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Aliases for TRIM40 Gene

Aliases for TRIM40 Gene

  • Tripartite Motif Containing 40 2 3 5
  • Probable E3 NEDD8-Protein Ligase 3 4
  • RING Finger Protein 35 3 4
  • RNF35 3 4
  • Tripartite Motif-Containing Protein 40 3
  • Tripartite Motif-Containing 40 2
  • Ring Finger RNF35 3

External Ids for TRIM40 Gene

Previous GeneCards Identifiers for TRIM40 Gene

  • GC06P030189
  • GC06P029875
  • GC06P030210
  • GC06P030212
  • GC06P030103
  • GC06P029920
  • GC06P030281
  • GC06P030317
  • GC06P030367
  • GC06P030517
  • GC06P030724
  • GC06P030883

Summaries for TRIM40 Gene

Entrez Gene Summary for TRIM40 Gene

  • This gene encodes a member of the tripartite motif (TRIM) protein family. The encoded protein may play a role as a negative regulator against inflammation and carcinogenesis in the gastrointestinal tract. Alternatively spliced transcript variants that encode different protein isoforms have been described. [provided by RefSeq, Feb 2014]

GeneCards Summary for TRIM40 Gene

TRIM40 (Tripartite Motif Containing 40) is a Protein Coding gene. GO annotations related to this gene include nucleotide binding.

UniProtKB/Swiss-Prot for TRIM40 Gene

  • May function as an E3 ubiquitin-protein ligase of the NEDD8 conjugation pathway. Promotes neddylation of IKBKG/NEMO, stabilizing NFKBIA, and inhibiting of NF-kappaB nuclear translocation and activity.

Additional gene information for TRIM40 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for TRIM40 Gene

Genomics for TRIM40 Gene

Regulatory Elements for TRIM40 Gene

Enhancers for TRIM40 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
GH06H030129 1.3 Ensembl ENCODE 38.4 -3.6 -3603 3 HDGF PKNOX1 MLX ARNT SIN3A ARID4B FEZF1 ZNF2 ZNF143 DEK TRIM40 TRIM31 TRIM31-AS1 TRIM10 TRIM15 HLA-A HCG18 ENSG00000252228 GC06M030317
GH06H030143 0.7 ENCODE 32.8 +10.0 10023 1 ATF1 FEZF1 ATF2 RARA PRDM6 SCRT2 MBD1 CREB1 BCL6 ATF7 HLA-U TRIM40 TRIM31 ZFP57 ENSG00000237669 IFITM4P TRIM15
GH06H030122 0.5 ENCODE 31.9 -11.4 -11420 1 PKNOX1 PRDM6 POLR3A HLF HLA-U TRIM40 VARS2 HLA-W GC06M030233 GC06M030235 GC06M030250 GC06M030269 GC06M030297 GC06M030300
GH06H030210 1.1 ENCODE 9.6 +78.4 78380 4 PKNOX1 MLX ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 ZNF143 FOS HLA-U TRIM31 MICD HLA-K HLA-W DHX16 ENSG00000233892 TRIM39 TRIM26 MDC1
GH06H030133 1 ENCODE 8.2 +1.1 1102 4 FOXA2 ATF1 ARID4B DMAP1 SLC30A9 ATF7 RUNX3 SP5 MIER2 PPARG TRIM31 HLA-K HLA-A ENSG00000237669 TRIM31-AS1 TRIM10 TRIM15 PPP1R10 TRIM39 TRIM26
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around TRIM40 on UCSC Golden Path with GeneCards custom track

Genomic Location for TRIM40 Gene

Chromosome:
6
Start:
30,134,510 bp from pter
End:
30,148,773 bp from pter
Size:
14,264 bases
Orientation:
Plus strand

Genomic View for TRIM40 Gene

Genes around TRIM40 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
TRIM40 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for TRIM40 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

Proteins for TRIM40 Gene

  • Protein details for TRIM40 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q6P9F5-TRI40_HUMAN
    Recommended name:
    Tripartite motif-containing protein 40
    Protein Accession:
    Q6P9F5
    Secondary Accessions:
    • Q5SRJ6
    • Q5SS36
    • Q8TD96

    Protein attributes for TRIM40 Gene

    Size:
    258 amino acids
    Molecular mass:
    29336 Da
    Quaternary structure:
    • Interacts with NEDD8.

    Alternative splice isoforms for TRIM40 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for TRIM40 Gene

Post-translational modifications for TRIM40 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for TRIM40 Gene

No data available for DME Specific Peptides for TRIM40 Gene

Domains & Families for TRIM40 Gene

Gene Families for TRIM40 Gene

Suggested Antigen Peptide Sequences for TRIM40 Gene

Graphical View of Domain Structure for InterPro Entry

Q6P9F5

UniProtKB/Swiss-Prot:

TRI40_HUMAN :
  • Belongs to the TRIM/RBCC family.
Family:
  • Belongs to the TRIM/RBCC family.
genes like me logo Genes that share domains with TRIM40: view

Function for TRIM40 Gene

Molecular function for TRIM40 Gene

UniProtKB/Swiss-Prot Function:
May function as an E3 ubiquitin-protein ligase of the NEDD8 conjugation pathway. Promotes neddylation of IKBKG/NEMO, stabilizing NFKBIA, and inhibiting of NF-kappaB nuclear translocation and activity.

Phenotypes From GWAS Catalog for TRIM40 Gene

Gene Ontology (GO) - Molecular Function for TRIM40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 21474709
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with TRIM40: view
genes like me logo Genes that share phenotypes with TRIM40: view

Animal Model Products

CRISPR Products

miRNA for TRIM40 Gene

miRTarBase miRNAs that target TRIM40

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for TRIM40 Gene

Localization for TRIM40 Gene

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 TRIM40 gene
Compartment Confidence
nucleus 3
cytosol 2

Gene Ontology (GO) - Cellular Components for TRIM40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005622 intracellular IEA --
GO:0008385 IkappaB kinase complex IDA 21474709
genes like me logo Genes that share ontologies with TRIM40: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Subcellular locations from the Human Protein Atlas (HPA) for TRIM40 Gene

Pathways & Interactions for TRIM40 Gene

SuperPathways for TRIM40 Gene

No Data Available

Gene Ontology (GO) - Biological Process for TRIM40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0030308 negative regulation of cell growth IEA --
GO:0032088 negative regulation of NF-kappaB transcription factor activity IDA 21474709
GO:0042177 negative regulation of protein catabolic process IDA 21474709
GO:0045116 protein neddylation IDA 21474709
GO:1900181 negative regulation of protein localization to nucleus IDA 21474709
genes like me logo Genes that share ontologies with TRIM40: view

No data available for Pathways by source and SIGNOR curated interactions for TRIM40 Gene

Drugs & Compounds for TRIM40 Gene

No Compound Related Data Available

Transcripts for TRIM40 Gene

mRNA/cDNA for TRIM40 Gene

(6) REFSEQ mRNAs :
(1) Additional mRNA sequences :
(5) Selected AceView cDNA sequences:
(4) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for TRIM40 Gene

Tripartite motif containing 40:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for TRIM40 Gene

No ASD Table

Relevant External Links for TRIM40 Gene

GeneLoc Exon Structure for
TRIM40
ECgene alternative splicing isoforms for
TRIM40

Expression for TRIM40 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for TRIM40 Gene

mRNA differential expression in normal tissues according to GTEx for TRIM40 Gene

This gene is overexpressed in Liver (x18.0), Small Intestine - Terminal Ileum (x13.9), Colon - Transverse (x13.0), and Testis (x4.7).

Protein differential expression in normal tissues from HIPED for TRIM40 Gene

This gene is overexpressed in Heart (60.4) and Platelet (8.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for TRIM40 Gene



Protein tissue co-expression partners for TRIM40 Gene

NURSA nuclear receptor signaling pathways regulating expression of TRIM40 Gene:

TRIM40

SOURCE GeneReport for Unigene cluster for TRIM40 Gene:

Hs.509439

mRNA Expression by UniProt/SwissProt for TRIM40 Gene:

Q6P9F5-TRI40_HUMAN
Tissue specificity: Highly expressed in normal gastrointestinal epithelia but that is down-regulated in gastrointestinal carcinomas and chronic inflammatory lesions of the gastrointestinal tract.
genes like me logo Genes that share expression patterns with TRIM40: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for TRIM40 Gene

Orthologs for TRIM40 Gene

This gene was present in the common ancestor of mammals.

Orthologs for TRIM40 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia TRIM40 33 34
  • 99.42 (n)
cow
(Bos Taurus)
Mammalia TRIM40 33 34
  • 80.99 (n)
mouse
(Mus musculus)
Mammalia Trim40 33 16 34
  • 77.01 (n)
rat
(Rattus norvegicus)
Mammalia Trim40 33
  • 74.25 (n)
oppossum
(Monodelphis domestica)
Mammalia TRIM40 34
  • 39 (a)
OneToOne
Species where no ortholog for TRIM40 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • tropical clawed frog (Silurana tropicalis)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for TRIM40 Gene

ENSEMBL:
Gene Tree for TRIM40 (if available)
TreeFam:
Gene Tree for TRIM40 (if available)

Paralogs for TRIM40 Gene

(1) SIMAP similar genes for TRIM40 Gene using alignment to 1 proteins:

genes like me logo Genes that share paralogs with TRIM40: view

No data available for Paralogs for TRIM40 Gene

Variants for TRIM40 Gene

Sequence variations from dbSNP and Humsavar for TRIM40 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000868084 -- 30,137,811(+) CTCTC(G/T)TTTTC intron-variant
rs1001100035 -- 30,146,202(+) TGGTC(A/G)TGGAG intron-variant
rs1001492369 -- 30,139,993(+) CTTTA(A/G)AGAAA intron-variant
rs1001725678 -- 30,145,868(+) CATTT(A/C)TTTTT intron-variant
rs1001762476 -- 30,134,433(+) GGATT(A/G)AAGGT upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for TRIM40 Gene

Variant ID Type Subtype PubMed ID
esv2731777 CNV deletion 23290073
esv3411275 CNV duplication 20981092
nsv1074389 CNV deletion 25765185
nsv1122126 CNV deletion 24896259
nsv1144137 CNV deletion 24896259
nsv601264 CNV loss 21841781

Variation tolerance for TRIM40 Gene

Residual Variation Intolerance Score: 83.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 6.21; 76.05% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for TRIM40 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
TRIM40

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for TRIM40 Gene

Disorders for TRIM40 Gene

Relevant External Links for TRIM40

Genetic Association Database (GAD)
TRIM40
Human Genome Epidemiology (HuGE) Navigator
TRIM40
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
TRIM40

No disorders were found for TRIM40 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for TRIM40 Gene

Publications for TRIM40 Gene

  1. TRIM40 promotes neddylation of IKKγ and is downregulated in gastrointestinal cancers. (PMID: 21474709) Noguchi K … Hatakeyama S (Carcinogenesis 2011) 3 4 60
  2. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. (PMID: 20593013) Cree BA … IMSGC (PloS one 2010) 3 45 60
  3. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos LF … Criswell LA (PLoS genetics 2009) 3 45 60
  4. Rapid evolution of major histocompatibility complex class I genes in primates generates new disease alleles in humans via hitchhiking diversity. (PMID: 16702430) Shiina T … Bahram S (Genetics 2006) 3 4 60
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60

Products for TRIM40 Gene

Sources for TRIM40 Gene

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