encodes a member of a small class of prenylated protein tyrosine phosphatases (PTPs), which contain a PTP domain and a characteristic C-terminal prenylation motif. The encoded protein is a cell signaling molecule that plays regulatory roles in a variety of cellular processes, including cell proliferation and migration. The protein may also be involved in cancer development and metastasis. This tyrosine phosphatase is a nuclear protein, but may associate with plasma membrane by means of its prenylation motif. Pseudogenes related to this gene are located on chromosomes 1, 2, 5, 7, 11 and X. [provided by RefSeq, Jun 2013]
    Expression
    Broad expression in liver (RPKM 141.5), adrenal (RPKM 72.5) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PTP4A1 in Genome Data Viewer
    Location:
    6q12
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (63516440..63583588)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (64662355..64729529)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (64226345..64293493)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene HNF1 motif-containing MPRA enhancer 15 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24717 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24718 Neighboring gene leucine rich repeat containing 59 pseudogene Neighboring gene lengsin, lens protein with glutamine synthetase domain Neighboring gene translation initiation factor IF-2-like Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64282845-64283580 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64283581-64284316 Neighboring gene uncharacterized LOC128125822 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64282109-64282844 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64281371-64282108 Neighboring gene Sharpr-MPRA regulatory region 1413 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24720 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24721 Neighboring gene eukaryotic translation elongation factor 1 beta 2 pseudogene 5 Neighboring gene NANOG hESC enhancer GRCh37_chr6:64344395-64344932 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:64345464-64346284 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17311 Neighboring gene ribosomal protein L7a pseudogene 34 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24722 Neighboring gene ribosomal protein L9 pseudogene 18 Neighboring gene PHD finger protein 3 Neighboring gene eyes shut homolog

    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. Potential effects of tetrodotoxin exposure to human glial cells postulated using microarray approach. Raghavendra Prasad HS, et al. Toxicon, 2004 Nov. PMID 15501285
    2. Phosphatase of regenerating liver maintains cellular magnesium homeostasis. Yoshida A, et al. Biochem J, 2018 Mar 26. PMID 29487165
    3. Phosphatase of Regenerating Liver-1 (PRL-1) Regulates Actin Dynamics During Immunological Synapse Assembly and T Cell Effector Function. Castro-Sánchez P, et al. Front Immunol, 2018. PMID 30515156, Free PMC Article
    4. PRL PTPs: mediators and markers of cancer progression. Bessette DC, et al. Cancer Metastasis Rev, 2008 Jun. PMID 18224294
    5. Phosphatase activity, trimerization, and the C-terminal polybasic region are all required for PRL1-mediated cell growth and migration. Sun JP, et al. J Biol Chem, 2007 Sep 28. PMID 17656357

    See all (89) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Endothelial PTP4A1 mitigates vascular inflammation via USF1/A20 axis-mediated NF-kappaB inactivation.
      Title: Endothelial PTP4A1 mitigates vascular inflammation via USF1/A20 axis-mediated NF-κB inactivation.
    2. GINS2 regulates the proliferation and apoptosis of colon cancer cells through PTP4A1.
      Title: GINS2 regulates the proliferation and apoptosis of colon cancer cells through PTP4A1.
    3. LncRNA NEAT1 promotes cell proliferation, migration, and invasion via the miR-186-5p/PTP4A1 axis in cholangiocarcinoma.
      Title: LncRNA NEAT1 promotes cell proliferation, migration, and invasion via the miR-186-5p/PTP4A1 axis in cholangiocarcinoma.
    4. These results provide evidence indicating a regulatory role of PRL-1 during Immunological Synapse assembly and highlight the involvement of PRLs in immune responses by mature T cells.
      Title: Phosphatase of Regenerating Liver-1 (PRL-1) Regulates Actin Dynamics During Immunological Synapse Assembly and T Cell Effector Function.
    5. Overexpression of miR-339-5p enhanced radiosensitivity of A549 and H460 cells by inhibiting cell viability, increasing apoptosis, inducing cell cycle arrest, and suppressing cell proliferation. Further exploration validated that miR-339-5p can target phosphatases of regenerating liver-1 (PRL-1) in lung cancer cells.
      Title: miR-339-5p Increases Radiosensitivity of Lung Cancer Cells by Targeting Phosphatases of Regenerating Liver-1 (PRL-1).
    6. PRL mRNA transcription was stimulated by Mg(2+) depletion. A series of analyses revealed the activation and the crucial importance of signal transducer and activator of transcription 1 in this process. Collectively, these results implicate PRL in maintaining cellular Mg(2+) homeostasis.
      Title: Phosphatase of regenerating liver maintains cellular magnesium homeostasis.
    7. PTP4A1 is a direct downstream target of miR-1271 in the hepatocellular carcinoma.
      Title: MicroRNA-1271 functions as a metastasis and epithelial-mesenchymal transition inhibitor in human HCC by targeting the PTP4A1/c-Src axis.
    8. PTP4A1 is highly expressed in fibroblasts from patients with systemic sclerosis and enhances pro-fibrotic TGFbeta signaling in these cells.
      Title: PTP4A1 promotes TGFβ signaling and fibrosis in systemic sclerosis.
    9. PTP4A1 was overexpressed in ICC and played an important role in the progression and metastasis of ICC. The functional role of PTP4A1 was assumed to be acted by activation PI3K/AKT signaling and promoting the EMT process through two pivotal transcriptional factors Zeb1 and Snail.
      Title: Protein tyrosine phosphatase PTP4A1 promotes proliferation and epithelial-mesenchymal transition in intrahepatic cholangiocarcinoma via the PI3K/AKT pathway.
    10. Results showed that SIAH1 and PTP4A1 expression was regulated by mir-944 in breast cancer cells. miR-944 binds directly the 3 UTR of their promotor region.
      Title: Suppression of cell migration is promoted by miR-944 through targeting of SIAH1 and PTP4A1 in breast cancer cells.
    Submit: New GeneRIF Correction See all GeneRIFs (34)

    Phenotypes

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    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

    Clone Names

    • DKFZp779M0721

    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 phosphatase activity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in positive regulation of cell migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein 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 cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasmic side of plasma membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in early endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in spindle IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein tyrosine phosphatase type IVA 1
    Names
    PVT1/PTP4A1 fusion
    phosphatase of regenerating liver 1
    protein tyrosine phosphatase type IVA protein 1
    protein tyrosine phosphatase type IVA, member 1
    protein-tyrosine phosphatase of regenerating liver 1
    NP_001372183.1
    NP_001372184.1
    NP_001372185.1
    NP_001372186.1
    NP_001372187.1
    NP_001372188.1
    NP_001372189.1
    NP_001372191.1
    NP_001372192.1
    NP_001372194.1
    NP_001372195.1
    NP_001372196.1
    NP_001372197.1
    NP_003454.1

    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_001385254.1 → NP_001372183.1  protein tyrosine phosphatase type IVA 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL135905
      Consensus CDS
      CCDS4965.1
      UniProtKB/Swiss-Prot
      B2R6C8, O00648, Q49A54, Q93096
      UniProtKB/TrEMBL
      B5BU78
      Conserved Domains (1) summary
      cd18537
      Location:1 → 167
      PTP-IVa1; protein tyrosine phosphatase type IVA 1

    2. NM_001385255.1 → NP_001372184.1  protein tyrosine phosphatase type IVA 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL135905
      Consensus CDS
      CCDS4965.1
      UniProtKB/Swiss-Prot
      B2R6C8, O00648, Q49A54, Q93096
      UniProtKB/TrEMBL
      B5BU78
      Conserved Domains (1) summary
      cd18537
      Location:1 → 167
      PTP-IVa1; protein tyrosine phosphatase type IVA 1

    3. NM_001385256.1 → NP_001372185.1  protein tyrosine phosphatase type IVA 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL135905
      Consensus CDS
      CCDS4965.1
      UniProtKB/Swiss-Prot
      B2R6C8, O00648, Q49A54, Q93096
      UniProtKB/TrEMBL
      B5BU78
      Related
      ENSP00000497588.1, ENST00000648894.1
      Conserved Domains (1) summary
      cd18537
      Location:1 → 167
      PTP-IVa1; protein tyrosine phosphatase type IVA 1

    4. NM_001385257.1 → NP_001372186.1  protein tyrosine phosphatase type IVA 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL135905
      Consensus CDS
      CCDS4965.1
      UniProtKB/Swiss-Prot
      B2R6C8, O00648, Q49A54, Q93096
      UniProtKB/TrEMBL
      B5BU78
      Conserved Domains (1) summary
      cd18537
      Location:1 → 167
      PTP-IVa1; protein tyrosine phosphatase type IVA 1

    5. NM_001385258.1 → NP_001372187.1  protein tyrosine phosphatase type IVA 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL135905
      Consensus CDS
      CCDS4965.1
      UniProtKB/Swiss-Prot
      B2R6C8, O00648, Q49A54, Q93096
      UniProtKB/TrEMBL
      B5BU78
      Conserved Domains (1) summary
      cd18537
      Location:1 → 167
      PTP-IVa1; protein tyrosine phosphatase type IVA 1

    6. NM_001385259.1 → NP_001372188.1  protein tyrosine phosphatase type IVA 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL135905
      Consensus CDS
      CCDS4965.1
      UniProtKB/Swiss-Prot
      B2R6C8, O00648, Q49A54, Q93096
      UniProtKB/TrEMBL
      B5BU78
      Related
      ENSP00000500859.1, ENST00000673199.1
      Conserved Domains (1) summary
      cd18537
      Location:1 → 167
      PTP-IVa1; protein tyrosine phosphatase type IVA 1

    7. NM_001385260.1 → NP_001372189.1  protein tyrosine phosphatase type IVA 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL135905
      Consensus CDS
      CCDS4965.1
      UniProtKB/Swiss-Prot
      B2R6C8, O00648, Q49A54, Q93096
      UniProtKB/TrEMBL
      B5BU78
      Related
      ENSP00000500952.1, ENST00000672924.1
      Conserved Domains (1) summary
      cd18537
      Location:1 → 167
      PTP-IVa1; protein tyrosine phosphatase type IVA 1

    8. NM_001385262.2 → NP_001372191.1  protein tyrosine phosphatase type IVA 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL135905
      Consensus CDS
      CCDS4965.1
      UniProtKB/Swiss-Prot
      B2R6C8, O00648, Q49A54, Q93096
      UniProtKB/TrEMBL
      B5BU78
      Conserved Domains (1) summary
      cd18537
      Location:1 → 167
      PTP-IVa1; protein tyrosine phosphatase type IVA 1

    9. NM_001385263.2 → NP_001372192.1  protein tyrosine phosphatase type IVA 1 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL135905
      UniProtKB/TrEMBL
      B5BU78
      Conserved Domains (1) summary
      cl28904
      Location:1 → 151
      PTP_DSP_cys; cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily

    10. NM_001385265.1 → NP_001372194.1  protein tyrosine phosphatase type IVA 1 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL135905
      Conserved Domains (1) summary
      cl28904
      Location:1 → 135
      PTP_DSP_cys; cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily

    11. NM_001385266.1 → NP_001372195.1  protein tyrosine phosphatase type IVA 1 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL135905
      Conserved Domains (1) summary
      cl28904
      Location:1 → 135
      PTP_DSP_cys; cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily

    12. NM_001385267.2 → NP_001372196.1  protein tyrosine phosphatase type IVA 1 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL135905
      Consensus CDS
      CCDS4965.1
      UniProtKB/Swiss-Prot
      B2R6C8, O00648, Q49A54, Q93096
      UniProtKB/TrEMBL
      B5BU78
      Conserved Domains (1) summary
      cd18537
      Location:1 → 167
      PTP-IVa1; protein tyrosine phosphatase type IVA 1

    13. NM_001385268.2 → NP_001372197.1  protein tyrosine phosphatase type IVA 1 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL135905
      UniProtKB/TrEMBL
      B5BU78
      Conserved Domains (1) summary
      cl28904
      Location:1 → 154
      PTP_DSP_cys; cys-based protein tyrosine phosphatase and dual-specificity phosphatase superfamily

    14. NM_003463.5 → NP_003454.1  protein tyrosine phosphatase type IVA 1 isoform 1

      See identical proteins and their annotated locations for NP_003454.1

      Status: VALIDATED

      Source sequence(s)
      AL135905
      Consensus CDS
      CCDS4965.1
      UniProtKB/Swiss-Prot
      B2R6C8, O00648, Q49A54, Q93096
      UniProtKB/TrEMBL
      B5BU78
      Related
      ENSP00000485687.1, ENST00000626021.3
      Conserved Domains (1) summary
      cd18537
      Location:1 → 167
      PTP-IVa1; protein tyrosine phosphatase type IVA 1

    RNA

    1. NR_169593.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL135905

    2. NR_169594.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL135905

    3. NR_169595.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL135905

    4. NR_169596.2 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL135905

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      63516440..63583588
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      64662355..64729529
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q93096.2 GenPept UniProtKB/Swiss-Prot:Q93096

    Gene LinkOut

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

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