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    Ppfia4 PTPRF interacting protein alpha 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 140592, updated on 2-May-2024

    Summary

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    Official Symbol
    Ppfia4provided by RGD
    Official Full Name
    PTPRF interacting protein alpha 4provided by RGD
    Primary source
    RGD:620055
    See related
    Ensembl:ENSRNOG00000003494 AllianceGenome:RGD:620055
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Summary
    Predicted to be involved in synapse organization. Predicted to be located in synapse. Predicted to be active in presynaptic active zone. Orthologous to human PPFIA4 (PTPRF interacting protein alpha 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in Brain (RPKM 70.0), Heart (RPKM 19.5) and 6 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    Location:
    13q13
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 13 NC_086031.1 (48305844..48354329, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 13 NC_051348.1 (45753827..45802305, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 13 NC_005112.4 (51134831..51183321, complement)

    Chromosome 13 - NC_086031.1Genomic Context describing neighboring genes Neighboring gene myosin binding protein H Neighboring gene adenosine A1 receptor Neighboring gene uncharacterized LOC120096189 Neighboring gene myogenin Neighboring gene transmembrane protein 183A Neighboring gene Mgat4 family, member E-like

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

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    Related articles in PubMed

    1. Differential expression of liprin-α family proteins in the brain suggests functional diversification. Spangler SA, et al. J Comp Neurol, 2011 Oct 15. PMID 21618222
    2. Identification and characterization of human PPFIA4 gene in silico. Katoh M, et al. Int J Mol Med, 2003 Dec. PMID 14612982
    3. Association of the kinesin motor KIF1A with the multimodular protein liprin-alpha. Shin H, et al. J Biol Chem, 2003 Mar 28. PMID 12522103
    4. RIM1alpha forms a protein scaffold for regulating neurotransmitter release at the active zone. Schoch S, et al. Nature, 2002 Jan 17. PMID 11797009
    5. Analyses of the spatiotemporal expression and subcellular localization of liprin-α proteins. Zürner M, et al. J Comp Neurol, 2011 Oct 15. PMID 21618221

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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 RGD

    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 cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in parallel fiber to Purkinje cell synapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in parallel fiber to Purkinje cell synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in presynapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in presynaptic active zone IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in synapse ISO
    Inferred from Sequence Orthology
    more info
    		  
    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-interacting protein alpha-4
    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_080409.1 → NP_536334.1  liprin-alpha-4

      Status: VALIDATED

      Source sequence(s)
      AY057064, BF285985, CB584337, JAXUCZ010000013
      UniProtKB/TrEMBL
      A0A8I6AIZ8
      Related
      ENSRNOP00000033209.6, ENSRNOT00000039540.7
      Conserved Domains (7) 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
      smart00454
      Location:827 → 893
      SAM; Sterile alpha motif
      pfam15619
      Location:174 → 355
      Lebercilin; Ciliary protein causing Leber congenital amaurosis disease
      cd16269
      Location:437 → 449
      GBP_C; coiled coil [structural motif]
      cl20817
      Location:258 → 470
      GBP_C; Guanylate-binding protein, C-terminal domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086031.1 Reference GRCr8

      Range
      48305844..48354329 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063271978.1 → XP_063128048.1  liprin-alpha-4 isoform X4

    2. XM_063271976.1 → XP_063128046.1  liprin-alpha-4 isoform X2

      UniProtKB/TrEMBL
      A6ICB3, F1M863

    3. XM_063271975.1 → XP_063128045.1  liprin-alpha-4 isoform X1

      UniProtKB/TrEMBL
      A0A8I5ZQL8

    4. XM_063271977.1 → XP_063128047.1  liprin-alpha-4 isoform X3

    5. XM_039090290.2 → XP_038946218.1  liprin-alpha-4 isoform X6

      Conserved Domains (2) summary
      COG1196
      Location:241 → 470
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:37 → 409
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    6. XM_039090289.2 → XP_038946217.1  liprin-alpha-4 isoform X5

      Conserved Domains (2) summary
      COG1196
      Location:241 → 470
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:37 → 409
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type

    RNA

    1. XR_005492195.2 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q91Z80.1 GenPept UniProtKB/Swiss-Prot:Q91Z80

    Gene LinkOut

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