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ASTN1 astrotactin 1 [ Homo sapiens (human) ]

Gene ID: 460, updated on 14-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 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

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