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    ALMS1 ALMS1 centrosome and basal body associated protein [ Homo sapiens (human) ]

    Gene ID: 7840, updated on 22-Jun-2019

    Summary

    Official Symbol
    ALMS1provided by HGNC
    Official Full Name
    ALMS1 centrosome and basal body associated proteinprovided by HGNC
    Primary source
    HGNC:HGNC:428
    See related
    Ensembl:ENSG00000116127 MIM:606844
    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
    ALSS
    Summary
    This gene encodes a protein containing a large tandem-repeat domain as well as additional low complexity regions. The encoded protein functions in microtubule organization, particularly in the formation and maintanance of cilia. Mutations in this gene cause Alstrom syndrome. There is a pseudogene for this gene located adjacent in the same region of chromosome 2. Alternative splice variants have been described but their full length nature has not been determined. [provided by RefSeq, Apr 2014]
    Expression
    Broad expression in testis (RPKM 15.5), ovary (RPKM 5.0) and 21 other tissues See more
    Orthologs

    Genomic context

    See ALMS1 in Genome Data Viewer
    Location:
    2p13.1
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (73385758..73609919)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (73612886..73837047)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 5299 Neighboring gene uncharacterized LOC105374804 Neighboring gene ribosomal protein SA pseudogene 28 Neighboring gene G protein subunit gamma 5 pseudogene 4 Neighboring gene ALMS1 intronic transcript 1 Neighboring gene ALMS1 pseudogene 1 Neighboring gene N-acetyltransferase 8 (putative)

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Alstrom syndrome
    MedGen: C0268425 OMIM: 203800 GeneReviews: Alstrom Syndrome
    not available

    NHGRI GWAS Catalog

    Description
    A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection.
    NHGRI GWA Catalog
    An atlas of genetic influences on human blood metabolites.
    NHGRI GWA Catalog
    Genetic loci influencing kidney function and chronic kidney disease.
    NHGRI GWA Catalog
    Genome-wide association study of a heart failure related metabolomic profile among African Americans in the Atherosclerosis Risk in Communities (ARIC) study.
    NHGRI GWA Catalog
    Genome-wide association study of metabolic traits reveals novel gene-metabolite-disease links.
    NHGRI GWA Catalog
    Human metabolic individuality in biomedical and pharmaceutical research.
    NHGRI GWA Catalog
    New loci associated with kidney function and chronic kidney disease.
    NHGRI GWA Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    retropepsin gag-pol HIV-1 PR is identified to have a physical interaction with Alstrom syndrome 1 (ALMS1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • AURKA Activation by TPX2, organism-specific biosystem (from REACTOME)
      AURKA Activation by TPX2, organism-specific biosystemTPX2 binds to aurora kinase A (AURKA) at centrosomes and promotes its activation by facilitating AURKA active conformation and autophosphorylation of the AURKA threonine residue T288 (Bayliss et al. ...
    • Anchoring of the basal body to the plasma membrane, organism-specific biosystem (from REACTOME)
      Anchoring of the basal body to the plasma membrane, organism-specific biosystemCilium biogenesis is initiated by the docking of basal bodies, a centriole-derived organelle, to the plasma membrane (reviewed in Reiter et al, 2012). The centriole consists of a multiprotein core su...
    • Cell Cycle, organism-specific biosystem (from REACTOME)
      Cell Cycle, organism-specific biosystem
      Cell Cycle
    • Cell Cycle, Mitotic, organism-specific biosystem (from REACTOME)
      Cell Cycle, Mitotic, organism-specific biosystemThe replication of the genome and the subsequent segregation of chromosomes into daughter cells are controlled by a series of events collectively known as the cell cycle. DNA replication is carried o...
    • Centrosome maturation, organism-specific biosystem (from REACTOME)
      Centrosome maturation, organism-specific biosystemThe centrosome is the primary microtubule organizing center (MTOC) in vertebrate cells and plays an important role in orchestrating the formation of the mitotic spindle. Centrosome maturation is an ...
    • Cilium Assembly, organism-specific biosystem (from REACTOME)
      Cilium Assembly, organism-specific biosystemCilia are membrane covered organelles that extend from the surface of eukaryotic cells. Cilia may be motile, such as respiratory cilia) or non-motile (such as the primary cilium) and are distinguishe...
    • G2/M Transition, organism-specific biosystem (from REACTOME)
      G2/M Transition, organism-specific biosystemCyclin A can also form complexes with Cdc2 (Cdk1). Together with three B-type cyclins, Cdc2 (Cdk1) regulates the transition from G2 into mitosis. These complexes are activated by dephosphorylation of...
    • Loss of Nlp from mitotic centrosomes, organism-specific biosystem (from REACTOME)
      Loss of Nlp from mitotic centrosomes, organism-specific biosystemDuring interphase, Nlp interacts with gamma-tubulin ring complexes (gamma-TuRC), and is thought to contribute to the organization of interphase microtubules (Casenghi et al.,2003). Plk1 is activated...
    • Loss of proteins required for interphase microtubule organization from the centrosome, organism-specific biosystem (from REACTOME)
      Loss of proteins required for interphase microtubule organization from the centrosome, organism-specific biosystemIn addition to recruiting proteins and complexes necessary for increased microtubule nucleation, centrosomal maturation involves the loss of proteins involved in interphase microtubule organization ...
    • Mitotic G2-G2/M phases, organism-specific biosystem (from REACTOME)
      Mitotic G2-G2/M phases, organism-specific biosystem
      Mitotic G2-G2/M phases
    • Organelle biogenesis and maintenance, organism-specific biosystem (from REACTOME)
      Organelle biogenesis and maintenance, organism-specific biosystemThis module describes the biogenesis of organelles. Organelles are subcellular structures of distinctive morphology and function. The organelles of human cells include: mitochondria, endoplasmic reti...
    • Recruitment of mitotic centrosome proteins and complexes, organism-specific biosystem (from REACTOME)
      Recruitment of mitotic centrosome proteins and complexes, organism-specific biosystemThe mitotic spindle becomes established once centrosomes have migrated to opposite poles and the nuclear envelope has broken down. During this stage, interphase centrosomes mature into mitotic centro...
    • Regulation of PLK1 Activity at G2/M Transition, organism-specific biosystem (from REACTOME)
      Regulation of PLK1 Activity at G2/M Transition, organism-specific biosystemThe kinase activity of PLK1 is required for cell cycle progression as PLK1 phosphorylates and regulates a number of cellular proteins during mitosis. Centrosomic AURKA (Aurora A kinase), catalyticall...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • KIAA0328, DKFZp686A118, DKFZp686D1828

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    alpha-actinin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    molecular_function ND
    No biological Data available
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    G2/M transition of mitotic cell cycle TAS
    Traceable Author Statement
    more info
     
    ciliary basal body-plasma membrane docking TAS
    Traceable Author Statement
    more info
     
    endosomal transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of cold-induced thermogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    regulation of G2/M transition of mitotic cell cycle TAS
    Traceable Author Statement
    more info
     
    regulation of centriole replication IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    regulation of stress fiber assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    centriole IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    colocalizes_with centriole IDA
    Inferred from Direct Assay
    more info
    PubMed 
    centrosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    centrosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cilium IEA
    Inferred from Electronic Annotation
    more info
     
    cytosol IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cytosol TAS
    Traceable Author Statement
    more info
     
    spindle pole IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    Alstrom syndrome protein 1
    Names
    Alstrom syndrome 1

    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.

    Genomic

    1. NG_011690.1 RefSeqGene

      Range
      5001..229167
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_741

    mRNA and Protein(s)

    1. NM_015120.4NP_055935.4  Alstrom syndrome protein 1

      Status: REVIEWED

      Source sequence(s)
      AC074008, AC092653, AC096546, AJ417593
      Consensus CDS
      CCDS42697.1
      UniProtKB/Swiss-Prot
      Q8TCU4
      Related
      ENSP00000482968.1, ENST00000613296.5
      Conserved Domains (2) summary
      pfam06583
      Location:14251573
      Neogenin_C; Neogenin C-terminus
      pfam15309
      Location:40344165
      ALMS_motif; ALMS motif

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

      Range
      73385758..73609919
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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