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    Ppfia1 PTPRF interacting protein alpha 1 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 293645, updated on 27-Nov-2024

    Summary

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    Symbol
    Ppfia1provided by RGD
    Full Name
    PTPRF interacting protein alpha 1provided by RGD
    Primary source
    RGD:1309009
    See related
    EnsemblRapid:ENSRNOG00000020857 AllianceGenome:RGD:1309009
    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
    Involved in regulation of postsynaptic membrane neurotransmitter receptor levels. Located in axon and dendrite. Part of protein-containing complex. Is active in Schaffer collateral - CA1 synapse and spine apparatus. Orthologous to human PPFIA1 (PTPRF interacting protein alpha 1). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Lung (RPKM 150.2), Kidney (RPKM 127.0) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Ppfia1 in Genome Data Viewer
    Location:
    1q42
    Exon count:
    32
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (209070608..209147740, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (199641277..199718371, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (217644259..217721285, complement)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene 60S ribosomal protein L21-like Neighboring gene SH3 and multiple ankyrin repeat domains 2 Neighboring gene cortactin Neighboring gene 60S ribosomal protein L7a pseudogene Neighboring gene Fas associated via death domain Neighboring gene anoctamin 1

    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. Liprin-α is involved in exocytosis and cell spreading in mast cells. Nomura H, et al. Immunol Lett, 2011 Sep 30. PMID 21683737
    2. Upregulation of liprin-α1 protein in the temporal neocortex of intractable epileptic patients and experimental rats. Yin H, et al. Synapse, 2011 Aug. PMID 21157931
    3. Cdk5-dependent phosphorylation of liprinα1 mediates neuronal activity-dependent synapse development. Huang H, et al. Proc Natl Acad Sci U S A, 2017 Aug 15. PMID 28760951, Free PMC Article
    4. A novel mechanism of hippocampal LTD involving muscarinic receptor-triggered interactions between AMPARs, GRIP and liprin-alpha. Dickinson BA, et al. Mol Brain, 2009 Jun 17. PMID 19534762, Free PMC Article
    5. Liprin-α controls stress fiber formation by binding to mDia and regulating its membrane localization. Sakamoto S, et al. J Cell Sci, 2012 Jan 1. PMID 22266902

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. liprin-alpha and TANC2 are not part of the KIF1A-cargo complex but capture dense core vesicles at dendritic spines.
      Title: Regulation of KIF1A-Driven Dense Core Vesicle Transport: Ca(2+)/CaM Controls DCV Binding and Liprin-α/TANC2 Recruits DCVs to Postsynaptic Sites.
    2. findings collectively demonstrate that the Cdk5-dependent phosphorylation of liprinalpha1 is important for the postsynaptic organization during activity-dependent synapse development.
      Title: Cdk5-dependent phosphorylation of liprinα1 mediates neuronal activity-dependent synapse development.
    3. liprin-alpha1 facilitates exocytosis and cell spreading, and these events might have correlated each other in mast cells.
      Title: Liprin-α is involved in exocytosis and cell spreading in mast cells.
    4. expression of Liprin-alpha1 in animals in the experimental group gradually increased from Days 1 to 30 postseizure induction and reached a stable level when spontaneous recurrent seizures (SRS) appeared
      Title: Upregulation of liprin-α1 protein in the temporal neocortex of intractable epileptic patients and experimental rats.
    5. These data indicate a novel mechanism of synaptic plasticity in which activation of M1 receptors results in AMPA receptor endocytosis, via a mechanism involving interactions between GluA2, GRIP and liprin-alpha.
      Title: A novel mechanism of hippocampal LTD involving muscarinic receptor-triggered interactions between AMPARs, GRIP and liprin-alpha.
    Submit: New GeneRIF Correction

    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

    Process Evidence Code Pubs
    involved_in cortical microtubule organization ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of protein localization to plasma membrane ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of stress fiber assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of postsynaptic membrane neurotransmitter receptor levels IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of postsynaptic membrane neurotransmitter receptor levels IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in synapse organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in Schaffer collateral - CA1 synapse IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in Schaffer collateral - CA1 synapse IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in axon IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cell cortex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in dendrite IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in focal adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in focal adhesion ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in presynaptic active zone IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in spine apparatus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    liprin-alpha-1
    Names
    liprin-alpha-1-like
    protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1
    protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein, alpha 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_001106320.2 → NP_001099790.2  liprin-alpha-1

      See identical proteins and their annotated locations for NP_001099790.2

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000001
      UniProtKB/TrEMBL
      A0A0G2K3L9, D3ZZ81
      Related
      ENSRNOP00000032648.4, ENSRNOT00000039677.6
      Conserved Domains (7) summary
      cd09562
      Location:874 → 944
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:961 → 1026
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1046 → 1117
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      smart00454
      Location:874 → 940
      SAM; Sterile alpha motif
      COG1842
      Location:302 → 515
      PspA; Phage shock protein A [Transcription, Signal transduction mechanisms]
      cl12013
      Location:323 → 444
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
      cl19219
      Location:423 → 518
      DUF342; Protein of unknown function (DUF342)

    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_086019.1 Reference GRCr8

      Range
      209070608..209147740 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006230723.5 → XP_006230785.1  liprin-alpha-1 isoform X16

      See identical proteins and their annotated locations for XP_006230785.1

      UniProtKB/TrEMBL
      A0A0G2K3L9, D3ZZ81
      Conserved Domains (7) summary
      cd09562
      Location:874 → 944
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:961 → 1026
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1046 → 1117
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      smart00454
      Location:874 → 940
      SAM; Sterile alpha motif
      COG1842
      Location:302 → 515
      PspA; Phage shock protein A [Transcription, Signal transduction mechanisms]
      cl12013
      Location:323 → 444
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
      cl19219
      Location:423 → 518
      DUF342; Protein of unknown function (DUF342)

    2. XM_006230722.5 → XP_006230784.1  liprin-alpha-1 isoform X15

      UniProtKB/TrEMBL
      A0A0G2K3L9
      Related
      ENSRNOP00000075947.3, ENSRNOT00000092748.3
      Conserved Domains (7) summary
      cd09562
      Location:874 → 944
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:961 → 1026
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1046 → 1117
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      smart00454
      Location:874 → 940
      SAM; Sterile alpha motif
      COG1842
      Location:302 → 515
      PspA; Phage shock protein A [Transcription, Signal transduction mechanisms]
      cl12013
      Location:323 → 444
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
      cl19219
      Location:423 → 518
      DUF342; Protein of unknown function (DUF342)

    3. XM_063286708.1 → XP_063142778.1  liprin-alpha-1 isoform X11

    4. XM_017589012.3 → XP_017444501.1  liprin-alpha-1 isoform X17

      UniProtKB/TrEMBL
      A0A1B0GWM2

    5. XM_006230720.5 → XP_006230782.1  liprin-alpha-1 isoform X8

      UniProtKB/TrEMBL
      A0A1B0GWM2
      Conserved Domains (7) summary
      cd09562
      Location:884 → 954
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:1001 → 1066
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1086 → 1157
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      smart00454
      Location:884 → 950
      SAM; Sterile alpha motif
      COG1842
      Location:302 → 515
      PspA; Phage shock protein A [Transcription, Signal transduction mechanisms]
      cl12013
      Location:323 → 444
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
      cl19219
      Location:423 → 518
      DUF342; Protein of unknown function (DUF342)

    6. XM_039108131.2 → XP_038964059.1  liprin-alpha-1 isoform X7

      UniProtKB/TrEMBL
      A0A1B0GWM2
      Conserved Domains (4) summary
      cd09562
      Location:884 → 954
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:1002 → 1067
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1087 → 1158
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      COG1196
      Location:171 → 516
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

    7. XM_063286716.1 → XP_063142786.1  liprin-alpha-1 isoform X14

      Related
      ENSRNOP00000075999.2, ENSRNOT00000092939.3

    8. XM_063286711.1 → XP_063142781.1  liprin-alpha-1 isoform X12

    9. XM_063286692.1 → XP_063142762.1  liprin-alpha-1 isoform X5

    10. XM_039108123.2 → XP_038964051.1  liprin-alpha-1 isoform X3

      UniProtKB/TrEMBL
      A0A1B0GWM2
      Conserved Domains (6) summary
      cd09562
      Location:899 → 969
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:1017 → 1082
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1102 → 1173
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      COG1196
      Location:45 → 418
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:246 → 545
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      TIGR02169
      Location:421 → 685
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type

    11. XM_063286712.1 → XP_063142782.1  liprin-alpha-1 isoform X13

    12. XM_006230721.5 → XP_006230783.1  liprin-alpha-1 isoform X10

      UniProtKB/TrEMBL
      A0A1B0GWM2
      Conserved Domains (7) summary
      cd09562
      Location:909 → 979
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:996 → 1061
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1081 → 1152
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      smart00454
      Location:909 → 975
      SAM; Sterile alpha motif
      COG1842
      Location:302 → 540
      PspA; Phage shock protein A [Transcription, Signal transduction mechanisms]
      cl12013
      Location:323 → 469
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
      cl19219
      Location:448 → 543
      DUF342; Protein of unknown function (DUF342)

    13. XM_039108139.2 → XP_038964067.1  liprin-alpha-1 isoform X9

      UniProtKB/TrEMBL
      A0A1B0GWM2
      Conserved Domains (6) summary
      cd09562
      Location:909 → 979
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:997 → 1062
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1082 → 1153
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      COG1196
      Location:45 → 418
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:246 → 545
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      TIGR02169
      Location:421 → 685
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type

    14. XM_017589010.3 → XP_017444499.1  liprin-alpha-1 isoform X4

      UniProtKB/TrEMBL
      A0A1B0GWM2

    15. XM_006230715.5 → XP_006230777.1  liprin-alpha-1 isoform X2

      UniProtKB/TrEMBL
      A0A1B0GWM2, A0A1B0GWS0
      Related
      ENSRNOP00000072693.3, ENSRNOT00000078810.3
      Conserved Domains (7) summary
      cd09562
      Location:909 → 979
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:1026 → 1091
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1111 → 1182
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      smart00454
      Location:909 → 975
      SAM; Sterile alpha motif
      COG1842
      Location:302 → 540
      PspA; Phage shock protein A [Transcription, Signal transduction mechanisms]
      cl12013
      Location:323 → 469
      BAR; The Bin/Amphiphysin/Rvs (BAR) domain, a dimerization module that binds membranes and detects membrane curvature
      cl19219
      Location:448 → 543
      DUF342; Protein of unknown function (DUF342)

    16. XM_039108128.2 → XP_038964056.1  liprin-alpha-1 isoform X6

      UniProtKB/TrEMBL
      A0A1B0GWM2
      Conserved Domains (6) summary
      cd09562
      Location:909 → 979
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:1027 → 1092
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1112 → 1183
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      COG1196
      Location:45 → 418
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:246 → 545
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      TIGR02169
      Location:421 → 685
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type

    17. XM_039108121.2 → XP_038964049.1  liprin-alpha-1 isoform X1

      UniProtKB/TrEMBL
      A0A1B0GWM2
      Conserved Domains (6) summary
      cd09562
      Location:909 → 979
      SAM_liprin-alpha1,2,3,4_repeat1; SAM domain of liprin-alpha1,2,3,4 proteins repeat 1
      cd09565
      Location:1027 → 1092
      SAM_liprin-alpha1,2,3,4_repeat2; SAM domain of liprin-alpha1,2,3,4 proteins repeat 2
      cd09568
      Location:1112 → 1183
      SAM_liprin-alpha1,2,3,4_repeat3; SAM domain of liprin-alpha1,2,3,4 proteins repeat 3
      COG1196
      Location:45 → 418
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      TIGR02168
      Location:246 → 545
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      TIGR02169
      Location:421 → 685
      SMC_prok_A; chromosome segregation protein SMC, primarily archaeal type
    Nucleotide Protein Strain
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