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Aliases for TRIM40 Gene

Aliases for TRIM40 Gene

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

External Ids for TRIM40 Gene

Previous GeneCards Identifiers for TRIM40 Gene

  • GC06P030189
  • GC06P029875
  • GC06P030210
  • GC06P030212
  • GC06P030103
  • GC06P029920

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.

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.

No data available for 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

Genomic Location for TRIM40 Gene

Start:
30,136,108 bp from pter
End:
30,148,735 bp from pter
Size:
12,628 bases
Orientation:
Plus strand

Genomic View for TRIM40 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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

Proteomics data for TRIM40 Gene at MOPED

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 for TRIM40 Gene

Gene Families for TRIM40 Gene

HGNC:
  • RNF :RING-type (C3HC4) zinc fingers
  • TRIM :Tripartite motif containing / Tripartite motif containing

Protein Domains for TRIM40 Gene

Suggested Antigen Peptide Sequences for TRIM40 Gene

Graphical View of Domain Structure for InterPro Entry

Q6P9F5

UniProtKB/Swiss-Prot:

TRI40_HUMAN :
  • Q6P9F5
Family:
  • Belongs to the TRIM/RBCC family.
Similarity:
  • Contains 1 B box-type zinc finger.
  • Contains 1 RING-type zinc finger.
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.

Gene Ontology (GO) - Molecular Function for TRIM40 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000166 nucleotide binding --
GO:0005515 protein binding IPI 21474709
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding --
genes like me logo Genes that share ontologies with TRIM40: view

Animal Model Products

CRISPR Products

miRNA for TRIM40 Gene

miRTarBase miRNAs that target TRIM40

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for TRIM40

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes , Animal Models , Transcription Factor Targeting and HOMER Transcription for TRIM40 Gene

Localization for TRIM40 Gene

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for TRIM40 Gene 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 --
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 for TRIM40 Gene

Pathways for TRIM40 Gene

SuperPathways for TRIM40 Gene

No Data Available

PCR Array Products

  • Pathway & Disease-focused RT² Profiler PCR Arrays

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 for TRIM40 Gene

Transcripts for TRIM40 Gene

mRNA/cDNA for TRIM40 Gene

(24) REFSEQ mRNAs :
(5) Selected AceView cDNA sequences:
(1) Additional mRNA 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

miRNA Products

Inhibitory RNA Products

  • Predesigned siRNA for gene silencing in human,mouse,rat for TRIM40

Primer Products

  • OriGene qSTAR qPCR primer pairs in human,mouse,rat for TRIM40
  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

Flow Cytometry 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 for TRIM40 Gene

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

This gene is overexpressed in Liver (18.0), Small Intestine - Terminal Ileum (13.9), Colon - Transverse (13.0), and Testis (4.7).

Integrated Proteomics: protein expression from ProteomicsDB and MOPED for TRIM40 Gene

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 expressions with TRIM40: view

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery 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 35
  • 99.42 (n)
  • 99.13 (a)
TRIM40 36
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia TRIM40 35
  • 80.99 (n)
  • 68.86 (a)
TRIM40 36
  • 51 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Trim40 35
  • 77.01 (n)
  • 67.67 (a)
Trim40 16
Trim40 36
  • 58 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia TRIM40 36
  • 39 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Trim40 35
  • 74.25 (n)
  • 64.23 (a)
Species with no ortholog for TRIM40:
  • 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

Selected 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 MAF
rs757259 -, - 30,147,765(-) TTTCT(C/T)CAACT missense, reference
rs757260 -- 30,147,427(-) CTCTG(A/G)GGTGC intron-variant
rs757261 -- 30,147,286(-) CACCT(C/T)CCAGA intron-variant
rs757262 -- 30,147,178(-) TGGCC(A/G)TCCTT reference, missense
rs1541267 -- 30,135,794(-) CCCAC(C/T)CCATT upstream-variant-2KB

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

Variant ID Type Subtype PubMed ID
esv2731777 CNV Deletion 23290073

Relevant External Links for TRIM40 Gene

HapMap Linkage Disequilibrium report
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
genes like me logo Genes that share disorders with TRIM40: view

No data available for UniProtKB/Swiss-Prot for TRIM40 Gene

Publications for TRIM40 Gene

  1. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4
  2. 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
  3. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. (PMID: 19851445) Barcellos L.F. … Criswell L.A. (PLoS Genet. 2009) 3 48
  4. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. (PMID: 20593013) Cree B.A. … . (PLoS ONE 2010) 3 48
  5. TRIM40 promotes neddylation of IKKgamma and is downregulated in gastrointestinal cancers. (PMID: 21474709) Noguchi K. … Hatakeyama S. (Carcinogenesis 2011) 3 4

Products for TRIM40 Gene

  • Pathway & Disease-focused RT² Profiler PCR Arrays
  • QIAGEN qRT-PCR Assays for microRNAs that regulate TRIM40
  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat
  • Predesigned siRNA for gene silencing in human,mouse,rat for TRIM40
  • Block miRNA regulation of TRIM40 using miScript Target Protectors

Sources for TRIM40 Gene

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