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Aliases for TM9SF3 Gene

Aliases for TM9SF3 Gene

  • Transmembrane 9 Superfamily Member 3 2 3 5
  • EP70-P-Iso 3 4
  • SMBP 3 4
  • Dinucleotide Oxidase Disulfide Thiol Exchanger 3 Superfamily Member 3 3
  • Endomembrane Protein Emp70 Precursor Isolog 3
  • SM-11044 Binding Protein 3
  • SM-11044-Binding Protein 4

External Ids for TM9SF3 Gene

Previous GeneCards Identifiers for TM9SF3 Gene

  • GC10M098267
  • GC10M091907

Summaries for TM9SF3 Gene

GeneCards Summary for TM9SF3 Gene

TM9SF3 (Transmembrane 9 Superfamily Member 3) is a Protein Coding gene. An important paralog of this gene is TM9SF4.

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TM9SF3 Gene

Genomics for TM9SF3 Gene

Regulatory Elements for TM9SF3 Gene

Enhancers for TM9SF3 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
GH10G096670 2 FANTOM5 Ensembl ENCODE dbSUPER 2.1 -86.7 -86696 8.1 HDGF PKNOX1 FOXA2 MLX ARID4B YY1 ZNF207 FOS ZNF263 MCM3 PIK3AP1 LCOR NPM1P26 TM9SF3 GC10M096631
GH10G096654 1.8 FANTOM5 Ensembl ENCODE dbSUPER 2.2 -69.2 -69210 3.9 HDGF ARID4B SIN3A DMAP1 FEZF1 ZNF48 YY1 SLC30A9 GLIS2 CBX5 PIK3AP1 LCOR RNU6-1274P MIR607 TM9SF3 GC10M096631
GH10G096644 1.6 FANTOM5 Ensembl ENCODE dbSUPER 2.2 -59.5 -59525 4.5 PKNOX1 KLF17 RAD21 YY1 ETV6 RELB CREM IKZF2 SMARCA5 JUNB PIK3AP1 LCOR MIR607 TM9SF3 GC10M096631
GH10G096716 1.7 FANTOM5 ENCODE dbSUPER 2 -131.6 -131604 5.4 HDGF PKNOX1 FOXA2 ARID4B SIN3A ZNF2 YY1 GLIS2 ZNF143 SP3 PIK3AP1 LCOR TM9SF3 GC10M096631
GH10G096708 1.7 FANTOM5 Ensembl ENCODE dbSUPER 2 -121.9 -121890 2.5 HDGF PTBP1 PKNOX1 SIN3A ZNF2 RAD21 RARA ZNF335 ZNF366 ZNF143 LCOR PIK3AP1 RNU6-1274P MIR607 TM9SF3 GC10M096631
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TM9SF3 on UCSC Golden Path with GeneCards custom track

Promoters for TM9SF3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for TM9SF3 Gene

96,518,109 bp from pter
96,587,452 bp from pter
69,344 bases
Minus strand

Genomic View for TM9SF3 Gene

Genes around TM9SF3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TM9SF3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TM9SF3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for TM9SF3 Gene

Proteins for TM9SF3 Gene

  • Protein details for TM9SF3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Transmembrane 9 superfamily member 3
    Protein Accession:
    Secondary Accessions:
    • Q5TB57
    • Q6UWE7
    • Q9NWL8
    • Q9P0G9
    • Q9UHW8

    Protein attributes for TM9SF3 Gene

    589 amino acids
    Molecular mass:
    67888 Da
    Quaternary structure:
    No Data Available
    • Sequence=AAF67014.1; Type=Frameshift; Positions=184, 198, 370, 446; Evidence={ECO:0000305}; Sequence=AAQ89178.1; Type=Frameshift; Positions=70; Evidence={ECO:0000305}; Sequence=BAA91362.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for TM9SF3 Gene

Post-translational modifications for TM9SF3 Gene

  • Ubiquitination at Lys59 and isoforms=210
  • Glycosylation at isoforms=174 and isoforms=419
  • Modification sites at PhosphoSitePlus

Other Protein References for TM9SF3 Gene

No data available for DME Specific Peptides for TM9SF3 Gene

Domains & Families for TM9SF3 Gene

Gene Families for TM9SF3 Gene

Protein Domains for TM9SF3 Gene


Graphical View of Domain Structure for InterPro Entry



  • Belongs to the nonaspanin (TM9SF) (TC 9.A.2) family.
  • Belongs to the nonaspanin (TM9SF) (TC 9.A.2) family.
genes like me logo Genes that share domains with TM9SF3: view

Function for TM9SF3 Gene

Phenotypes for TM9SF3 Gene

genes like me logo Genes that share phenotypes with TM9SF3: view

Animal Model Products

  • Taconic Biosciences Mouse Models for TM9SF3

CRISPR Products

miRNA for TM9SF3 Gene

miRTarBase miRNAs that target TM9SF3

Inhibitory RNA Products

Clone Products

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TM9SF3 Gene

Localization for TM9SF3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for TM9SF3 Gene

Membrane; Multi-pass membrane protein.

Subcellular locations from

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 TM9SF3 gene
Compartment Confidence
plasma membrane 3
golgi apparatus 2

Gene Ontology (GO) - Cellular Components for TM9SF3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016021 integral component of membrane IEA,IBA --
genes like me logo Genes that share ontologies with TM9SF3: view

Pathways & Interactions for TM9SF3 Gene

SuperPathways for TM9SF3 Gene

No Data Available

Interacting Proteins for TM9SF3 Gene

Gene Ontology (GO) - Biological Process for TM9SF3 Gene


No data available for Pathways by source and SIGNOR curated interactions for TM9SF3 Gene

Drugs & Compounds for TM9SF3 Gene

No Compound Related Data Available

Transcripts for TM9SF3 Gene

Unigene Clusters for TM9SF3 Gene

Transmembrane 9 superfamily member 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for TM9SF3 Gene

No ASD Table

Relevant External Links for TM9SF3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for TM9SF3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TM9SF3 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for TM9SF3 Gene

This gene is overexpressed in Nasal epithelium (41.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for TM9SF3 Gene

Protein tissue co-expression partners for TM9SF3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of TM9SF3 Gene:


SOURCE GeneReport for Unigene cluster for TM9SF3 Gene:


Evidence on tissue expression from TISSUES for TM9SF3 Gene

  • Liver(4.5)
  • Adrenal gland(4.3)
  • Muscle(4.3)
  • Nervous system(4.2)
  • Intestine(3.5)
  • Lung(3)
  • Kidney(2.5)
  • Stomach(2.1)
  • Blood(2)
  • Eye(2)
genes like me logo Genes that share expression patterns with TM9SF3: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for TM9SF3 Gene

Orthologs for TM9SF3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for TM9SF3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia TM9SF3 34 35
  • 99.82 (n)
(Bos Taurus)
Mammalia TM9SF3 34 35
  • 95.91 (n)
(Canis familiaris)
Mammalia TM9SF3 34 35
  • 95.8 (n)
(Monodelphis domestica)
Mammalia TM9SF3 35
  • 95 (a)
(Ornithorhynchus anatinus)
Mammalia TM9SF3 35
  • 95 (a)
(Rattus norvegicus)
Mammalia Tm9sf3 34
  • 92.67 (n)
(Mus musculus)
Mammalia Tm9sf3 34 16 35
  • 92.22 (n)
(Gallus gallus)
Aves TM9SF3 34 35
  • 86.43 (n)
(Anolis carolinensis)
Reptilia TM9SF3 35
  • 96 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia tm9sf3 34
  • 83.45 (n)
Str.6006 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.12856 34
(Danio rerio)
Actinopterygii tm9sf3 34 35
  • 80.4 (n)
Dr.26978 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004882 34
  • 67.93 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG10590 34 35
  • 65.84 (n)
(Caenorhabditis elegans)
Secernentea Y41D4A.4 34 35
  • 63.59 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes EMP70 35
  • 25 (a)
TMN2 35
  • 24 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons TMN1 34
  • 60.57 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.3627 34
(Glycine max)
eudicotyledons Gma.5446 34
(Oryza sativa)
Liliopsida Os12g0175700 34
  • 60.18 (n)
(Hordeum vulgare)
Liliopsida Hv.4691 34
(Zea mays)
Liliopsida Zm.4030 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.9350 35
  • 76 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4192 34
Species where no ortholog for TM9SF3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • 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 blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for TM9SF3 Gene

Gene Tree for TM9SF3 (if available)
Gene Tree for TM9SF3 (if available)

Paralogs for TM9SF3 Gene

Paralogs for TM9SF3 Gene

(4) SIMAP similar genes for TM9SF3 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with TM9SF3: view

Variants for TM9SF3 Gene

Sequence variations from dbSNP and Humsavar for TM9SF3 Gene

SNP ID Clin Chr 10 pos Sequence Context AA Info Type
rs1000087737 -- 96,571,422(+) AGGAA(C/T)AGCAG intron-variant
rs1000111854 -- 96,564,803(+) ATTGG(A/C)ATTAA intron-variant
rs1000167062 -- 96,577,335(+) TACAG(A/G)GGACA intron-variant
rs1000196670 -- 96,577,694(+) AGACA(C/T)TAATT intron-variant
rs1000213294 -- 96,587,622(+) CTTCC(C/T)AGTCA nc-transcript-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for TM9SF3 Gene

Variant ID Type Subtype PubMed ID
esv1534879 CNV insertion 17803354
esv3337079 CNV insertion 20981092
esv3577627 CNV gain 25503493
esv3579086 CNV loss 25503493
nsv1110852 OTHER inversion 24896259
nsv481191 CNV novel sequence insertion 20440878
nsv509363 CNV insertion 20534489
nsv825530 CNV loss 20364138
nsv948151 CNV duplication 23825009

Variation tolerance for TM9SF3 Gene

Residual Variation Intolerance Score: 15.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.71; 15.17% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TM9SF3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TM9SF3 Gene

Disorders for TM9SF3 Gene

Relevant External Links for TM9SF3

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:

No disorders were found for TM9SF3 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TM9SF3 Gene

Publications for TM9SF3 Gene

  1. The iodocyanopindolol and SM-11044 binding protein belongs to the TM9SF multispanning membrane protein superfamily. (PMID: 11595169) Sugasawa T. … Nahmias C. (Gene 2001) 2 3 22 64
  2. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PMID: 16385451) Grupe A. … Goate A. (Am. J. Hum. Genet. 2006) 3 46 64
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  4. The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment. (PMID: 12975309) Clark H.F. … Gray A.M. (Genome Res. 2003) 3 4 64
  5. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. (PMID: 25609649) Li X. … Chen J. (Mol. Syst. Biol. 2015) 3 64

Products for TM9SF3 Gene

Sources for TM9SF3 Gene

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