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    PPFIBP1 PTPRF interacting protein, binding protein 1 (liprin beta 1) [ Homo sapiens ]

    Gene ID: 8496, updated on 11-May-2012
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    Summary

    Official Symbol
    PPFIBP1provided by HGNC
    Official Full Name
    PTPRF interacting protein, binding protein 1 (liprin beta 1)provided by HGNC
    Primary source
    HGNC:9249
    See related
    Ensembl:ENSG00000110841; HPRD:04390; MIM:603141; Vega:OTTHUMG00000169207
    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
    L2; SGT2; hSGT2; hSgt2p
    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. It has been proposed that liprins are multivalent proteins that form complex structures and act as scaffolds for the recruitment and anchoring of LAR family of tyrosine phosphatases. This protein was found to interact with S100A4, a calcium-binding protein related to tumor invasiveness and metastasis. In vitro experiment demonstrated that the interaction inhibited the phosphorylation of this protein by protein kinase C and protein kinase CK2. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
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    Genomic context

    Location :
    12p12.1
    Sequence :
    Chromosome: 12; NC_000012.11 (27677045..27848497)
    See PPFIBP1 in Epigenomics, MapViewer

    Chromosome 12 - NC_000012.11Genomic Context describing neighboring genes Neighboring gene aryl hydrocarbon receptor nuclear translocator-like 2 Neighboring gene chromosome 12 open reading frame 70 Neighboring gene arginyl-tRNA synthetase pseudogene Neighboring gene uncharacterized protein C12orf71-like Neighboring gene high mobility group box 1 pseudogene 49 Neighboring gene RAB15 effector protein

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    Genomic regions, transcripts, and products

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details
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    Bibliography

    Related articles in PubMed

    1. Systematic and quantitative assessment of the ubiquitin-modified proteome. Kim W, et al. Mol Cell, 2011 Oct 21. PMID 21906983.
    2. Liprin-mediated large signaling complex organization revealed by the liprin-α/CASK and liprin-α/liprin-β complex structures. Wei Z, et al. Mol Cell, 2011 Aug 19. PMID 21855798.
    3. Pulmonary inflammatory myofibroblastic tumor expressing a novel fusion, PPFIBP1-ALK: reappraisal of anti-ALK immunohistochemistry as a tool for novel ALK fusion identification. Takeuchi K, et al. Clin Cancer Res, 2011 May 15. PMID 21430068.
    4. Mass spectrometric analysis of lysine ubiquitylation reveals promiscuity at site level. Danielsen JM, et al. Mol Cell Proteomics, 2011 Mar. PMID 21139048.
    5. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614.

    See all (18) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. Liprins can mediate assembly of target proteins into large protein complexes capable of regulating numerous cellular activities.
      Title: Liprin-mediated large signaling complex organization revealed by the liprin-α/CASK and liprin-α/liprin-β complex structures.
    2. Novel ALK fusions are being identified in various tumors in addition to inflammatory myofibroblastic tumor.
      Title: Pulmonary inflammatory myofibroblastic tumor expressing a novel fusion, PPFIBP1-ALK: reappraisal of anti-ALK immunohistochemistry as a tool for novel ALK fusion identification.
    3. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    4. liprin beta1, a member of the family of LAR transmembrane tyrosine phosphatase-interacting proteins, as highly expressed in intestinal lymphatic endothelial cells in vitro and lymphatic vasculature in vivo
      Title: Liprin (beta)1 is highly expressed in lymphatic vasculature and is important for lymphatic vessel integrity.
    5. new molecular target of the S100A4 protein, liprin beta1
      Title: Liprin beta 1, a member of the family of LAR transmembrane tyrosine phosphatase-interacting proteins, is a new target for the metastasis-associated protein S100A4 (Mts1).
    Submit: New GeneRIF Correction
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    Phenotypes

    Review eQTL and phenotype association data in this region using PheGenI

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    Interactions

    Products Interactant Other Gene Complex Source Pubs Description
    Q86W92 Q13136 PPFIA1    HPRD  PubMed  
    Q86W92 O75334 PPFIA2    HPRD  PubMed  
    Q86W92 O75145 PPFIA3    HPRD  PubMed  
    Q86W92 Q86W92 PPFIBP1    HPRD  PubMed  
    Q86W92 P28827 PTPRM    HPRD  PubMed  
    Q86W92 P26447 S100A4    HPRD  PubMed  
    Q86W92 P61981 YWHAG    HPRD  PubMed  
    BioGRID:114068 BioGRID:114072 PPFIA1    BioGRID  PubMed Reconstituted Complex 
    BioGRID:114068 BioGRID:114071 PPFIA2    BioGRID  PubMed Reconstituted Complex 
    BioGRID:114068 BioGRID:114068 PPFIBP1    BioGRID  PubMed Reconstituted Complex 
    BioGRID:114068 BioGRID:112183 S100A4    BioGRID  PubMed Affinity Capture-Western 
    BioGRID:114068 BioGRID:109072 SFN    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:114068 BioGRID:113164 UBC    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:114068 BioGRID:113364 YWHAG    BioGRID  PubMed Affinity Capture-MS 
    BioGRID:114068 BioGRID:116168 YWHAQ    BioGRID  PubMed Affinity Capture-MS 
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    General gene information

    Markers

    Genotypes

    Homology

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    cell adhesion TAS
    Traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    plasma membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
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    General protein information

    Preferred Names
    liprin-beta-1
    Names
    liprin-beta-1
    liprin-beta 1
    liprin related protein
    PTPRF-interacting protein-binding protein 1
    protein tyrosine phosphatase receptor type f polypeptide-interacting protein-binding protein 1
    protein-tyrosine phosphatase receptor-type f polypeptide-interacting protein-binding protein 1
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    NCBI Reference Sequences (RefSeq)

    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_001198915.1 → NP_001185844.1  liprin-beta-1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 2. The resulting isoform (3) is shorter at the N-terminus compared to isoform 2.
      Source sequence(s)
      AB033056, AC087257, BQ777042, CA442440
      Consensus CDS
      CCDS55814.1
      UniProtKB/Swiss-Prot
      Q86W92
      Related
      ENSP00000445425, OTTHUMP00000240410, ENST00000537927, OTTHUMT00000402876
      Conserved Domains (6) summary
      TIGR02168
      Location:2 – 178
      Blast Score: 110
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd09563
      Location:491 – 554
      Blast Score: 306
      SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
      cd09569
      Location:650 – 721
      Blast Score: 398
      SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
      smart00454
      Location:491 – 555
      Blast Score: 152
      SAM; Sterile alpha motif.
      pfam07647
      Location:654 – 721
      Blast Score: 139
      SAM_2; SAM domain (Sterile alpha motif)
      cl15755
      Location:565 – 627
      Blast Score: 236
      SAM_superfamily; SAM (Sterile alpha motif )

    2. NM_001198916.1 → NP_001185845.1  liprin-beta-1 isoform 4

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame exon compared to variant 2. The resulting isoform (4) has the same N- and C-termini but is shorter compared to isoform 2.
      Source sequence(s)
      AB033056, AC009509, AK314350, BQ777042, CA442440
      Consensus CDS
      CCDS55813.1
      UniProtKB/Swiss-Prot
      Q86W92
      Related
      ENSP00000443442, OTTHUMP00000240413, ENST00000542629, OTTHUMT00000402879
      Conserved Domains (6) summary
      TIGR02168
      Location:53 – 307
      Blast Score: 107
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      cd09563
      Location:613 – 676
      Blast Score: 307
      SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
      cd09569
      Location:772 – 843
      Blast Score: 397
      SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
      smart00454
      Location:613 – 677
      Blast Score: 152
      SAM; Sterile alpha motif.
      pfam07647
      Location:776 – 843
      Blast Score: 140
      SAM_2; SAM domain (Sterile alpha motif)
      cl15755
      Location:687 – 749
      Blast Score: 236
      SAM_superfamily; SAM (Sterile alpha motif )

    3. NM_003622.3 → NP_003613.3  liprin-beta-1 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) has multiple differences in the coding sequence compared to variant 2. The resulting isoform (1) has the same N- and C-termini but is 6 aa shorter compared to isoform 2.
      Source sequence(s)
      AB033056, AC009509, AF034802, BQ777042, CA442440
      Consensus CDS
      CCDS8713.1
      UniProtKB/Swiss-Prot
      Q86W92
      Related
      ENSP00000228425, OTTHUMP00000240414, ENST00000228425, OTTHUMT00000402880
      Conserved Domains (6) summary
      COG1196
      Location:62 – 308
      Blast Score: 116
      Smc; Chromosome segregation ATPases [Cell division and chromosome partitioning]
      cd09563
      Location:638 – 701
      Blast Score: 307
      SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
      cd09569
      Location:797 – 868
      Blast Score: 398
      SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
      smart00454
      Location:638 – 702
      Blast Score: 152
      SAM; Sterile alpha motif.
      pfam07647
      Location:801 – 868
      Blast Score: 140
      SAM_2; SAM domain (Sterile alpha motif)
      cl15755
      Location:712 – 774
      Blast Score: 237
      SAM_superfamily; SAM (Sterile alpha motif )

    4. NM_177444.2 → NP_803193.2  liprin-beta-1 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longest transcript and encodes the longest isoform (2).
      Source sequence(s)
      AB033056, AC009509, BC050281, BQ777042, CA442440
      Consensus CDS
      CCDS55812.1
      UniProtKB/Swiss-Prot
      Q86W92
      Related
      ENSP00000314724, OTTHUMP00000240411, ENST00000318304, OTTHUMT00000402877
      Conserved Domains (6) summary
      COG1196
      Location:102 – 338
      Blast Score: 109
      Smc; Chromosome segregation ATPases [Cell division and chromosome partitioning]
      cd09563
      Location:644 – 707
      Blast Score: 305
      SAM_liprin-beta1,2_repeat1; SAM domain of liprin-beta1,2 proteins repeat 1
      cd09569
      Location:803 – 874
      Blast Score: 397
      SAM_liprin-beta1,2_repeat3; SAM domain of liprin-beta proteins repeat 3
      smart00454
      Location:644 – 708
      Blast Score: 151
      SAM; Sterile alpha motif.
      pfam07647
      Location:807 – 874
      Blast Score: 139
      SAM_2; SAM domain (Sterile alpha motif)
      cl15755
      Location:718 – 780
      Blast Score: 236
      SAM_superfamily; SAM (Sterile alpha motif )

    RefSeqs of Annotated Genomes: Build 37.3

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

    Reference GRCh37.p5 Primary Assembly

    Genomic

    1. NC_000012.11 Reference GRCh37.p5 Primary Assembly

      Range
      27677045..27848497
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000144.1 Alternate HuRef

      Range
      27445920..27617349
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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    Related Sequences

    Nucleotide Protein
    Heading Accession and Version
    genomic AC009509.7 (16828..109465) None
    genomic AC068794.25 (119275..137042) None
    genomic AC087257.13 (109070..170115) None
    genomic CH471094.1 EAW96558.1
      EAW96559.1
      EAW96560.1
      EAW96561.1
      EAW96562.1
    mRNA AB033056.2 BAA86544.2
    mRNA AB049149.1 BAB39690.1
    mRNA AF034802.1 AAC26103.1
    mRNA AJ276680.1 CAB77544.1
    mRNA AK000807.1 None
    mRNA AK294267.1 BAG57559.1
    mRNA AK314350.1 None
    mRNA BC001560.1 None
    mRNA BC022873.1 AAH22873.1
    mRNA BC046159.1 AAH46159.1
    mRNA BC050281.1 AAH50281.1
    mRNA BM272389.1 None
    mRNA BQ777042.1 None
    mRNA BX648761.1 None
    mRNA CA442440.1 None
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q05CN4 GenPept UniProtKB/TrEMBL:Q05CN4
    Q86W92.2 GenPept UniProtKB/Swiss-Prot:Q86W92
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    Additional Links

    Gene LinkOut

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

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