TMEM9 transmembrane protein 9 [Homo sapiens (human)] - Gene

Summary

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, Oct 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

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_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TMEM9 activates Rab9-dependent alternative autophagy through interaction with Beclin1.
Title: TMEM9 activates Rab9-dependent alternative autophagy through interaction with Beclin1.
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.
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.
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.
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.
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.
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.
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.
TMEM9 knockdown by RNA interference resulted in G1 arrest.
Title: Effects of TMEM9 gene on cell progression in hepatocellular carcinoma by RNA interference.
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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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

HSC2QF012 (e-PCR)
- UniSTS:36977

D1S2716 (e-PCR), detects polymorphism
- UniSTS:53372

WI-11986 (e-PCR)
- UniSTS:7320

RH76360 (e-PCR)
- UniSTS:88497

RH119854 (e-PCR)
- UniSTS:133599

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)

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
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
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
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
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
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
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
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
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

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
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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

201134772..201171558 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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
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

NC_060925.1 Alternate T2T-CHM13v2.0

Range

200391754..200428535 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

B1ALM5
XM_054335755.1 → XP_054191730.1 proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform X1

UniProtKB/TrEMBL

B1ALM5
XM_054335753.1 → XP_054191728.1 proton-transporting V-type ATPase complex assembly regulator TMEM9 isoform X1

UniProtKB/TrEMBL

B1ALM5