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TRIM40 tripartite motif containing 40 [ Homo sapiens (human) ]

Gene ID: 135644, updated on 3-Apr-2024

Summary

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Official Symbol
TRIM40provided by HGNC
Official Full Name
tripartite motif containing 40provided by HGNC
Primary source
HGNC:HGNC:18736
See related
Ensembl:ENSG00000204614 MIM:616976; AllianceGenome:HGNC:18736
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RNF35
Summary
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]
Expression
Biased expression in small intestine (RPKM 3.6), duodenum (RPKM 3.4) and 4 other tissues See more
Orthologs
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Genomic context

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Location:
6p22.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (30136140..30148735)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (30000415..30013010)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (30103917..30116512)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene TRIM31 antisense RNA 1 Neighboring gene tripartite motif containing 31 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr6:30080310-30081509 Neighboring gene small nucleolar RNA SNORA48 Neighboring gene tripartite motif containing 10 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:30139523-30140072 Neighboring gene tripartite motif containing 15 Neighboring gene tripartite motif containing 26 Neighboring gene PAIP1 pseudogene 1

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. TRIM40 is a pathogenic driver of inflammatory bowel disease subverting intestinal barrier integrity. Kang S, et al. Nat Commun, 2023 Feb 9. PMID 36755029, Free PMC Article
  2. TRIM40 inhibits IgA1-induced proliferation of glomerular mesangial cells by inactivating NLRP3 inflammasome through ubiquitination. Shen J, et al. Mol Immunol, 2021 Dec. PMID 34763147
  3. The E3 Ubiquitin Ligase TRIM40 Attenuates Antiviral Immune Responses by Targeting MDA5 and RIG-I. Zhao C, et al. Cell Rep, 2017 Nov 7. PMID 29117565
  4. TRIM40 promotes neddylation of IKKγ and is downregulated in gastrointestinal cancers. Noguchi K, et al. Carcinogenesis, 2011 Jul. PMID 21474709
  5. A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01. Cree BA, et al. PLoS One, 2010 Jun 25. PMID 20593013, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. TRIM40 is a pathogenic driver of inflammatory bowel disease subverting intestinal barrier integrity.
    Title: TRIM40 is a pathogenic driver of inflammatory bowel disease subverting intestinal barrier integrity.
  2. TRIM40 inhibits IgA1-induced proliferation of glomerular mesangial cells by inactivating NLRP3 inflammasome through ubiquitination.
    Title: TRIM40 inhibits IgA1-induced proliferation of glomerular mesangial cells by inactivating NLRP3 inflammasome through ubiquitination.
  3. findings suggest that TRIM40 inhibits NF-kappaB activity via neddylation of inhibitor of nuclear factor kappaB kinase subunit gamma and that TRIM40 prevents inflammation-associated carcinogenesis in the gastrointestinal tract
    Title: TRIM40 promotes neddylation of IKKγ and is downregulated in gastrointestinal cancers.
  4. Observational study of gene-disease association. (HuGE Navigator)
    Title: A major histocompatibility Class I locus contributes to multiple sclerosis susceptibility independently from HLA-DRB1*15:01.
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
Genome-wide association study of proneness to anger.
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

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables ubiquitin protein ligase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in innate immune response IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of NF-kappaB transcription factor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in negative regulation of NF-kappaB transcription factor activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of cell growth IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of non-canonical NF-kappaB signal transduction NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in negative regulation of protein catabolic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of protein localization to nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein neddylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein ubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
part_of IkappaB kinase complex IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
E3 ubiquitin ligase TRIM40
Names
RING finger protein 35
probable E3 NEDD8-protein ligase
ring finger RNF35
NP_001273562.1
NP_619645.1
XP_011512608.1
XP_011512611.1
XP_054184422.1
XP_054184423.1
XP_054184424.1
XP_054185712.1
XP_054185713.1
XP_054186210.1
XP_054186500.1
XP_054186501.1
XP_054186502.1
XP_054186748.1
XP_054186749.1
XP_054186984.1
XP_054186985.1
XP_054187251.1
XP_054187252.1
XP_054210303.1
XP_054210304.1
XP_054210305.1

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.

Genomic

  1. NG_033972.1 RefSeqGene

    Range
    5033..17621
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001286633.2 → NP_001273562.1  E3 ubiquitin ligase TRIM40 isoform a

    See identical proteins and their annotated locations for NP_001273562.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AL669914, BC060785
    Consensus CDS
    CCDS69069.1
    UniProtKB/Swiss-Prot
    Q5SRJ6, Q5SS36, Q6P9F5, Q8TD96
    UniProtKB/TrEMBL
    A0A1U9X8S7, A0A1U9X8U1
    Related
    ENSP00000379826.1, ENST00000396581.6
    Conserved Domains (1) summary
    cd16583
    Location:13 → 58
    RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins

  2. NM_138700.4 → NP_619645.1  E3 ubiquitin ligase TRIM40 isoform b

    See identical proteins and their annotated locations for NP_619645.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' UTR and uses an alternate in-frame splice site in the 3' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
    Source sequence(s)
    AF489517, AL669914, BC060785
    Consensus CDS
    CCDS4675.1
    UniProtKB/TrEMBL
    A0A140T9D5
    Related
    ENSP00000308310.4, ENST00000307859.4
    Conserved Domains (1) summary
    cd00162
    Location:14 → 60
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    30136140..30148735
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514309.2 → XP_011512611.1  E3 ubiquitin ligase TRIM40 isoform X2

    See identical proteins and their annotated locations for XP_011512611.1

    UniProtKB/TrEMBL
    A0A1U9X8S7
    Conserved Domains (1) summary
    cd00162
    Location:14 → 60
    RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

  2. XM_011514306.2 → XP_011512608.1  E3 ubiquitin ligase TRIM40 isoform X1

    See identical proteins and their annotated locations for XP_011512608.1

    UniProtKB/Swiss-Prot
    Q5SRJ6, Q5SS36, Q6P9F5, Q8TD96
    UniProtKB/TrEMBL
    A0A1U9X8S7, A0A1U9X8U1
    Conserved Domains (1) summary
    cd16583
    Location:13 → 58
    RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    1394236..1406831
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054328447.1 → XP_054184422.1  E3 ubiquitin ligase TRIM40 isoform X1

    UniProtKB/Swiss-Prot
    Q5SRJ6, Q5SS36, Q6P9F5, Q8TD96
    UniProtKB/TrEMBL
    A0A1U9X8U1

  2. XM_054328449.1 → XP_054184424.1  E3 ubiquitin ligase TRIM40 isoform X2

  3. XM_054328448.1 → XP_054184423.1  E3 ubiquitin ligase TRIM40 isoform X1

    UniProtKB/Swiss-Prot
    Q5SRJ6, Q5SS36, Q6P9F5, Q8TD96
    UniProtKB/TrEMBL
    A0A1U9X8U1

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    1615945..1628543
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329738.1 → XP_054185713.1  E3 ubiquitin ligase TRIM40 isoform X2

  2. XM_054329737.1 → XP_054185712.1  E3 ubiquitin ligase TRIM40 isoform X1

    UniProtKB/Swiss-Prot
    Q5SRJ6, Q5SS36, Q6P9F5, Q8TD96
    UniProtKB/TrEMBL
    A0A1U9X8U1

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    1391916..1404652
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330235.1 → XP_054186210.1  E3 ubiquitin ligase TRIM40 isoform X1

    UniProtKB/TrEMBL
    A0A0G2JIV5

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    1446862..1459457
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330525.1 → XP_054186500.1  E3 ubiquitin ligase TRIM40 isoform X1

    UniProtKB/Swiss-Prot
    Q5SRJ6, Q5SS36, Q6P9F5, Q8TD96
    UniProtKB/TrEMBL
    A0A1U9X8U1

  2. XM_054330527.1 → XP_054186502.1  E3 ubiquitin ligase TRIM40 isoform X2

  3. XM_054330526.1 → XP_054186501.1  E3 ubiquitin ligase TRIM40 isoform X1

    UniProtKB/Swiss-Prot
    Q5SRJ6, Q5SS36, Q6P9F5, Q8TD96
    UniProtKB/TrEMBL
    A0A1U9X8U1

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    1480229..1492817
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330773.1 → XP_054186748.1  E3 ubiquitin ligase TRIM40 isoform X1

    UniProtKB/TrEMBL
    A0A0G2JMU7

  2. XM_054330774.1 → XP_054186749.1  E3 ubiquitin ligase TRIM40 isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    1391268..1403864
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331010.1 → XP_054186985.1  E3 ubiquitin ligase TRIM40 isoform X2

  2. XM_054331009.1 → XP_054186984.1  E3 ubiquitin ligase TRIM40 isoform X1

    UniProtKB/Swiss-Prot
    Q5SRJ6, Q5SS36, Q6P9F5, Q8TD96
    UniProtKB/TrEMBL
    A0A1U9X8U1

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    1435079..1447667
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331276.1 → XP_054187251.1  E3 ubiquitin ligase TRIM40 isoform X1

    UniProtKB/TrEMBL
    A0A0G2JMU7

  2. XM_054331277.1 → XP_054187252.1  E3 ubiquitin ligase TRIM40 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    30000415..30013010
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054354329.1 → XP_054210304.1  E3 ubiquitin ligase TRIM40 isoform X1

    UniProtKB/Swiss-Prot
    Q5SRJ6, Q5SS36, Q6P9F5, Q8TD96
    UniProtKB/TrEMBL
    A0A1U9X8U1

  2. XM_054354330.1 → XP_054210305.1  E3 ubiquitin ligase TRIM40 isoform X2

  3. XM_054354328.1 → XP_054210303.1  E3 ubiquitin ligase TRIM40 isoform X1

    UniProtKB/Swiss-Prot
    Q5SRJ6, Q5SS36, Q6P9F5, Q8TD96
    UniProtKB/TrEMBL
    A0A1U9X8U1
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6P9F5.3 GenPept UniProtKB/Swiss-Prot:Q6P9F5

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