U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

    PPFIA3 PTPRF interacting protein alpha 3 [ Homo sapiens (human) ]

    Gene ID: 8541, updated on 9-Dec-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    PPFIA3provided by HGNC
    Official Full Name
    PTPRF interacting protein alpha 3provided by HGNC
    Primary source
    HGNC:HGNC:9247
    See related
    Ensembl:ENSG00000177380 MIM:603144; AllianceGenome:HGNC:9247
    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
    LPNA3
    Summary
    The protein encoded by this gene is a member of the LAR protein-tyrosine phosphatase-interacting protein (liprin) family. Liprins interact with members of LAR family of transmembrane protein tyrosine phosphatases, which are known to be important for axon guidance and mammary gland development. Liprin family protein has been shown to localize phosphatase LAR to cell focal adhesions and may be involved in the molecular organization of presynaptic active zones. [provided by RefSeq, Jul 2008]
    Expression
    Biased expression in brain (RPKM 10.8), skin (RPKM 6.5) and 10 other tissues See more
    Orthologs
    mouse all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    See PPFIA3 in Genome Data Viewer
    Location:
    19q13.33
    Exon count:
    29
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (49119544..49151026)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (52114278..52145758)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (49622801..49654283)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14926 Neighboring gene small nuclear ribonucleoprotein U1 subunit 70 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49603173-49604028 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49604029-49604882 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49610053-49610894 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10912 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49621711-49622222 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10913 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49623585-49624085 Neighboring gene chromosome 19 open reading frame 73 Neighboring gene lin-7 homolog B, crumbs cell polarity complex component Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10914 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49635887-49636531 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49640079-49640585 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49644909-49645502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14927 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49654589-49655198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49660783-49661404 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:49662088-49662274 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49668584-49669227 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49669228-49669870 Neighboring gene histidine rich calcium binding protein Neighboring gene transient receptor potential cation channel subfamily M member 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49691645-49692146 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:49692147-49692646 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:49700016-49700342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:49713888-49714526

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • 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

    Go to the top of the pageHelp

    Related articles in PubMed

    1. A syndromic neurodevelopmental disorder caused by rare variants in PPFIA3. Paul MS, et al. Am J Hum Genet, 2024 Jan 4. PMID 38181735, Free PMC Article
    2. Detection of OSR2, VAV3, and PPFIA3 Methylation in the Serum of Patients with Gastric Cancer. Li WH, et al. Dis Markers, 2016. PMID 27143812, Free PMC Article
    3. Liprin α3: a putative estrogen regulated acrosomal protein. Joshi CS, et al. Histochem Cell Biol, 2013 Apr. PMID 23124857
    4. Interaction of the ERC family of RIM-binding proteins with the liprin-alpha family of multidomain proteins. Ko J, et al. J Biol Chem, 2003 Oct 24. PMID 12923177
    5. Liprins, a family of LAR transmembrane protein-tyrosine phosphatase-interacting proteins. Serra-Pagès C, et al. J Biol Chem, 1998 Jun 19. PMID 9624153

    See all (36) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

    Go to the top of the page Help

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

    Go to the top of the page Help

    See Variation Viewer (GRCh37.p13)

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Clone Names

    • KIAA0654, MGC126567, MGC126569

    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 neurotransmitter secretion ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of short-term neuronal synaptic plasticity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in synapse organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptic vesicle docking IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in acrosomal vesicle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in epididymosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    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 presynaptic active zone cytoplasmic component IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    liprin-alpha-3
    Names
    liprin
    protein tyrosine phosphatase receptor type f polypeptide-interacting protein alpha-3
    protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 3
    protein tyrosine phosphatase, receptor type, f polypeptide, alpha 3

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    NEW Try the new Transcript table

    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_003660.4 → NP_003651.1  liprin-alpha-3

      See identical proteins and their annotated locations for NP_003651.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes a functional protein.
      Source sequence(s)
      AB014554, AI346749, BX111585, DA236900
      Consensus CDS
      CCDS12758.1
      UniProtKB/Swiss-Prot
      A8K142, O75145, Q3MJA0, Q9H8B5, Q9UEW4
      Related
      ENSP00000335614.3, ENST00000334186.9
      Conserved Domains (7) summary
      cd09562
      Location:835 → 905
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:952 → 1017
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1037 → 1108
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      smart00454
      Location:1040 → 1107
      SAM; Sterile alpha motif
      pfam09728
      Location:239 → 499
      Taxilin; Myosin-like coiled-coil protein
      cl03951
      Location:398 → 498
      CDC37_N; Cdc37 N terminal kinase binding
      cl12013
      Location:237 → 419
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    RNA

    1. NR_103842.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AB014554, AI346749, BC143470, BX111585, DA236900
      Related
      ENST00000602655.5

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      49119544..49151026
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439582.1 → XP_047295538.1  liprin-alpha-3 isoform X1

      UniProtKB/Swiss-Prot
      A8K142, O75145, Q3MJA0, Q9H8B5, Q9UEW4

    2. XM_047439583.1 → XP_047295539.1  liprin-alpha-3 isoform X2

    3. XM_017027407.2 → XP_016882896.1  liprin-alpha-3 isoform X2

      UniProtKB/Swiss-Prot
      O75145
      Related
      ENSP00000473622.1, ENST00000602351.5
      Conserved Domains (8) summary
      cd09562
      Location:835 → 905
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:943 → 1008
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1028 → 1099
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      smart00454
      Location:1031 → 1098
      SAM; Sterile alpha motif
      COG1340
      Location:32 → 345
      COG1340; Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]
      pfam09728
      Location:239 → 499
      Taxilin; Myosin-like coiled-coil protein
      cl03951
      Location:398 → 498
      CDC37_N; Cdc37 N terminal kinase binding
      cl12013
      Location:237 → 419
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature

    RNA

    1. XR_007067023.1 RNA Sequence

    2. XR_007067024.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      52114278..52145758
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322460.1 → XP_054178435.1  liprin-alpha-3 isoform X1

    2. XM_054322462.1 → XP_054178437.1  liprin-alpha-3 isoform X2

    3. XM_054322461.1 → XP_054178436.1  liprin-alpha-3 isoform X2

    RNA

    1. XR_008485214.1 RNA Sequence

    2. XR_008485215.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75145.3 GenPept UniProtKB/Swiss-Prot:O75145

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous