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

Gene ID: 293645, updated on 13-Apr-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
Ensembl: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
Predicted to be involved in synapse organization. Predicted to act upstream of or within negative regulation of protein localization to plasma membrane and negative regulation of stress fiber assembly. Located in axon and dendrite. Part of protein-containing complex. Orthologous to human PPFIA1 (PTPRF interacting protein alpha 1). [provided by Alliance of Genome Resources, Apr 2022]
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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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
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 cytoplasm IEA
Inferred from Electronic Annotation
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, ENSRNOT00000039677.5
    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
    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

  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
    ENSRNOP00000075999.1
    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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