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

Summary

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: mouse all
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Genomic context

Location:: 6p22.1

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (30136140..30148735)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (30000415..30013010)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (30103917..30116512)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TRIM40 interacts with ROCK1 directly and inhibits colorectal cancer cell proliferation through the c-Myc/p21 axis.
Title: TRIM40 interacts with ROCK1 directly and inhibits colorectal cancer cell proliferation through the c-Myc/p21 axis.
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.
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.
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.
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.

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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 EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D6S2965 (e-PCR)
- UniSTS:464169

D6S2849 (e-PCR)
- UniSTS:464170

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	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 regulation of gene expression	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

EC 2.3.2.27

NP_619645.1

EC 2.3.2.27

XP_011512608.1

EC 2.3.2.27

XP_011512611.1

EC 2.3.2.27

XP_054184422.1

EC 2.3.2.27

XP_054184423.1

EC 2.3.2.27

XP_054184424.1

EC 2.3.2.27

XP_054185712.1

EC 2.3.2.27

XP_054185713.1

EC 2.3.2.27

XP_054186210.1

EC 2.3.2.27

XP_054186500.1

EC 2.3.2.27

XP_054186501.1

EC 2.3.2.27

XP_054186502.1

EC 2.3.2.27

XP_054186748.1

EC 2.3.2.27

XP_054186749.1

EC 2.3.2.27

XP_054186984.1

EC 2.3.2.27

XP_054186985.1

EC 2.3.2.27

XP_054187251.1

EC 2.3.2.27

XP_054187252.1

EC 2.3.2.27

XP_054210303.1

EC 2.3.2.27

XP_054210304.1

EC 2.3.2.27

XP_054210305.1

EC 2.3.2.27

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

NG_033972.1 RefSeqGene

Range

5033..17621

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

30136140..30148735

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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 ...
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

NT_167244.2 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

1394236..1406831

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

Q5SRJ6, Q5SS36, Q6P9F5, Q8TD96

UniProtKB/TrEMBL

A0A1U9X8U1
XM_054328449.1 → XP_054184424.1 E3 ubiquitin ligase TRIM40 isoform X2
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

NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

1615945..1628543

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

Range

1391916..1404652

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A0G2JIV5

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

Range

1446862..1459457

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

Q5SRJ6, Q5SS36, Q6P9F5, Q8TD96

UniProtKB/TrEMBL

A0A1U9X8U1
XM_054330527.1 → XP_054186502.1 E3 ubiquitin ligase TRIM40 isoform X2
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

NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

Range

1480229..1492817

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A0G2JMU7
XM_054330774.1 → XP_054186749.1 E3 ubiquitin ligase TRIM40 isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

Range

1391268..1403864

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

Range

1435079..1447667

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A0G2JMU7
XM_054331277.1 → XP_054187252.1 E3 ubiquitin ligase TRIM40 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

30000415..30013010

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/Swiss-Prot

Q5SRJ6, Q5SS36, Q6P9F5, Q8TD96

UniProtKB/TrEMBL

A0A1U9X8U1
XM_054354330.1 → XP_054210305.1 E3 ubiquitin ligase TRIM40 isoform X2
XM_054354328.1 → XP_054210303.1 E3 ubiquitin ligase TRIM40 isoform X1

UniProtKB/Swiss-Prot

Q5SRJ6, Q5SS36, Q6P9F5, Q8TD96

UniProtKB/TrEMBL

A0A1U9X8U1