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    LSP1 lymphocyte specific protein 1 [ Homo sapiens (human) ]

    Gene ID: 4046, updated on 2-Nov-2024

    Summary

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    Official Symbol
    LSP1provided by HGNC
    Official Full Name
    lymphocyte specific protein 1provided by HGNC
    Primary source
    HGNC:HGNC:6707
    See related
    Ensembl:ENSG00000130592 MIM:153432; AllianceGenome:HGNC:6707
    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
    WP34; pp52
    Summary
    This gene encodes an intracellular F-actin binding protein. The protein is expressed in lymphocytes, neutrophils, macrophages, and endothelium and may regulate neutrophil motility, adhesion to fibrinogen matrix proteins, and transendothelial migration. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in spleen (RPKM 60.6), appendix (RPKM 43.3) and 19 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LSP1 in Genome Data Viewer
    Location:
    11p15.5
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (1853084..1892263)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (1938882..1978157)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (1874314..1913493)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3062 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3063 Neighboring gene uncharacterized LOC107984299 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4290 Neighboring gene troponin I2, fast skeletal type Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1870712-1871698 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4291 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4292 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4293 Neighboring gene microRNA 4298 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1891831-1892369 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1892370-1892907 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1896777-1897673 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1897674-1898570 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4294 Neighboring gene microRNA 7847 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:1908437-1908603 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr11:1918050-1919249 Neighboring gene proline rich 33 Neighboring gene long intergenic non-protein coding RNA 1150 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1927717-1928218 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:1928219-1928718 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3064 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 4295 Neighboring gene troponin T3, fast skeletal type Neighboring gene ReSE screen-validated silencer GRCh37_chr11:1956346-1956534 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:1956988-1957585

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues 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

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    Related articles in PubMed

    1. LSP1 promotes the progression of acute myelogenous leukemia by regulating KSR/ERK signaling pathway and cell migration. Li T, et al. Hematology, 2024 Dec. PMID 38511641
    2. Developmental regulation of lymphocyte-specific protein 1 (LSP1) expression in thymus during human T-cell maturation. Palker TJ, et al. Hybridoma, 1998 Dec. PMID 9890705
    3. The LSP1 rs3817198 T > C polymorphism contributes to increased breast cancer risk: a meta-analysis of twelve studies. Tang J, et al. Oncotarget, 2016 Sep 27. PMID 27590509, Free PMC Article
    4. Lymphocyte-specific protein 1: a specific marker of human leucocytes. Pulford K, et al. Immunology, 1999 Feb. PMID 10233704, Free PMC Article
    5. The 47-kD protein increased in neutrophil actin dysfunction with 47- and 89-kD protein abnormalities is lymphocyte-specific protein. Howard T, et al. Blood, 1994 Jan 1. PMID 8274738

    See all (84) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. LSP1 promotes the progression of acute myelogenous leukemia by regulating KSR/ERK signaling pathway and cell migration.
      Title: LSP1 promotes the progression of acute myelogenous leukemia by regulating KSR/ERK signaling pathway and cell migration.
    2. Lymphocyte-Specific Protein 1 Regulates Expression and Stability of Endothelial Nitric Oxide Synthase.
      Title: Lymphocyte-Specific Protein 1 Regulates Expression and Stability of Endothelial Nitric Oxide Synthase.
    3. Tim-3 Is Differentially Expressed during Cell Activation and Interacts with the LSP-1 Protein in Human Macrophages.
      Title: Tim-3 Is Differentially Expressed during Cell Activation and Interacts with the LSP-1 Protein in Human Macrophages.
    4. The correlation of leukocyte-specific protein 1 (LSP1) rs3817198(T>C) polymorphism with breast cancer: A meta-analysis.
      Title: The correlation of leukocyte-specific protein 1 (LSP1) rs3817198(T>C) polymorphism with breast cancer: A meta-analysis.
    5. Identification of Diagnostic Signatures and Immune Cell Infiltration Characteristics in Rheumatoid Arthritis by Integrating Bioinformatic Analysis and Machine-Learning Strategies.
      Title: Identification of Diagnostic Signatures and Immune Cell Infiltration Characteristics in Rheumatoid Arthritis by Integrating Bioinformatic Analysis and Machine-Learning Strategies.
    6. MiR-920 and LSP1 co-regulate the growth and migration of glioblastoma cells by modulation of JAK2/STAT5 pathway.
      Title: MiR-920 and LSP1 co-regulate the growth and migration of glioblastoma cells by modulation of JAK2/STAT5 pathway.
    7. Lymphocyte-specific protein 1 (LSP1) regulates bone marrow stromal cell antigen 2 (BST-2)-mediated intracellular trafficking of HIV-1 in dendritic cells.
      Title: Lymphocyte-specific protein 1 (LSP1) regulates bone marrow stromal cell antigen 2 (BST-2)-mediated intracellular trafficking of HIV-1 in dendritic cells.
    8. Predictive and prognostic value of LSP1 rs3817198 in sporadic breast cancer in northeastern population of Iran.
      Title: Predictive and prognostic value of LSP1 rs3817198 in sporadic breast cancer in northeastern population of Iran.
    9. Differential gene expression by SFRP2(+), FMO1(+), and COL11A1(+) fibroblasts suggests roles in matrix deposition, inflammatory cell retention, and connective tissue cell differentiation, respectively.
      Title: SFRP2/DPP4 and FMO1/LSP1 Define Major Fibroblast Populations in Human Skin.
    10. LSP1 rs3817198 T > C polymorphism is associated with increased risk of breast cancer, especially in Caucasian and Asian populations [meta-analysis]
      Title: The LSP1 rs3817198 T > C polymorphism contributes to increased breast cancer risk: a meta-analysis of twelve studies.
    Submit: New GeneRIF Correction See all GeneRIFs (32)

    Phenotypes

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

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    A possible mechanism behind autoimmune disorders discovered by genome-wide linkage and association analysis in celiac disease.
    EBI GWAS Catalog
    Genome-wide association study identifies five new breast cancer susceptibility loci.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple loci associated with bladder cancer risk.
    EBI GWAS Catalog
    Genome-wide association study identifies multiple loci associated with both mammographic density and breast cancer risk.
    EBI GWAS Catalog
    Genome-wide association study identifies novel breast cancer susceptibility loci.
    EBI GWAS Catalog
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    EBI GWAS Catalog
    Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
    EBI GWAS Catalog
    Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env HIV-1 gp120 upregulates the expression of lymphocyte-specific protein 1 (LSP1) in human B cells PubMed
    env Inhibition of M-tropic HIV-1 gp120-induced transendothelial migration by SLIT2N involves SLIT2N-mediated enhancement of co-localization of Robo1 with WASp and LSP1 in immature monocyte-derived dendritic cells PubMed
    env SLIT2N, an active fragment of SLIT2, inhibits M-tropic HIV-1 gp120-induced association of LSP1, Wiskott-Aldrich Syndrome protein (WASp), Actin-Related Protein 2/3 (Arp2/3), and beta-actin in immature monocyte-derived dendritic cells PubMed
    env HIV-1 gp120-induced migration of dendritic cells is regulated by a novel kinase cascade involving Pyk2, p38 MAP kinase, and LSP1 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

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    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 GOA

    Function Evidence Code Pubs
    enables actin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cellular defense response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in cellular response to interleukin-7 IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chemotaxis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in actin cytoskeleton TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in membrane HDA PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lymphocyte-specific protein 1
    Names
    47 kDa actin binding protein
    52 kDa phosphoprotein
    F-actin binding and cytoskeleton associated protein
    leufactin (leukocyte F-actin binding protein)
    leukocyte-specific protein 1
    lymphocyte-specific antigen WP34

    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.

    Genomic

    1. NG_011509.1 RefSeqGene

      Range
      5115..44294
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001013253.2 → NP_001013271.1  lymphocyte-specific protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001013271.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate exon and lacks two exons in the 5' region, and uses a downstream start codon, compared to variant 5. The resulting protein (isoform 2) has a shorter N-terminus compared to isoform 3. Variants 2, 3, 4 and 6 encode the same protein (isoform 2).
      Source sequence(s)
      AC051649, BC001785
      Consensus CDS
      CCDS31335.1
      UniProtKB/TrEMBL
      A8K7L8
      Related
      ENSP00000383932.2, ENST00000405957.6
      Conserved Domains (1) summary
      pfam02029
      Location:129 → 252
      Caldesmon; Caldesmon

    2. NM_001013254.1 → NP_001013272.1  lymphocyte-specific protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001013272.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate exon and lacks two exons in the 5' region, and uses a downstream start codon, compared to variant 5. The resulting protein (isoform 2) has a shorter N-terminus compared to isoform 3. Variants 2, 3, 4 and 6 encode the same protein (isoform 2).
      Source sequence(s)
      AC051649, AK056576, BC001785
      Consensus CDS
      CCDS31335.1
      UniProtKB/TrEMBL
      A8K7L8
      Related
      ENSP00000384022.2, ENST00000406638.6
      Conserved Domains (1) summary
      pfam02029
      Location:129 → 252
      Caldesmon; Caldesmon

    3. NM_001013255.1 → NP_001013273.1  lymphocyte-specific protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001013273.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate exon and lacks two exons in the 5' region, and uses a downstream start codon, compared to variant 5. The resulting protein (isoform 2) has a shorter N-terminus compared to isoform 3. Variants 2, 3, 4 and 6 encode the same protein (isoform 2).
      Source sequence(s)
      AC051649, BC001785, BQ893821
      Consensus CDS
      CCDS31335.1
      UniProtKB/TrEMBL
      A8K7L8
      Conserved Domains (1) summary
      pfam02029
      Location:129 → 252
      Caldesmon; Caldesmon

    4. NM_001242932.2 → NP_001229861.1  lymphocyte-specific protein 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) represents the longest transcript and encodes the longest isoform (3).
      Source sequence(s)
      AC051649, AK092071, BC001785, BE043985, BQ893037
      Consensus CDS
      CCDS58110.1
      UniProtKB/Swiss-Prot
      P33241
      Related
      ENSP00000371194.1, ENST00000381775.5
      Conserved Domains (1) summary
      pfam02029
      Location:319 → 413
      Caldesmon; Caldesmon

    5. NM_001289005.2 → NP_001275934.1  lymphocyte-specific protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001275934.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) contains a distinct 5' UTR and lacks an in-frame portion of the 5' coding region, compared to variant 5. The resulting isoform (2) has a shorter N-terminus, compared to isoform 3. Variants 2, 3, 4 and 6 encode the same protein (isoform 2).
      Source sequence(s)
      AC051649, AI817126, AK222733, AK292033
      Consensus CDS
      CCDS31335.1
      UniProtKB/TrEMBL
      A8K7L8
      Related
      ENSP00000484140.1, ENST00000612798.4
      Conserved Domains (1) summary
      pfam02029
      Location:129 → 252
      Caldesmon; Caldesmon

    6. NM_002339.3 → NP_002330.1  lymphocyte-specific protein 1 isoform 1

      See identical proteins and their annotated locations for NP_002330.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) contains an alternate exon and lacks two exons in the 5' coding region compared to variant 5. The resulting protein (isoform 1) has a distinct N-terminus and is shorter than isoform 3.
      Source sequence(s)
      AC051649, BC001785
      Consensus CDS
      CCDS31334.1
      UniProtKB/Swiss-Prot
      B3KPP1, B3KRR6, E9PBV6, E9PFP3, P33241, Q16096, Q53H48, Q6FHM3, Q9BUY8
      UniProtKB/TrEMBL
      A8K2L4
      Related
      ENSP00000308383.4, ENST00000311604.8
      Conserved Domains (1) summary
      pfam02029
      Location:191 → 314
      Caldesmon; Caldesmon

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      1853084..1892263
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_021160004.1 Reference GRCh38.p14 PATCHES

      Range
      43587..82766
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      1938882..1978157
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P33241.1 GenPept UniProtKB/Swiss-Prot:P33241

    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