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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
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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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