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Aliases for LST1 Gene

Aliases for LST1 Gene

  • Leukocyte Specific Transcript 1 2 3 5
  • B144 3 4
  • Leukocyte-Specific Transcript 1 Protein 3
  • Lymphocyte Antigen 117 3
  • Protein B144 4
  • D6S49E 3
  • LST-1 3

External Ids for LST1 Gene

Previous GeneCards Identifiers for LST1 Gene

  • GC06P031617
  • GC06P031324
  • GC06P031658
  • GC06P031661
  • GC06P031556
  • GC06P031557
  • GC06P031340
  • GC06P031558
  • GC06P031568
  • GC06P031718
  • GC06P031760
  • GC06P031615
  • GC06P031625
  • GC06P031630
  • GC06P031643
  • GC06P031659
  • GC06P031669
  • GC06P031679
  • GC06P031997

Summaries for LST1 Gene

Entrez Gene Summary for LST1 Gene

  • The protein encoded by this gene is a membrane protein that can inhibit the proliferation of lymphocytes. Expression of this gene is enhanced by lipopolysaccharide, interferon-gamma, and bacteria. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

GeneCards Summary for LST1 Gene

LST1 (Leukocyte Specific Transcript 1) is a Protein Coding gene.

UniProtKB/Swiss-Prot for LST1 Gene

  • Possible role in modulating immune responses. Induces morphological changes including production of filopodia and microspikes when overexpressed in a variety of cell types and may be involved in dendritic cell maturation. Isoform 1 and isoform 2 have an inhibitory effect on lymphocyte proliferation.

Gene Wiki entry for LST1 Gene

Additional gene information for LST1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LST1 Gene

Genomics for LST1 Gene

GeneHancer (GH) Regulatory Elements for LST1 Gene

Promoters and enhancers for LST1 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH06J031567 Promoter/Enhancer 2.8 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 656.5 -7.7 -7705 22.2 HDGF PKNOX1 SMAD1 MLX ZFP64 ARID4B SIN3A DMAP1 YBX1 ZNF2 TNF ATP6V1G2 LST1 GC06P032155 GC06P032156 GC06P032157 GC06P032158 GC06P032160 GC06P032161 GC06P032163
GH06J031614 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE 12.5 +29.7 29710 3.7 HDGF HDAC1 ELF3 FOXA2 IRF4 ZNF335 ZNF121 ATF7 ETV6 BCLAF1 AIF1 BAG6 LY6G5B DDX39B SKIV2L CSNK2B HLA-DRB1 NRM DHX16 LY6G5C
GH06J031557 Enhancer 1.2 Ensembl ENCODE 13.2 -26.5 -26533 4.2 HDGF ATF1 SMAD1 IRF4 NCOA2 TCF12 E2F8 ZNF207 ZNF143 ATF7 LTA CSNK2B DDX39B LST1 NCR3 UQCRHP1 AIF1 LTB SNORD117 PSORS1C2
GH06J031733 Promoter/Enhancer 2.7 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 4.8 +151.3 151331 8.5 CLOCK MLX ZFP64 YBX1 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 MSH5 CLIC1 MSH5-SAPCD1 DDX39B LY6G5B ATF6B LSM2 SKIV2L CSNK2B GPANK1
GH06J031591 Promoter/Enhancer 1.4 EPDnew Ensembl ENCODE 6.9 +7.0 6958 2.3 HDGF ZSCAN4 EBF1 CDC5L ZFHX2 CTBP1 POLR2A EGR1 EED IKZF2 NCR3 DDX39B ATF6B LY6G5B LSM2 MDC1 MICA-AS1 MICA PPP1R10 SKIV2L
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LST1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LST1 gene promoter:
  • AP-1
  • ATF-2
  • c-Jun
  • p53
  • PPAR-gamma1

Genomic Locations for LST1 Gene

Genomic Locations for LST1 Gene
chr6:31,586,124-31,588,909
(GRCh38/hg38)
Size:
2,786 bases
Orientation:
Plus strand
chr6:31,553,901-31,556,686
(GRCh37/hg19)
Size:
2,786 bases
Orientation:
Plus strand

Genomic View for LST1 Gene

Genes around LST1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LST1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LST1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for LST1 Gene

  • Protein details for LST1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O00453-LST1_HUMAN
    Recommended name:
    Leukocyte-specific transcript 1 protein
    Protein Accession:
    O00453
    Secondary Accessions:
    • B0S8E0
    • B0S8E1
    • B0S8E5
    • O00452
    • O00454
    • Q13669
    • Q2HNT3
    • Q5HYS9
    • Q5SP24
    • Q5STA5
    • Q5STA6
    • Q5STA7
    • Q5STA8
    • Q5STW6
    • Q9UJR5
    • Q9UJR6
    • Q9UJR7
    • Q9UJR8
    • Q9UJS1

    Protein attributes for LST1 Gene

    Size:
    97 amino acids
    Molecular mass:
    10792 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAX45332.1; Type=Erroneous termination; Positions=47; Note=Translated as Gln.; Evidence={ECO:0000305};

    Alternative splice isoforms for LST1 Gene

neXtProt entry for LST1 Gene

Post-translational modifications for LST1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LST1 Gene

Domains & Families for LST1 Gene

Gene Families for LST1 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Predicted secreted proteins

Protein Domains for LST1 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LST1 Gene

Graphical View of Domain Structure for InterPro Entry

O00453

UniProtKB/Swiss-Prot:

LST1_HUMAN :
  • Belongs to the LST1 family.
Family:
  • Belongs to the LST1 family.
genes like me logo Genes that share domains with LST1: view

Function for LST1 Gene

Molecular function for LST1 Gene

UniProtKB/Swiss-Prot Function:
Possible role in modulating immune responses. Induces morphological changes including production of filopodia and microspikes when overexpressed in a variety of cell types and may be involved in dendritic cell maturation. Isoform 1 and isoform 2 have an inhibitory effect on lymphocyte proliferation.
UniProtKB/Swiss-Prot Induction:
By IFNG/IFN-gamma. Up-regulated upon autoimmune and bacterially-induced inflammation.
GENATLAS Biochemistry:
leukocyte specific transcript 1,with several alternatively spliced isoforms,homolog of the mouse B144 transcript,predominantly expressed in monocytes

Phenotypes From GWAS Catalog for LST1 Gene

genes like me logo Genes that share phenotypes with LST1: view

Animal Model Products

  • Taconic Biosciences Mouse Models for LST1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for LST1 Gene

Localization for LST1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for LST1 Gene

Membrane; Single-pass membrane protein. Golgi apparatus membrane; Single-pass membrane protein. Endomembrane system; Single-pass membrane protein. Note=Also detected in a perinuclear region corresponding to the localization of the Golgi apparatus and throughout the cytoplasm.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for LST1 gene
Compartment Confidence
extracellular 3
nucleus 2

Gene Ontology (GO) - Cellular Components for LST1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005737 cytoplasm IDA 11478849
GO:0005794 Golgi apparatus NAS 11478849
GO:0012505 endomembrane system IEA --
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with LST1: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for LST1 Gene

Pathways & Interactions for LST1 Gene

No Data Available

Gene Ontology (GO) - Biological Process for LST1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000902 cell morphogenesis IEA --
GO:0002376 immune system process IEA --
GO:0006955 immune response NAS,IEA 7590964
GO:0008360 regulation of cell shape IEA --
GO:0009653 anatomical structure morphogenesis NAS 10944527
genes like me logo Genes that share ontologies with LST1: view

No data available for Pathways by source and SIGNOR curated interactions for LST1 Gene

Drugs & Compounds for LST1 Gene

(1) Drugs for LST1 Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Abacavir Approved, Investigational Pharma 222
genes like me logo Genes that share compounds with LST1: view

Transcripts for LST1 Gene

Unigene Clusters for LST1 Gene

Leukocyte specific transcript 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for LST1 Gene

No ASD Table

Relevant External Links for LST1 Gene

GeneLoc Exon Structure for
LST1
ECgene alternative splicing isoforms for
LST1

Expression for LST1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LST1 Gene

mRNA differential expression in normal tissues according to GTEx for LST1 Gene

This gene is overexpressed in Whole Blood (x33.4) and Spleen (x6.0).

Protein differential expression in normal tissues from HIPED for LST1 Gene

This gene is overexpressed in Urine (36.9), Monocytes (17.5), and Peripheral blood mononuclear cells (12.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LST1 Gene



Protein tissue co-expression partners for LST1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of LST1 Gene:

LST1

SOURCE GeneReport for Unigene cluster for LST1 Gene:

Hs.436066

mRNA Expression by UniProt/SwissProt for LST1 Gene:

O00453-LST1_HUMAN
Tissue specificity: Expressed in lung, tonsil, thymus, placenta, kidney, fetal spleen, fetal liver and brain.

Evidence on tissue expression from TISSUES for LST1 Gene

  • Bone marrow(2.2)
  • Spleen(2)
genes like me logo Genes that share expression patterns with LST1: view

No data available for Phenotype-based relationships between genes and organs from Gene ORGANizer for LST1 Gene

Orthologs for LST1 Gene

This gene was present in the common ancestor of mammals.

Orthologs for LST1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LST1 33
  • 99.31 (n)
dog
(Canis familiaris)
Mammalia LST1 34
  • 77 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Lst1 34
  • 53 (a)
OneToOne
Species where no ortholog for LST1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • cow (Bos Taurus)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • oppossum (Monodelphis domestica)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for LST1 Gene

ENSEMBL:
Gene Tree for LST1 (if available)
TreeFam:
Gene Tree for LST1 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LST1: view image

Paralogs for LST1 Gene

No data available for Paralogs for LST1 Gene

Variants for LST1 Gene

Sequence variations from dbSNP and Humsavar for LST1 Gene

SNP ID Clin Chr 06 pos Variation AA Info Type
rs1000228388 -- 31,588,957(+) A/G downstream_transcript_variant
rs1000791610 -- 31,587,071(+) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1001966262 -- 31,586,604(+) C/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1002410742 -- 31,586,819(+) T/C genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1003587055 -- 31,584,601(+) C/A upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for LST1 Gene

Variant ID Type Subtype PubMed ID
dgv10403n54 CNV loss 21841781
dgv10404n54 CNV loss 21841781
nsv1073969 CNV deletion 25765185
nsv1112900 CNV deletion 24896259
nsv1126749 CNV deletion 24896259
nsv830627 CNV loss 17160897

Variation tolerance for LST1 Gene

Residual Variation Intolerance Score: 85.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.94; 59.67% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LST1 Gene

Human Gene Mutation Database (HGMD)
LST1
SNPedia medical, phenotypic, and genealogical associations of SNPs for
LST1

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LST1 Gene

Disorders for LST1 Gene

Additional Disease Information for LST1

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for LST1 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for LST1 Gene

Publications for LST1 Gene

  1. LST1 and NCR3 expression in autoimmune inflammation and in response to IFN-gamma, LPS and microbial infection. (PMID: 16362817) Mulcahy H … O'Gara F (Immunogenetics 2006) 3 4 22 58
  2. LST1: a gene with extensive alternative splicing and immunomodulatory function. (PMID: 10706707) Rollinger-Holzinger I … Zwierzina H (Journal of immunology (Baltimore, Md. : 1950) 2000) 3 4 22 58
  3. Complex expression pattern of the TNF region gene LST1 through differential regulation, initiation, and alternative splicing. (PMID: 9367684) de Baey A … Weiss EH (Genomics 1997) 2 3 4 58
  4. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 44 58
  5. A strong genetic association between the tumor necrosis factor locus and proliferative vitreoretinopathy: the retina 4 project. (PMID: 20663564) Rojas J … Carracedo A (Ophthalmology 2010) 3 44 58

Products for LST1 Gene

Sources for LST1 Gene

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