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    ASTN1 astrotactin 1 [ Homo sapiens (human) ]

    Gene ID: 460, updated on 27-Nov-2024

    Summary

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    Official Symbol
    ASTN1provided by HGNC
    Official Full Name
    astrotactin 1provided by HGNC
    Primary source
    HGNC:HGNC:773
    See related
    Ensembl:ENSG00000152092 MIM:600904; AllianceGenome:HGNC:773
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ASTN
    Summary
    Astrotactin is a neuronal adhesion molecule required for glial-guided migration of young postmitotic neuroblasts in cortical regions of developing brain, including cerebrum, hippocampus, cerebellum, and olfactory bulb (Fink et al., 1995).[supplied by OMIM, Jun 2009]
    Expression
    Biased expression in brain (RPKM 17.5), adrenal (RPKM 5.3) and 1 other tissue See more
    Orthologs
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    Genomic context

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    See ASTN1 in Genome Data Viewer
    Location:
    1q25.2
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (176857321..177164712, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (176211993..176519385, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (176826457..177133848, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1571 Neighboring gene mortality factor 4 like 1 pseudogene 7 Neighboring gene pappalysin 2 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr1:176525984-176527183 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1572 Neighboring gene PTP4A1 pseudogene 7 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:176694898-176695118 Neighboring gene NANOG hESC enhancer GRCh37_chr1:176702698-176703199 Neighboring gene MPRA-validated peak474 silencer Neighboring gene GATA motif-containing MPRA enhancer 65 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:176873531-176874030 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:176873029-176873530 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:177013479-177014043 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:177017656-177018356 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:177029877-177031076 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr1:177034489-177035123 Neighboring gene microRNA 488 Neighboring gene OCT4-H3K4me1 hESC enhancer GRCh37_chr1:177139732-177140321 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:177140322-177140910 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:177150672-177151233 Neighboring gene uncharacterized LOC105371625 Neighboring gene BMP/retinoic acid inducible neural specific 2 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:177224616-177225815 Neighboring gene long intergenic non-protein coding RNA 1645

    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
    • 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. Astrotactin: a novel neuronal cell surface antigen that mediates neuron-astroglial interactions in cerebellar microcultures. Edmondson JC, et al. J Cell Biol, 1988 Feb. PMID 3276720, Free PMC Article
    2. ASTN1 and alcohol dependence: family-based association analysis in multiplex alcohol dependence families. Hill SY, et al. Am J Med Genet B Neuropsychiatr Genet, 2012 Jun. PMID 22488871, Free PMC Article
    3. ASTN1 is associated with immune infiltrates in hepatocellular carcinoma, and inhibits the migratory and invasive capacity of liver cancer via the Wnt/β‑catenin signaling pathway. Chen QF, et al. Oncol Rep, 2020 Oct. PMID 32945491, Free PMC Article
    4. Astrotactin (ASTN), a gene for glial-guided neuronal migration, maps to human chromosome 1q25.2. Fink JM, et al. Genomics, 1997 Feb 15. PMID 9070947
    5. Association analysis of schizophrenia on 18 genes involved in neuronal migration: MDGA1 as a new susceptibility gene. Kähler AK, et al. Am J Med Genet B Neuropsychiatr Genet, 2008 Oct 5. PMID 18384059

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. ASTN1 is associated with immune infiltrates in hepatocellular carcinoma, and inhibits the migratory and invasive capacity of liver cancer via the Wnt/betacatenin signaling pathway.
      Title: ASTN1 is associated with immune infiltrates in hepatocellular carcinoma, and inhibits the migratory and invasive capacity of liver cancer via the Wnt/β‑catenin signaling pathway.
    2. Family-based association analysis shows the ASTN1 gene significantly associated with alcohol dependence.
      Title: ASTN1 and alcohol dependence: family-based association analysis in multiplex alcohol dependence families.
    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. Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.
    5. Observational study of gene-disease association. (HuGE Navigator)
      Title: Identification of new putative susceptibility genes for several psychiatric disorders by association analysis of regulatory and non-synonymous SNPs of 306 genes involved in neurotransmission and neurodevelopment.
    Submit: New GeneRIF Correction

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Clone Names

    • KIAA1747

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in locomotory behavior IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in neuron cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neuron migration IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in clathrin-coated vesicle IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in external side of plasma membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in perikaryon IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    astrotactin-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_001286164.2 → NP_001273093.1  astrotactin-1 isoform 3 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR and uses an alternate exon in the 3' coding region. The encoded isoform (3) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL021398, AL022145, AL031290, BC032870
      Consensus CDS
      CCDS65732.1
      UniProtKB/TrEMBL
      A6H8Y4, B1AJS1
      Related
      ENSP00000356629.3, ENST00000367657.7
      Conserved Domains (2) summary
      smart00457
      Location:804 → 991
      MACPF; membrane-attack complex / perforin
      pfam14670
      Location:652 → 699
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    2. NM_001364856.2 → NP_001351785.1  astrotactin-1 isoform 4 precursor

      Status: VALIDATED

      Source sequence(s)
      AL021398, AL022145, AL031290, AL136983
      UniProtKB/Swiss-Prot
      A5PL12, B4DHI9, E9PFR8, O14525, O60799, Q5W0V7, Q5W0V8
      UniProtKB/TrEMBL
      A6H8Y4
      Conserved Domains (2) summary
      smart00457
      Location:812 → 999
      MACPF; membrane-attack complex / perforin
      pfam14670
      Location:660 → 707
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    3. NM_004319.3 → NP_004310.1  astrotactin-1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_004310.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and it encodes the longest isoform (1).
      Source sequence(s)
      AL021398, AL031290, BC146795, BF507471
      Consensus CDS
      CCDS1319.1
      UniProtKB/TrEMBL
      A6H8Y4
      Related
      ENSP00000354536.2, ENST00000361833.7
      Conserved Domains (2) summary
      smart00457
      Location:804 → 991
      MACPF; membrane-attack complex / perforin
      pfam14670
      Location:652 → 699
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    4. NM_207108.3 → NP_996991.1  astrotactin-1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_996991.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses a different splice site in the 3' coding region and 3' UTR, compared to variant 1. The resulting protein (isoform 2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AL021398, AL031290, BC142697
      Consensus CDS
      CCDS44280.1
      UniProtKB/TrEMBL
      A6H8Y4
      Related
      ENSP00000395041.2, ENST00000424564.2
      Conserved Domains (2) summary
      smart00457
      Location:804 → 991
      MACPF; membrane-attack complex / perforin
      pfam14670
      Location:652 → 699
      FXa_inhibition; Coagulation Factor Xa inhibitory site

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      176857321..177164712 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017001341.3 → XP_016856830.1  astrotactin-1 isoform X1

      UniProtKB/TrEMBL
      A6H8Y4

    RNA

    1. XR_001737193.3 RNA Sequence

    2. XR_921796.4 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      176211993..176519385 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054336732.1 → XP_054192707.1  astrotactin-1 isoform X1

    RNA

    1. XR_008486049.1 RNA Sequence

    2. XR_008486050.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O14525.3 GenPept UniProtKB/Swiss-Prot:O14525

    Gene LinkOut

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

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