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    PPFIA4 PTPRF interacting protein alpha 4 [ Homo sapiens (human) ]

    Gene ID: 8497, updated on 5-Mar-2024

    Summary

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    Official Symbol
    PPFIA4provided by HGNC
    Official Full Name
    PTPRF interacting protein alpha 4provided by HGNC
    Primary source
    HGNC:HGNC:9248
    See related
    Ensembl:ENSG00000143847 MIM:603145; AllianceGenome:HGNC:9248
    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
    PPFIA4, or liprin-alpha-4, belongs to the liprin-alpha gene family. See liprin-alpha-1 (LIP1, or PPFIA1; MIM 611054) for background on liprins.[supplied by OMIM, Mar 2008]
    Expression
    Biased expression in brain (RPKM 8.9), heart (RPKM 8.4) and 10 other tissues See more
    Orthologs
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    Genomic context

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    See PPFIA4 in Genome Data Viewer
    Location:
    1q32.1
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (203026491..203078736)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (202289215..202341489)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (202995619..203047864)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene MGAT4 family member F, pseudogene Neighboring gene CRISPRi-validated cis-regulatory element chr1.10803 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2339 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:202975854-202976628 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:202976629-202977401 Neighboring gene ribosomal protein S20 pseudogene 8 Neighboring gene transmembrane protein 183A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:202995545-202996066 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2340 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203010223-203010724 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203010725-203011224 Neighboring gene Sharpr-MPRA regulatory region 9252 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203013943-203014581 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203014582-203015219 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:203015372-203015574 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203017091-203017988 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203020635-203021176 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:203023677-203024428 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203024429-203025180 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:203030137-203030721 Neighboring gene uncharacterized LOC105371687 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2341 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203044947-203045682 Neighboring gene NANOG hESC enhancer GRCh37_chr1:203056459-203056976 Neighboring gene myogenin promoter associated myogenic regulatory antisense long non coding RNA Neighboring gene myogenin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203096578-203097558 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203103311-203104198 Neighboring gene adenosine A1 receptor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203112572-203113072 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:203114546-203115227 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:203134798-203134977 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203135305-203135815 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:203135816-203136326

    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. Liprin-α4 as a Possible New Therapeutic Target for Pancreatic Cancer. Yamasaki A, et al. Anticancer Res, 2017 Dec. PMID 29187440
    2. Liprin-α4 is required for nickel induced receptor protein tyrosine phosphatase-leukocyte antigen related receptor F (RPTP-LAR) activity. Kiok K, et al. PLoS One, 2011. PMID 21829649, Free PMC Article
    3. Liprin-α4 is a new hypoxia-inducible target gene required for maintenance of cell-cell contacts. Mattauch S, et al. Exp Cell Res, 2010 Oct 15. PMID 20599943
    4. Liprin-α4 as a New Therapeutic Target for SCLC as an Upstream Mediator of HIF1α. Onishi H, et al. Anticancer Res, 2019 Mar. PMID 30842147
    5. Korean atrial fibrillation network genome-wide association study for early-onset atrial fibrillation identifies novel susceptibility loci. Lee JY, et al. Eur Heart J, 2017 Sep 7. PMID 28460022

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PPFIA4 Promotes Proliferation, Migration and Glycolysis of Esophageal Cancer Cells.
      Title: PPFIA4 Promotes Proliferation, Migration and Glycolysis of Esophageal Cancer Cells.
    2. Hypoxia appears to up-regulate the expression of liprin-alpha4, which induces the expression of HIF1alpha. HIF1alpha contributes to increased proliferation and lower chemosensitivity. Therefore, inhibition of liprin-alpha4 or HIF1alpha led to reduced proliferation and increased chemosensitivity of SBC-5 cells.
      Title: Liprin-α4 as a New Therapeutic Target for SCLC as an Upstream Mediator of HIF1α.
    3. The results identify PP1IFA4 loci associated with early onset atrial fibrillation in a Korean population.
      Title: Korean atrial fibrillation network genome-wide association study for early-onset atrial fibrillation identifies novel susceptibility loci.
    4. Data show that liprin-alpha4 plays a pivotal role in inducing malignant phenotypes such as increased proliferation and invasion in pancreatic cancer, and that liprin-alpha4 could be a new effective therapeutic target for pancreatic cancer.
      Title: Liprin-α4 as a Possible New Therapeutic Target for Pancreatic Cancer.
    5. presence of Liprin-alpha4 and nickel increased tyrosine phosphatase activity that reduced the global levels of tyrosine phosphorylation in the cell
      Title: Liprin-α4 is required for nickel induced receptor protein tyrosine phosphatase-leukocyte antigen related receptor F (RPTP-LAR) activity.
    6. liprin-alpha4 is a hypoxia-induced gene potentially involved in cell-cell adhesion
      Title: Liprin-α4 is a new hypoxia-inducible target gene required for maintenance of cell-cell contacts.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Follow-up of a major linkage peak on chromosome 1 reveals suggestive QTLs associated with essential hypertension: GenNet study.
    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

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in synapse organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cell surface IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    is_active_in presynaptic active zone IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in presynaptic active zone TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    liprin-alpha-4
    Names
    protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4

    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_001304331.2 → NP_001291260.1  liprin-alpha-4 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AB020704, AC096632, AC105940, AK295757, AL540093, DA327222, EF428334
      Consensus CDS
      CCDS91145.1
      UniProtKB/TrEMBL
      A0A8J8YUZ5, B1APN9
      Related
      ENSP00000295706.5, ENST00000295706.9
      Conserved Domains (5) summary
      cd09562
      Location:848 → 918
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:965 → 1030
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1050 → 1121
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      smart00454
      Location:848 → 914
      SAM; Sterile alpha motif
      cl02488
      Location:338 → 493
      SPEC; Spectrin repeats, found in several proteins involved in cytoskeletal structure; family members include spectrin, alpha-actinin and dystrophin; the spectrin repeat forms a three helix bundle with the second helix interrupted by proline in some sequences; ...

    2. NM_001304332.2 → NP_001291261.1  liprin-alpha-4 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC096632, AC105940, AK023365, AK295757, AL540093, BC144262, DA327222, EF428334
      UniProtKB/TrEMBL
      B1APN9
      Conserved Domains (5) summary
      cd09562
      Location:848 → 918
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:956 → 1021
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1041 → 1112
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      COG0419
      Location:25 → 490
      SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
      COG1196
      Location:262 → 491
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

    3. NM_001393950.1 → NP_001380879.1  liprin-alpha-4 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC096632, AC105940, AL451082
      UniProtKB/TrEMBL
      B1APN9
      Conserved Domains (4) summary
      cd09562
      Location:839 → 909
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:956 → 1021
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1041 → 1112
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      COG1196
      Location:161 → 484
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

    4. NM_001393951.1 → NP_001380880.1  liprin-alpha-4 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC096632, AC105940, AL451082
      UniProtKB/TrEMBL
      A0A8I5QJ45
      Related
      ENSP00000508419.1, ENST00000692772.1
      Conserved Domains (5) summary
      cd09562
      Location:827 → 897
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:944 → 1009
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1029 → 1100
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      COG0419
      Location:36 → 470
      SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
      COG1196
      Location:262 → 470
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

    5. NM_001393952.1 → NP_001380881.1  liprin-alpha-4 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AC096632, AC105940, AL451082
      UniProtKB/TrEMBL
      B1APN9
      Conserved Domains (5) summary
      cd09562
      Location:848 → 918
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:965 → 1030
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      COG0419
      Location:25 → 490
      SbcC; DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair]
      COG1196
      Location:262 → 491
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      cl15755
      Location:1050 → 1108
      SAM_superfamily; SAM (Sterile alpha motif )

    6. NM_001393953.1 → NP_001380882.1  liprin-alpha-4 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AC096632, AC105940, AL451082
      UniProtKB/TrEMBL
      A0A8I5QJ45
      Conserved Domains (5) summary
      cd09562
      Location:803 → 873
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:920 → 985
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1005 → 1076
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      COG1196
      Location:161 → 448
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam15921
      Location:21 → 615
      CCDC158; Coiled-coil domain-containing protein 158

    7. NM_001393954.1 → NP_001380883.1  liprin-alpha-4 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AC096632, AC105940, AL451082
      UniProtKB/TrEMBL
      B1APN9
      Conserved Domains (5) summary
      cd09562
      Location:803 → 873
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:920 → 985
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1005 → 1076
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      COG1196
      Location:161 → 448
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam15921
      Location:21 → 615
      CCDC158; Coiled-coil domain-containing protein 158

    8. NM_001393955.1 → NP_001380884.1  liprin-alpha-4 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AC096632, AC105940, AL451082
      UniProtKB/TrEMBL
      A0A8I5QJ45
      Conserved Domains (5) summary
      cd09562
      Location:782 → 852
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:899 → 964
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:984 → 1055
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      TIGR02168
      Location:147 → 424
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam15921
      Location:21 → 594
      CCDC158; Coiled-coil domain-containing protein 158

    9. NM_001393956.1 → NP_001380885.1  liprin-alpha-4 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AC096632, AC105940, AL451082
      UniProtKB/TrEMBL
      B1APN9
      Conserved Domains (5) summary
      cd09562
      Location:782 → 852
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:890 → 955
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:975 → 1046
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      TIGR02168
      Location:147 → 424
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam15921
      Location:21 → 594
      CCDC158; Coiled-coil domain-containing protein 158

    10. NM_001393957.1 → NP_001380886.1  liprin-alpha-4 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AC096632, AC105940, AL451082
      UniProtKB/TrEMBL
      A0A8I5QJ45
      Conserved Domains (5) summary
      cd09562
      Location:759 → 829
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:876 → 941
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:961 → 1032
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      COG1196
      Location:145 → 404
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam15921
      Location:21 → 571
      CCDC158; Coiled-coil domain-containing protein 158

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      203026491..203078736
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      202289215..202341489
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_015053.1: Suppressed sequence

      Description
      NM_015053.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75335.3 GenPept UniProtKB/Swiss-Prot:O75335

    Gene LinkOut

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

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