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TMEM9 transmembrane protein 9 [ Homo sapiens (human) ]

Gene ID: 252839, updated on 3-Apr-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, Apr 2022]
Expression
Ubiquitous expression in brain (RPKM 25.4), thyroid (RPKM 25.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
1q32.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (201134772..201171558, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (200391754..200428535, complement)
105.20220307 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. 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
  2. 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
  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. MicroRNA-346-5p Regulates Differentiation of Bone Marrow-Derived Mesenchymal Stem Cells by Inhibiting Transmembrane Protein 9. Zhang Y, et al. Biomed Res Int, 2020. PMID 33299881, Free PMC Article
  5. The lysosomal transmembrane protein 9B regulates the activity of inflammatory signaling pathways. Dodeller F, et al. J Biol Chem, 2008 Aug 1. PMID 18541524

See all (46) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. TMEM9 knockdown by RNA interference resulted in G1 arrest.
    Title: Effects of TMEM9 gene on cell progression in hepatocellular carcinoma by RNA interference.
  8. 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.
  9. TMEM9B is a key component of inflammatory signaling pathways and suggest that endosomal or lysosomal compartments regulate these pathways
    Title: The lysosomal transmembrane protein 9B regulates the activity of inflammatory signaling pathways.
  10. phylogenetically conserved, widely expressed transmembrane protein with a potential, but unknown function in intracellular transport that localizes to lysosomes and late endosomes
    Title: Characterization of the novel human transmembrane protein 9 (TMEM9) that localizes to lysosomes and late endosomes.
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)

Genotypes

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 molecular_function ND
No biological Data available
more info
  
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_2023_10

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

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

    UniProtKB/TrEMBL
    B1ALM5

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

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

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