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TM9SF4 transmembrane 9 superfamily member 4 [ Homo sapiens (human) ]

Gene ID: 9777, updated on 3-Apr-2024

Summary

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Official Symbol
TM9SF4provided by HGNC
Official Full Name
transmembrane 9 superfamily member 4provided by HGNC
Primary source
HGNC:HGNC:30797
See related
Ensembl:ENSG00000101337 MIM:617727; AllianceGenome:HGNC:30797
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
dJ836N17.2
Summary
Involved in several processes, including positive regulation of protein localization; regulation of intracellular pH; and vacuolar proton-transporting V-type ATPase complex assembly. Located in Golgi apparatus and early endosome. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in placenta (RPKM 20.7), brain (RPKM 16.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
20q11.21
Exon count:
18
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (32109714..32167256)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (33834368..33891894)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (30697517..30755059)

Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12774 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:30641518-30641717 Neighboring gene RNA, 5S ribosomal pseudogene 482 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17707 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17708 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17709 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12775 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12776 Neighboring gene HCK proto-oncogene, Src family tyrosine kinase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30659475-30659975 Neighboring gene MPRA-validated peak4189 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30672211-30672710 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30678826-30679621 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30688747-30689248 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:30696834-30698033 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:30708941-30709834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17711 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30737033-30737924 Neighboring gene Sharpr-MPRA regulatory region 10464 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30747197-30748088 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30752983-30753483 Neighboring gene Sharpr-MPRA regulatory region 8915 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30762883-30763484 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr20:30763485-30764084 Neighboring gene ribosomal L24 domain containing 1 pseudogene 6 Neighboring gene ReSE screen-validated silencer GRCh37_chr20:30768259-30768439 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:30769860-30770360 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:30776057-30776872 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12777 Neighboring gene testis specific protein Y-linked 26, pseudogene

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. TM9SF4 is an F-actin disassembly factor that promotes tumor progression and metastasis. Meng Z, et al. Nat Commun, 2022 Sep 29. PMID 36175399, Free PMC Article
  2. Knockdown of TM9SF4 boosts ER stress to trigger cell death of chemoresistant breast cancer cells. Zhu Y, et al. Oncogene, 2019 Jul. PMID 31249383
  3. TM9SF4 levels determine sorting of transmembrane domains in the early secretory pathway. Vernay A, et al. J Cell Sci, 2018 Nov 5. PMID 30301779
  4. TM9SF4 Is a Crucial Regulator of Inflammation and ER Stress in Inflammatory Bowel Disease. Xie M, et al. Cell Mol Gastroenterol Hepatol, 2022. PMID 35398597, Free PMC Article
  5. The human homologue of Dictyostelium discoideum phg1A is expressed by human metastatic melanoma cells. Lozupone F, et al. EMBO Rep, 2009 Dec. PMID 19893578, Free PMC Article

See all (39) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TM9SF4 is an F-actin disassembly factor that promotes tumor progression and metastasis.
    Title: TM9SF4 is an F-actin disassembly factor that promotes tumor progression and metastasis.
  2. TM9SF4 Is a Crucial Regulator of Inflammation and ER Stress in Inflammatory Bowel Disease.
    Title: TM9SF4 Is a Crucial Regulator of Inflammation and ER Stress in Inflammatory Bowel Disease.
  3. results uncovered a novel role of TM9SF4 proteins in alleviating endoplasmic reticulum stress and protecting chemoresistant breast cancer cells from apoptotic/necrotic cell death
    Title: Knockdown of TM9SF4 boosts ER stress to trigger cell death of chemoresistant breast cancer cells.
  4. Results show that TM9SF4 controls the sorting of TMDs at the ER-Golgi interface. Remarkably, sorting of T-R1 in HCT116 cells was different from that in HEK cells: in HCT116 cells, a substantial fraction of T-R1 was localized to the Golgi complex, and it was relocated to the ER by genetic ablation of TM9SF4.
    Title: TM9SF4 levels determine sorting of transmembrane domains in the early secretory pathway.
  5. The TM9SF4 functions to facilitate mTOR inactivation, resulting in an enhanced autophagic flux, which serves to protect cells from apoptotic cell death.
    Title: TM9SF4 is a novel factor promoting autophagic flux under amino acid starvation.
  6. TM9SF4 is a direct target of HIF-1alpha, down-regulated in leukemic cells by hypoxia and involved in cell adhesion.
    Title: Human TM9SF4 Is a New Gene Down-Regulated by Hypoxia and Involved in Cell Adhesion of Leukemic Cells.
  7. Our study shows for the first time the important role of TM9SF4 in the aberrant constitutive activation of the V-ATPase, and the development of a malignant phenotype.
    Title: TM9SF4 is a novel V-ATPase-interacting protein that modulates tumor pH alterations associated with drug resistance and invasiveness of colon cancer cells.
  8. TM9SF4 is a new marker of malignancy, representing a potential new target for anti-tumour strategies with a specific role in tumour cannibalism and in the establishment of a metastatic phenotype.
    Title: The human homologue of Dictyostelium discoideum phg1A is expressed by human metastatic melanoma cells.
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

EBI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
EBI GWAS Catalog

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

Clone Names

  • KIAA0255

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 cell adhesion IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in phagocytosis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of protein exit from endoplasmic reticulum IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of protein localization to cell surface IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein localization to membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of intracellular pH IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in response to hypoxia IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in vacuolar proton-transporting V-type ATPase complex assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in early endosome IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
transmembrane 9 superfamily member 4
Names
dinucleotide oxidase disulfide thiol exchanger 3 superfamily member 4
transmembrane 9 superfamily protein member 4
tumor cannibalism associated protein 1

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_001363731.2 → NP_001350660.1  transmembrane 9 superfamily member 4 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL049539, BC021107, BM976438, D87444, DC377969
    Consensus CDS
    CCDS86943.1
    UniProtKB/TrEMBL
    A0A0C4DFM1, B4DKC1
    Related
    ENSP00000217315.5, ENST00000217315.9
    Conserved Domains (1) summary
    pfam02990
    Location:38 → 582
    EMP70; Endomembrane protein 70

  2. NM_014742.4 → NP_055557.2  transmembrane 9 superfamily member 4 isoform 1 precursor

    See identical proteins and their annotated locations for NP_055557.2

    Status: VALIDATED

    Source sequence(s)
    BC021107, BM976438, D87444, DC381660
    Consensus CDS
    CCDS13196.2
    UniProtKB/Swiss-Prot
    B0QYT7, Q92544, Q9NUA3
    UniProtKB/TrEMBL
    A0A024QYR3, B4DKC1
    Related
    ENSP00000381104.2, ENST00000398022.7
    Conserved Domains (1) summary
    pfam02990
    Location:55 → 599
    EMP70; Endomembrane protein 70

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_000020.11 Reference GRCh38.p14 Primary Assembly

    Range
    32109714..32167256
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017028155.2 → XP_016883644.1  transmembrane 9 superfamily member 4 isoform X2

    UniProtKB/TrEMBL
    B4DKC1
    Conserved Domains (1) summary
    pfam02990
    Location:38 → 554
    EMP70; Endomembrane protein 70

  2. XM_017028154.2 → XP_016883643.1  transmembrane 9 superfamily member 4 isoform X1

    UniProtKB/TrEMBL
    B4DKC1
    Conserved Domains (1) summary
    pfam02990
    Location:55 → 571
    EMP70; Endomembrane protein 70

  3. XM_017028156.2 → XP_016883645.1  transmembrane 9 superfamily member 4 isoform X3

    UniProtKB/TrEMBL
    B4DH88, B4DKC1
    Conserved Domains (1) summary
    pfam02990
    Location:1 → 506
    EMP70; Endomembrane protein 70

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060944.1 Alternate T2T-CHM13v2.0

    Range
    33834368..33891894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054324291.1 → XP_054180266.1  transmembrane 9 superfamily member 4 isoform X2

  2. XM_054324290.1 → XP_054180265.1  transmembrane 9 superfamily member 4 isoform X1

  3. XM_054324292.1 → XP_054180267.1  transmembrane 9 superfamily member 4 isoform X3

    UniProtKB/TrEMBL
    B4DH88
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92544.2 GenPept UniProtKB/Swiss-Prot:Q92544

Gene LinkOut

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