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Aliases for TM9SF4 Gene

Aliases for TM9SF4 Gene

  • Transmembrane 9 Superfamily Member 4 2 3 5
  • Tumor Cannibalism Associated Protein 1 3 4
  • Dinucleotide Oxidase Disulfide Thiol Exchanger 3 Superfamily Member 4 3
  • Transmembrane 9 Superfamily Protein Member 4 3
  • DJ836N17.2 3
  • KIAA0255 4
  • TUCAP1 4

External Ids for TM9SF4 Gene

Previous GeneCards Identifiers for TM9SF4 Gene

  • GC20P031395
  • GC20P031442
  • GC20P030161
  • GC20P030184
  • GC20P030697
  • GC20P027486

Summaries for TM9SF4 Gene

GeneCards Summary for TM9SF4 Gene

TM9SF4 (Transmembrane 9 Superfamily Member 4) is a Protein Coding gene. Diseases associated with TM9SF4 include Melanoma. An important paralog of this gene is TM9SF2.

UniProtKB/Swiss-Prot for TM9SF4 Gene

  • Associates with proteins harboring glycine-rich transmembrane domains and ensures their efficient localization to the cell surface (PubMed:25999474). Regulates the assembly and activity of V-ATPase in colon cancer cells via its interaction with V-type proton ATPase subunit H (ATP6V1H) and contributes to V-ATPase-mediated pH alterations in cancer cells which play an important role in drug resistance and invasiveness of colon cancer cells (PubMed:25659576). Plays an important role in an atypical phagocytic activity of metastatic melanoma cells called cannibalism and is involved in the pH regulation of the intracellular vesicles in tumor cells (PubMed:19893578).

Additional gene information for TM9SF4 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TM9SF4 Gene

Genomics for TM9SF4 Gene

Regulatory Elements for TM9SF4 Gene

Enhancers for TM9SF4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH20H031709 2.1 FANTOM5 Ensembl ENCODE dbSUPER 41.4 -392.3 -392318 14 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D SSRP1 TM9SF4 ASXL1 PLAGL2 MYLK2 COX4I2 DEFB121 RNU1-94P DEFB122 DEFB123 DEFB118
GH20H031601 2.3 VISTA FANTOM5 ENCODE dbSUPER 31.6 -502.1 -502055 11 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A MEF2D ASXL1 TM9SF4 MYLK2 COX4I2 HM13 RNU6-384P HM13-AS1 PLAGL2 POFUT1 ID1
GH20H031894 1.5 FANTOM5 Ensembl ENCODE 36.1 -214.2 -214173 1 HDGF ATF1 ZNF493 ZFP64 ZNF133 RFX5 ZNF302 ZNF354C ZNF143 ATF7 ASXL1 TM9SF4 MCTS2P DNMT3B REM1 TSPY26P BAK1P1 RSL24D1P6 PDRG1 C20orf203
GH20H031565 1.7 Ensembl ENCODE dbSUPER 30.1 -539.3 -539317 9 MLX ZFP64 FEZF1 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC MEF2D ASXL1 TM9SF4 HM13 COX4I2 ID1 MCTS2P MYLK2 HM13-AS1 PIR57123 HM13-IT1
GH20H032631 0.9 dbSUPER 37.9 +523.7 523667 3 TBP TBL1XR1 NFRKB TCF12 ZNF766 ZSCAN5C ATF7 SMARCA5 SMAD5 CEBPB TM9SF4 ASXL1 POFUT1 CDK5RAP1 NOL4L ENSG00000233293 PLAGL2 C20orf203 COMMD7 DNMT3B
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TM9SF4 on UCSC Golden Path with GeneCards custom track

Promoters for TM9SF4 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000136096 395 1400 MLX ZFP64 DMAP1 YY1 SLC30A9 ZNF143 SP3 NFYC ZC3H11A MEF2D

Genomic Location for TM9SF4 Gene

Chromosome:
20
Start:
32,109,506 bp from pter
End:
32,167,258 bp from pter
Size:
57,753 bases
Orientation:
Plus strand

Genomic View for TM9SF4 Gene

Genes around TM9SF4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TM9SF4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TM9SF4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TM9SF4 Gene

Proteins for TM9SF4 Gene

  • Protein details for TM9SF4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q92544-TM9S4_HUMAN
    Recommended name:
    Transmembrane 9 superfamily member 4
    Protein Accession:
    Q92544
    Secondary Accessions:
    • B0QYT7
    • Q9NUA3

    Protein attributes for TM9SF4 Gene

    Size:
    642 amino acids
    Molecular mass:
    74519 Da
    Quaternary structure:
    • Interacts with ATP6V1H in colon cancer cells (PubMed:25659576).
    SequenceCaution:
    • Sequence=AAH21107.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAA13385.2; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for TM9SF4 Gene

Post-translational modifications for TM9SF4 Gene

  • Ubiquitination at Lys72
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for TM9SF4 Gene

Domains & Families for TM9SF4 Gene

Gene Families for TM9SF4 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted membrane proteins
  • Transporters

Protein Domains for TM9SF4 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for TM9SF4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q92544

UniProtKB/Swiss-Prot:

TM9S4_HUMAN :
  • Belongs to the nonaspanin (TM9SF) (TC 9.A.2) family.
Family:
  • Belongs to the nonaspanin (TM9SF) (TC 9.A.2) family.
genes like me logo Genes that share domains with TM9SF4: view

Function for TM9SF4 Gene

Molecular function for TM9SF4 Gene

UniProtKB/Swiss-Prot Function:
Associates with proteins harboring glycine-rich transmembrane domains and ensures their efficient localization to the cell surface (PubMed:25999474). Regulates the assembly and activity of V-ATPase in colon cancer cells via its interaction with V-type proton ATPase subunit H (ATP6V1H) and contributes to V-ATPase-mediated pH alterations in cancer cells which play an important role in drug resistance and invasiveness of colon cancer cells (PubMed:25659576). Plays an important role in an atypical phagocytic activity of metastatic melanoma cells called cannibalism and is involved in the pH regulation of the intracellular vesicles in tumor cells (PubMed:19893578).
UniProtKB/Swiss-Prot Induction:
Transcriptionally repressed following hypoxia by HIF1A in leukemic cells.

Phenotypes From GWAS Catalog for TM9SF4 Gene

Gene Ontology (GO) - Molecular Function for TM9SF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25659576
genes like me logo Genes that share ontologies with TM9SF4: view
genes like me logo Genes that share phenotypes with TM9SF4: view

Animal Models for TM9SF4 Gene

MGI Knock Outs for TM9SF4:

Animal Model Products

  • Taconic Biosciences Mouse Models for TM9SF4

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for TM9SF4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for TM9SF4 Gene

Localization for TM9SF4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TM9SF4 Gene

Membrane; Multi-pass membrane protein. Golgi apparatus. Early endosome.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for TM9SF4 gene
Compartment Confidence
golgi apparatus 5
endosome 5
plasma membrane 3
mitochondrion 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for TM9SF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005768 endosome IEA --
GO:0005769 early endosome IDA,IEA 19893578
GO:0005794 Golgi apparatus IEA,IDA 25999474
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IBA,IEA --
genes like me logo Genes that share ontologies with TM9SF4: view

Pathways & Interactions for TM9SF4 Gene

SuperPathways for TM9SF4 Gene

No Data Available

Gene Ontology (GO) - Biological Process for TM9SF4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001666 response to hypoxia IDA 25961573
GO:0006909 phagocytosis IMP 19893578
GO:0007155 cell adhesion IMP 25961573
GO:0051453 regulation of intracellular pH IMP 19893578
GO:0070072 vacuolar proton-transporting V-type ATPase complex assembly IMP 25659576
genes like me logo Genes that share ontologies with TM9SF4: view

No data available for Pathways by source and SIGNOR curated interactions for TM9SF4 Gene

Drugs & Compounds for TM9SF4 Gene

No Compound Related Data Available

Transcripts for TM9SF4 Gene

Unigene Clusters for TM9SF4 Gene

Transmembrane 9 superfamily protein member 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for TM9SF4
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for TM9SF4 Gene

No ASD Table

Relevant External Links for TM9SF4 Gene

GeneLoc Exon Structure for
TM9SF4
ECgene alternative splicing isoforms for
TM9SF4

Expression for TM9SF4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TM9SF4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TM9SF4 Gene

This gene is overexpressed in Liver (9.1) and Adrenal (7.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TM9SF4 Gene



Protein tissue co-expression partners for TM9SF4 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TM9SF4 Gene:

TM9SF4

SOURCE GeneReport for Unigene cluster for TM9SF4 Gene:

Hs.654665

mRNA Expression by UniProt/SwissProt for TM9SF4 Gene:

Q92544-TM9S4_HUMAN
Tissue specificity: Highly expressed in metastatic melanoma cells whereas it is undetectable in primary melanoma cells, healthy skin tissues and peripheral blood lymphocytes. Expressed in CD34(+) hematopoietic progenitor cells and during monocyte and granulocyte differentiation. Overexpressed in acute myeloid leukemia, in particular in those displaying granulocytic differentiation (at protein level).

Evidence on tissue expression from TISSUES for TM9SF4 Gene

  • Nervous system(4.9)
  • Bone marrow(4.2)
  • Muscle(4.2)
  • Blood(4.1)
  • Intestine(3)
genes like me logo Genes that share expression patterns with TM9SF4: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for TM9SF4 Gene

Orthologs for TM9SF4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TM9SF4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TM9SF4 33 34
  • 99.79 (n)
dog
(Canis familiaris)
Mammalia TM9SF4 33 34
  • 93.2 (n)
cow
(Bos Taurus)
Mammalia TM9SF4 33 34
  • 93.09 (n)
rat
(Rattus norvegicus)
Mammalia Tm9sf4 33
  • 91.8 (n)
mouse
(Mus musculus)
Mammalia Tm9sf4 33 16 34
  • 91.48 (n)
oppossum
(Monodelphis domestica)
Mammalia TM9SF4 34
  • 86 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 54 (a)
ManyToMany
chicken
(Gallus gallus)
Aves TM9SF4 33 34
  • 81.38 (n)
lizard
(Anolis carolinensis)
Reptilia TM9SF4 34
  • 90 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia LOC398864 33
zebrafish
(Danio rerio)
Actinopterygii tm9sf4 33 34
  • 76.56 (n)
zgc66234 33
fruit fly
(Drosophila melanogaster)
Insecta TM9SF4 33 34
  • 65.47 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010029 33
  • 62.38 (n)
worm
(Caenorhabditis elegans)
Secernentea ZK858.6 33 34
  • 58.22 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes EMP70 34 36
  • 36 (a)
ManyToMany
TMN2 34
  • 33 (a)
ManyToMany
thale cress
(Arabidopsis thaliana)
eudicotyledons TMN7 33
  • 59.06 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 57 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4614 33
Species where no ortholog for TM9SF4 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)

Evolution for TM9SF4 Gene

ENSEMBL:
Gene Tree for TM9SF4 (if available)
TreeFam:
Gene Tree for TM9SF4 (if available)

Paralogs for TM9SF4 Gene

Paralogs for TM9SF4 Gene

(4) SIMAP similar genes for TM9SF4 Gene using alignment to 3 proteins:

genes like me logo Genes that share paralogs with TM9SF4: view

Variants for TM9SF4 Gene

Sequence variations from dbSNP and Humsavar for TM9SF4 Gene

SNP ID Clin Chr 20 pos Sequence Context AA Info Type
rs1000009335 -- 32,163,771(+) CACGC(C/T)CGGCT intron-variant
rs1000043001 -- 32,133,667(+) GGTTG(C/T)CCCCC intron-variant
rs1000051545 -- 32,109,505(+) AGGCT(A/C)AGTTT upstream-variant-2KB
rs1000102415 -- 32,116,073(+) TGCCT(C/T)AGCCT intron-variant
rs1000120765 -- 32,129,129(+) AAAAA(A/C)GGAAT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for TM9SF4 Gene

Variant ID Type Subtype PubMed ID
nsv833953 CNV loss 17160897
nsv833954 CNV loss 17160897

Variation tolerance for TM9SF4 Gene

Residual Variation Intolerance Score: 12.1% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.46; 28.54% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TM9SF4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TM9SF4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TM9SF4 Gene

Disorders for TM9SF4 Gene

MalaCards: The human disease database

(1) MalaCards diseases for TM9SF4 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
melanoma
  • malignant melanoma
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for TM9SF4

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TM9SF4
genes like me logo Genes that share disorders with TM9SF4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for TM9SF4 Gene

Publications for TM9SF4 Gene

  1. TM9 family proteins control surface targeting of glycine-rich transmembrane domains. (PMID: 25999474) Perrin J … Cosson P (Journal of cell science 2015) 2 3 4 60
  2. TM9SF4 is a novel V-ATPase-interacting protein that modulates tumor pH alterations associated with drug resistance and invasiveness of colon cancer cells. (PMID: 25659576) Lozupone F … Fais S (Oncogene 2015) 2 3 4 60
  3. The human homologue of Dictyostelium discoideum phg1A is expressed by human metastatic melanoma cells. (PMID: 19893578) Lozupone F … Fais S (EMBO reports 2009) 3 4 22 60
  4. Prediction of the coding sequences of unidentified human genes. VI. The coding sequences of 80 new genes (KIAA0201-KIAA0280) deduced by analysis of cDNA clones from cell line KG-1 and brain. (PMID: 9039502) Nagase T … Nomura N (DNA research : an international journal for rapid publication of reports on genes and genomes 1996) 2 3 4 60
  5. Human TM9SF4 Is a New Gene Down-Regulated by Hypoxia and Involved in Cell Adhesion of Leukemic Cells. (PMID: 25961573) Paolillo R … Labbaye C (PloS one 2015) 3 4 60

Products for TM9SF4 Gene

Sources for TM9SF4 Gene

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