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    TMEM9 transmembrane protein 9 [ Homo sapiens (human) ]

    Gene ID: 252839, updated on 10-Dec-2024

    Summary

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    Official Symbol
    TMEM9provided by HGNC
    Official Full Name
    transmembrane protein 9provided by HGNC
    Primary source
    HGNC:HGNC:18823
    See related
    Ensembl:ENSG00000116857 MIM:616877; AllianceGenome:HGNC:18823
    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
    DERM4; TMEM9A
    Summary
    Involved in intracellular pH reduction; positive regulation of canonical Wnt signaling pathway; and proton-transporting V-type ATPase complex assembly. Located in bounding membrane of organelle; intercellular bridge; and mitotic spindle. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in brain (RPKM 25.4), thyroid (RPKM 25.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See TMEM9 in Genome Data Viewer
    Location:
    1q32.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (201134772..201171558, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (200391754..200428535, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (201103900..201140686, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene calcium voltage-gated channel subunit alpha1 S Neighboring gene uncharacterized LOC124904481 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201070239-201070740 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201070741-201071240 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201072987-201073503 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1686 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201084381-201084901 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:201095506-201096496 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:201096497-201097487 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:201103675-201103881 Neighboring gene achaete-scute family bHLH transcription factor 5 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2309 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1687 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2310 Neighboring gene immunoglobulin like and fibronectin type III domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1688 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201194684-201195676 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:201252475-201253004 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201271917-201272422 Neighboring gene plakophilin 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:201290713-201291214

    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. TMEM9 promotes lung adenocarcinoma progression via activating the MEK/ERK/STAT3 pathway to induce VEGF expression. Wang Z, et al. Cell Death Dis, 2024 Apr 25. PMID 38664392, Free PMC Article
    2. Tumor-Promoting Properties of TMEM9A in Breast Cancer Progression via Activating the Wnt/β-Catenin Signaling Pathway. He J, et al. Biol Pharm Bull, 2023. PMID 36596527
    3. Effects of TMEM9 gene on cell progression in hepatocellular carcinoma by RNA interference. Zhang Y, et al. Oncol Rep, 2016 Jul. PMID 27220462
    4. TMEM9 mediates IL-6 and IL-1β secretion and is modulated by the Wnt pathway. Wei W, et al. Int Immunopharmacol, 2018 Oct. PMID 30119033
    5. TMEM9 activates Rab9-dependent alternative autophagy through interaction with Beclin1. Baek S, et al. Cell Mol Life Sci, 2024 Jul 30. PMID 39078420, Free PMC Article

    See all (52) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. TMEM9 activates Rab9-dependent alternative autophagy through interaction with Beclin1.
      Title: TMEM9 activates Rab9-dependent alternative autophagy through interaction with Beclin1.
    2. TMEM9 promotes lung adenocarcinoma progression via activating the MEK/ERK/STAT3 pathway to induce VEGF expression.
      Title: TMEM9 promotes lung adenocarcinoma progression via activating the MEK/ERK/STAT3 pathway to induce VEGF expression.
    3. Lysosomal TMEM9-LAMTOR4-controlled mTOR signaling integrity is required for mammary tumorigenesis.
      Title: Lysosomal TMEM9-LAMTOR4-controlled mTOR signaling integrity is required for mammary tumorigenesis.
    4. Tumor-Promoting Properties of TMEM9A in Breast Cancer Progression via Activating the Wnt/beta-Catenin Signaling Pathway.
      Title: Tumor-Promoting Properties of TMEM9A in Breast Cancer Progression via Activating the Wnt/β-Catenin Signaling Pathway.
    5. TMEM9-v-ATPase Activates Wnt/beta-Catenin Signaling Via APC Lysosomal Degradation for Liver Regeneration and Tumorigenesis.
      Title: TMEM9-v-ATPase Activates Wnt/β-Catenin Signaling Via APC Lysosomal Degradation for Liver Regeneration and Tumorigenesis.
    6. TMEM9-activated v-ATPase downregulates APC via lysosomal degradation, which hyperactivates WNT/beta-Catenin signaling.
      Title: TMEM9-v-ATPase Activates Wnt/β-Catenin Signaling Via APC Lysosomal Degradation for Liver Regeneration and Tumorigenesis.
    7. Data show that TMEM9 binds to and facilitates assembly of vacuolar-ATPase (v-ATPase), a vacuolar proton pump, resulting in enhanced vesicular acidification and trafficking.
      Title: TMEM9 promotes intestinal tumorigenesis through vacuolar-ATPase-activated Wnt/β-catenin signalling.
    8. TMEM9 plays a significant role in TNF-alpha-enhanced cytokines (IL-6 and IL-1beta) secretion in LX-2 cells and that the canonical Wnt/beta-catenin signaling pathway is involved in the induction of these cytokine expressions.
      Title: TMEM9 mediates IL-6 and IL-1β secretion and is modulated by the Wnt pathway.
    9. TMEM9 knockdown by RNA interference resulted in G1 arrest.
      Title: Effects of TMEM9 gene on cell progression in hepatocellular carcinoma by RNA interference.
    10. 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.
    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)

    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 protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in endosomal lumen acidification IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in lysosomal lumen acidification IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of canonical Wnt signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in proton-transporting V-type ATPase complex assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of protein catabolic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in intercellular bridge IDA
    Inferred from Direct Assay
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lysosomal membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in microtubule cytoskeleton IDA
    Inferred from Direct Assay
    more info
    		  
    located_in mitotic spindle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in multivesicular body membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    proton-transporting V-type ATPase complex assembly regulator TMEM9
    Names
    dermal papilla-derived protein 4
    v-ATPase assembly regulator TMEM9

    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_001288564.2 → NP_001275493.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform a precursor

      See identical proteins and their annotated locations for NP_001275493.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1-7 encode the same isoform (a).
      Source sequence(s)
      AI201238, AK054883, DA141558
      Consensus CDS
      CCDS1408.1
      UniProtKB/Swiss-Prot
      B1ALM6, Q96NQ9, Q9BQF5, Q9P0T7
      UniProtKB/TrEMBL
      Q6IAJ3
      Related
      ENSP00000356302.2, ENST00000367333.6
      Conserved Domains (1) summary
      pfam05434
      Location:44 → 182
      Tmemb_9; TMEM9

    2. NM_001288565.2 → NP_001275494.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform a precursor

      See identical proteins and their annotated locations for NP_001275494.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR, compared to variant 1. Variants 1-7 encode the same isoform (a).
      Source sequence(s)
      AI201238, AK054883, AK091726, CX751563, DA160051, DA364005
      Consensus CDS
      CCDS1408.1
      UniProtKB/Swiss-Prot
      B1ALM6, Q96NQ9, Q9BQF5, Q9P0T7
      UniProtKB/TrEMBL
      Q6IAJ3
      Related
      ENSP00000356299.1, ENST00000367330.6
      Conserved Domains (1) summary
      pfam05434
      Location:44 → 182
      Tmemb_9; TMEM9

    3. NM_001288566.2 → NP_001275495.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform a precursor

      See identical proteins and their annotated locations for NP_001275495.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, compared to variant 1. Variants 1-7 encode the same isoform (a).
      Source sequence(s)
      AI201238, AK054883, DA364005, DB031447
      Consensus CDS
      CCDS1408.1
      UniProtKB/Swiss-Prot
      B1ALM6, Q96NQ9, Q9BQF5, Q9P0T7
      UniProtKB/TrEMBL
      Q6IAJ3
      Conserved Domains (1) summary
      pfam05434
      Location:44 → 182
      Tmemb_9; TMEM9

    4. NM_001288567.2 → NP_001275496.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform a precursor

      See identical proteins and their annotated locations for NP_001275496.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, compared to variant 1. Variants 1-7 encode the same isoform (a).
      Source sequence(s)
      AI201238, AK054883, AL516746, DA160051, DA364005
      Consensus CDS
      CCDS1408.1
      UniProtKB/Swiss-Prot
      B1ALM6, Q96NQ9, Q9BQF5, Q9P0T7
      UniProtKB/TrEMBL
      Q6IAJ3
      Related
      ENSP00000476893.1, ENST00000485839.6
      Conserved Domains (1) summary
      pfam05434
      Location:44 → 182
      Tmemb_9; TMEM9

    5. NM_001288568.2 → NP_001275497.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform a precursor

      See identical proteins and their annotated locations for NP_001275497.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 5' UTR, compared to variant 1. Variants 1-7 encode the same isoform (a).
      Source sequence(s)
      AI201238, AK054883, BE782946, DA364005, DA625212
      Consensus CDS
      CCDS1408.1
      UniProtKB/Swiss-Prot
      B1ALM6, Q96NQ9, Q9BQF5, Q9P0T7
      UniProtKB/TrEMBL
      Q6IAJ3
      Conserved Domains (1) summary
      pfam05434
      Location:44 → 182
      Tmemb_9; TMEM9

    6. NM_001288569.2 → NP_001275498.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform a precursor

      See identical proteins and their annotated locations for NP_001275498.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) differs in the 5' UTR, compared to variant 1. Variants 1-7 encode the same isoform (a).
      Source sequence(s)
      AF151020, AI201238, AK054883, DA364005
      Consensus CDS
      CCDS1408.1
      UniProtKB/Swiss-Prot
      B1ALM6, Q96NQ9, Q9BQF5, Q9P0T7
      UniProtKB/TrEMBL
      Q6IAJ3
      Conserved Domains (1) summary
      pfam05434
      Location:44 → 182
      Tmemb_9; TMEM9

    7. NM_001288570.2 → NP_001275499.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform b precursor

      See identical proteins and their annotated locations for NP_001275499.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (b) is longer, compared to isoform a.
      Source sequence(s)
      AI201238, AK054883
      Consensus CDS
      CCDS73001.1
      UniProtKB/TrEMBL
      B1ALM5, Q6IAJ3
      Related
      ENSP00000356301.1, ENST00000367332.5
      Conserved Domains (1) summary
      pfam05434
      Location:47 → 185
      Tmemb_9; TMEM9

    8. NM_001288571.2 → NP_001275500.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform c precursor

      See identical proteins and their annotated locations for NP_001275500.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9) uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (c) is longer, compared to isoform a.
      Source sequence(s)
      AI201238, AK054883, AK303843, AL139159
      UniProtKB/TrEMBL
      B4E1H4, Q6IAJ3
      Conserved Domains (1) summary
      pfam05434
      Location:69 → 207
      Tmemb_9; TMEM9

    9. NM_016456.5 → NP_057540.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform a precursor

      See identical proteins and their annotated locations for NP_057540.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes isoform (a). Variants 1-7 encode the same isoform.
      Source sequence(s)
      AF151020, AI201238, AK054883
      Consensus CDS
      CCDS1408.1
      UniProtKB/Swiss-Prot
      B1ALM6, Q96NQ9, Q9BQF5, Q9P0T7
      UniProtKB/TrEMBL
      Q6IAJ3
      Related
      ENSP00000356303.5, ENST00000367334.9
      Conserved Domains (1) summary
      pfam05434
      Location:44 → 182
      Tmemb_9; TMEM9

    RNA

    1. NR_109920.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (10) includes an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI201238, AK054883, BM928361, DA364005

    2. NR_109921.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (11) uses an alternate 5'-terminal exon structure, and an alternate splice site at an internal exon, compared ot variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI201238, AK054883, BX337142, CX751563, DA364005, DA625212

    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
      201134772..201171558 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011509386.3 → XP_011507688.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform X1

      See identical proteins and their annotated locations for XP_011507688.1

      UniProtKB/TrEMBL
      B1ALM5, Q6IAJ3
      Conserved Domains (1) summary
      pfam05434
      Location:47 → 185
      Tmemb_9; TMEM9

    2. XM_011509387.3 → XP_011507689.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform X1

      See identical proteins and their annotated locations for XP_011507689.1

      UniProtKB/TrEMBL
      B1ALM5, Q6IAJ3
      Conserved Domains (1) summary
      pfam05434
      Location:47 → 185
      Tmemb_9; TMEM9

    3. XM_011509385.3 → XP_011507687.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform X1

      See identical proteins and their annotated locations for XP_011507687.1

      UniProtKB/TrEMBL
      B1ALM5, Q6IAJ3
      Conserved Domains (1) summary
      pfam05434
      Location:47 → 185
      Tmemb_9; TMEM9

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      200391754..200428535 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335754.1 → XP_054191729.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform X1

      UniProtKB/TrEMBL
      B1ALM5, Q6IAJ3

    2. XM_054335755.1 → XP_054191730.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform X1

      UniProtKB/TrEMBL
      B1ALM5, Q6IAJ3

    3. XM_054335753.1 → XP_054191728.1  proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform X1

      UniProtKB/TrEMBL
      B1ALM5, Q6IAJ3
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9P0T7.1 GenPept UniProtKB/Swiss-Prot:Q9P0T7

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