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    ATG9B autophagy related 9B [ Homo sapiens (human) ]

    Gene ID: 285973, updated on 31-Mar-2024

    Summary

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    Official Symbol
    ATG9Bprovided by HGNC
    Official Full Name
    autophagy related 9Bprovided by HGNC
    Primary source
    HGNC:HGNC:21899
    See related
    Ensembl:ENSG00000181652 MIM:612205; AllianceGenome:HGNC:21899
    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
    SONE; APG9L2; NOS3AS
    Summary
    This gene functions in the regulation of autophagy, a lysosomal degradation pathway. This gene also functions as an antisense transcript in the posttranscriptional regulation of the endothelial nitric oxide synthase 3 gene, which has 3' overlap with this gene on the opposite strand. Mutations in this gene and disruption of the autophagy process have been associated with multiple cancers. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Sep 2012]
    Expression
    Broad expression in skin (RPKM 9.1), placenta (RPKM 8.7) and 15 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ATG9B in Genome Data Viewer
    Location:
    7q36.1
    Exon count:
    19
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (151012209..151024499, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (152185332..152201351, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (150709297..150721586, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105375567 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150549187-150549758 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150553923-150554766 Neighboring gene amine oxidase copper containing 1 Neighboring gene Sharpr-MPRA regulatory region 11983 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150607062-150607562 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:150642260-150643002 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150643003-150643744 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150645973-150646713 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150651428-150652026 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150654831-150655332 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150658991-150659600 Neighboring gene VISTA enhancer hs2192 Neighboring gene potassium voltage-gated channel subfamily H member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150669129-150669642 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18785 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18786 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18787 Neighboring gene uncharacterized LOC124901776 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150672781-150673707 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18788 Neighboring gene NOS3 5' regulatory region Neighboring gene ReSE screen-validated silencer GRCh37_chr7:150697314-150697476 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr7:150698330-150699529 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150703744-150704324 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150704325-150704905 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26844 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:150710378-150711069 Neighboring gene nitric oxide synthase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18790 Neighboring gene uncharacterized LOC124901777 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:150722492-150723096 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:150723702-150724305 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr7:150724306-150724910 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:150725516-150726120 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:150726121-150726724 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:150736215-150736999 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:150737000-150737783 Neighboring gene ATP binding cassette subfamily B member 8

    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. Polymorphisms in autophagy genes and susceptibility to tuberculosis. Songane M, et al. PLoS One, 2012. PMID 22879892, Free PMC Article
    2. Induction of cellular senescence by doxorubicin is associated with upregulated miR-375 and induction of autophagy in K562 cells. Yang MY, et al. PLoS One, 2012. PMID 22606351, Free PMC Article
    3. Genetic polymorphisms in oxidative stress pathway genes and modification of BMI and risk of non-Hodgkin lymphoma. Kim C, et al. Cancer Epidemiol Biomarkers Prev, 2012 May. PMID 22374993, Free PMC Article
    4. Comprehensive analysis of expression pattern and promoter regulation of human autophagy-related genes. Kusama Y, et al. Apoptosis, 2009 Oct. PMID 19657746
    5. Hypoxia-inducible expression of a natural cis-antisense transcript inhibits endothelial nitric-oxide synthase. Fish JE, et al. J Biol Chem, 2007 May 25. PMID 17403686

    See all (32) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Depletion of CPNE7 sensitizes colorectal cancer to 5-fluorouracil by downregulating ATG9B expression.
      Title: Depletion of CPNE7 sensitizes colorectal cancer to 5-fluorouracil by downregulating ATG9B expression.
    2. ATG9B is a tissue-specific homotrimeric lipid scramblase that can compensate for ATG9A.
      Title: ATG9B is a tissue-specific homotrimeric lipid scramblase that can compensate for ATG9A.
    3. Contribution of NOS3AS Variants to Susceptibility to Essential Hypertension: A Study in Kermanshah Province, Western Iran.
      Title: Contribution of NOS3AS Variants to Susceptibility to Essential Hypertension: A Study in Kermanshah Province, Western Iran.
    4. Aging is associated with a decline in Atg9b-mediated autophagosome formation and appearance of enlarged mitochondria in the heart.
      Title: Aging is associated with a decline in Atg9b-mediated autophagosome formation and appearance of enlarged mitochondria in the heart.
    5. This study highlights the transcriptional inactivation mechanisms of ATG2B, ATG4D, ATG9A and ATG9B promoter methylation status and the possible origin of autophagy signal pathway repression in invasive ductal carcinomas.
      Title: Aberrant methylation of ATG2B, ATG4D, ATG9A and ATG9B CpG island promoter is associated with decreased mRNA expression in sporadic breast carcinoma.
    6. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    7. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
      Title: Polymorphisms in innate immunity genes and risk of childhood leukemia.
    8. The role of Atg9 trafficking in yeast and mammalian autophagy, is summarised.
      Title: New insights into the function of Atg9.
    9. Observational study of gene-disease association, gene-gene interaction, gene-environment interaction, and genetic testing. (HuGE Navigator)
      Title: Integrative predictive model of coronary artery calcification in atherosclerosis.
    10. Observational study of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Genetic polymorphisms in nitric oxide synthase genes modify the relationship between vegetable and fruit intake and risk of non-Hodgkin lymphoma.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    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)

    Genotypes

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Macrophage exposure to infectious or AT-2 inactivated HIV-1 increases expression of the TFEB targets ATG9B, UVRAG (both autophagy genes) and MCOLN1 (a lysosomal gene) at 24 hours post-exposure. 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 phospholipid scramblase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within autophagosome assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in autophagy of mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in bone morphogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in piecemeal microautophagy of the nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in plasma membrane phospholipid scrambling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in programmed necrotic cell death ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein localization to phagophore assembly site IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in reticulophagy IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in autophagosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in endoplasmic reticulum membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in phagophore assembly site IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in phagophore assembly site membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in recycling endosome membrane ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in trans-Golgi network ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    autophagy-related protein 9B
    Names
    APG9-like 2
    ATG9 autophagy related 9 homolog B
    autophagy 9-like 2 protein
    endothelial nitric oxide synthase antisense
    nitric oxide synthase 3-overlapping antisense gene protein

    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_030317.1 RefSeqGene

      Range
      5006..14349
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001317056.2 → NP_001303985.1  autophagy-related protein 9B

      Status: REVIEWED

      Source sequence(s)
      AC010973, AY515311, BM821239, BU741121, BX380863, BX420361
      Consensus CDS
      CCDS83242.1
      UniProtKB/Swiss-Prot
      A1A5D3, Q674R7, Q6JRW5, Q8N8I8
      Related
      ENSP00000491504.1, ENST00000639579.2
      Conserved Domains (1) summary
      pfam04109
      Location:323 → 679
      APG9; Autophagy protein Apg9

    RNA

    1. NR_073169.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) has alternate 5' exon structure, lacks an internal exon in the central region, and uses alternate exons in the 3' region, compared to variant 3. This variant is represented as non-coding because use of the expected translational start codon, as used in variant 1, results in a significantly truncated ORF and renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI221785, AI243432, AY515311, BC128587

    2. NR_133652.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) uses an alternate 3' structure compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC010973, AY515311

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      151012209..151024499 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011516065.3 → XP_011514367.3  autophagy-related protein 9B isoform X1

      UniProtKB/Swiss-Prot
      A1A5D3, Q674R7, Q6JRW5, Q8N8I8
      Related
      ENSP00000475737.2, ENST00000605952.5

    RNA

    1. XR_007060009.1 RNA Sequence

    2. XR_002956421.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      152185332..152201351 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054357935.1 → XP_054213910.1  autophagy-related protein 9B isoform X2

    2. XM_054357938.1 → XP_054213913.1  autophagy-related protein 9B isoform X2

    3. XM_054357936.1 → XP_054213911.1  autophagy-related protein 9B isoform X2

    4. XM_054357937.1 → XP_054213912.1  autophagy-related protein 9B isoform X2

    5. XM_054357939.1 → XP_054213914.1  autophagy-related protein 9B isoform X1

      UniProtKB/Swiss-Prot
      A1A5D3, Q674R7, Q6JRW5, Q8N8I8

    RNA

    1. XR_008487566.1 RNA Sequence

    2. XR_008487565.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q674R7.1 GenPept UniProtKB/Swiss-Prot:Q674R7

    Gene LinkOut

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

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