Trim40 tripartite motif-containing 40 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Trim40provided by MGI
Official Full Name: tripartite motif-containing 40provided by MGI
Primary source: MGI:MGI:2684881
See related: Ensembl:ENSMUSG00000073399 AllianceGenome:MGI:2684881
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Gm35; Gm319; Gm865
Summary: Predicted to enable ubiquitin protein ligase activity. Predicted to be involved in several processes, including negative regulation of NF-kappaB transcription factor activity; negative regulation of protein localization to nucleus; and protein modification by small protein conjugation. Predicted to be part of IkappaB kinase complex. Predicted to be active in cytoplasm. Orthologous to human TRIM40 (tripartite motif containing 40). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in large intestine adult (RPKM 19.3), small intestine adult (RPKM 8.6) and 2 other tissues See more
Orthologs: human all
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Genomic context

Location:: 17 B1; 17 19.16 cM

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	17	NC_000083.7 (37192488..37201049, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	17	NC_000083.6 (36881596..36890157, complement)

Chromosome 17 - NC_000083.7 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: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Riok3 inhibits the antiviral immune response by facilitating TRIM40-mediated RIG-I and MDA5 degradation.
Title: Riok3 inhibits the antiviral immune response by facilitating TRIM40-mediated RIG-I and MDA5 degradation.
TRIM40 binds to MDA5 and RIG-I and promotes their K27- and K48-linked polyubiquitination via its E3 ligase activity, leading to their proteasomal degradation. TRIM40 deficiency enhances RLR-triggered signaling.
Title: The E3 Ubiquitin Ligase TRIM40 Attenuates Antiviral Immune Responses by Targeting MDA5 and RIG-I.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables transferase activity	IEA Inferred from Electronic Annotation more info
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	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell growth	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein catabolic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of protein localization to nucleus	ISO Inferred from Sequence Orthology more info
involved_in protein neddylation	ISO Inferred from Sequence Orthology more info
involved_in protein ubiquitination	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of IkappaB kinase complex	ISO Inferred from Sequence Orthology more info
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: probable E3 NEDD8-protein ligase; ring finger RNF35; tripartite motif-containing protein 40

NP_001028407.1

EC 2.3.2.27

NP_001165639.1

EC 2.3.2.27

XP_006523965.1

EC 2.3.2.27

XP_006523966.1

EC 2.3.2.27

XP_006523967.1

EC 2.3.2.27

XP_006523969.1

EC 2.3.2.27

XP_006523970.1

EC 2.3.2.27

XP_006523971.1

EC 2.3.2.27

XP_006523972.1

EC 2.3.2.27

XP_017172846.1

EC 2.3.2.27

XP_017172847.1

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.

mRNA and Protein(s)

NM_001033235.3 → NP_001028407.1 E3 ubiquitin ligase TRIM40 isoform 1

See identical proteins and their annotated locations for NP_001028407.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AK136498, CR956641

Consensus CDS

CCDS28727.1

UniProtKB/Swiss-Prot

B2RVT3, Q3UWA4

Related

ENSMUSP00000084400.5, ENSMUST00000087158.11

Conserved Domains (2) summary

cd16583
Location:11 → 56

RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins

cl00034
Location:66 → 108

Bbox_SF; B-box-type zinc finger superfamily
NM_001172168.1 → NP_001165639.1 E3 ubiquitin ligase TRIM40 isoform 2

See identical proteins and their annotated locations for NP_001165639.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.

Source sequence(s)

BC172037, CJ053960, CR956641

Consensus CDS

CCDS57080.1

UniProtKB/TrEMBL

B7ZWG4

Conserved Domains (2) summary

cd16583
Location:11 → 56

RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins

cl00034
Location:66 → 108

Bbox_SF; B-box-type zinc finger superfamily

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000083.7 Reference GRCm39 C57BL/6J

Range

37192488..37201049 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017317357.2 → XP_017172846.1 E3 ubiquitin ligase TRIM40 isoform X2

UniProtKB/Swiss-Prot

B2RVT3, Q3UWA4

Conserved Domains (2) summary

cd16583
Location:11 → 56

RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins

cl00034
Location:66 → 108

Bbox_SF; B-box-type zinc finger superfamily
XM_017317358.1 → XP_017172847.1 E3 ubiquitin ligase TRIM40 isoform X5

UniProtKB/TrEMBL

B7ZWG4

Related

ENSMUSP00000133581.2, ENSMUST00000172711.2

Conserved Domains (2) summary

cd16583
Location:11 → 56

RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins

cl00034
Location:66 → 108

Bbox_SF; B-box-type zinc finger superfamily
XM_006523908.4 → XP_006523971.1 E3 ubiquitin ligase TRIM40 isoform X3

Conserved Domains (2) summary

cl00034
Location:33 → 75

Bbox_SF; B-box-type zinc finger superfamily

cl17238
Location:1 → 23

RING_Ubox; The superfamily of RING finger (Really Interesting New Gene) domain and U-box domain
XM_006523903.3 → XP_006523966.1 E3 ubiquitin ligase TRIM40 isoform X1

See identical proteins and their annotated locations for XP_006523966.1

Conserved Domains (2) summary

cd16583
Location:11 → 56

RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins

cl00034
Location:66 → 108

Bbox_SF; B-box-type zinc finger superfamily
XM_006523907.4 → XP_006523970.1 E3 ubiquitin ligase TRIM40 isoform X1

See identical proteins and their annotated locations for XP_006523970.1

Conserved Domains (2) summary

cd16583
Location:11 → 56

RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins

cl00034
Location:66 → 108

Bbox_SF; B-box-type zinc finger superfamily
XM_006523906.4 → XP_006523969.1 E3 ubiquitin ligase TRIM40 isoform X1

See identical proteins and their annotated locations for XP_006523969.1

Conserved Domains (2) summary

cd16583
Location:11 → 56

RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins

cl00034
Location:66 → 108

Bbox_SF; B-box-type zinc finger superfamily
XM_006523904.4 → XP_006523967.1 E3 ubiquitin ligase TRIM40 isoform X1

See identical proteins and their annotated locations for XP_006523967.1

Conserved Domains (2) summary

cd16583
Location:11 → 56

RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins

cl00034
Location:66 → 108

Bbox_SF; B-box-type zinc finger superfamily
XM_006523902.4 → XP_006523965.1 E3 ubiquitin ligase TRIM40 isoform X1

See identical proteins and their annotated locations for XP_006523965.1

Conserved Domains (2) summary

cd16583
Location:11 → 56

RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins

cl00034
Location:66 → 108

Bbox_SF; B-box-type zinc finger superfamily
XM_006523909.4 → XP_006523972.1 E3 ubiquitin ligase TRIM40 isoform X4

See identical proteins and their annotated locations for XP_006523972.1

Conserved Domains (2) summary

cd16583
Location:11 → 56

RING-HC_TRIM40-C-V; RING finger, HC subclass, found in tripartite motif-containing protein 40 (TRIM40) and similar proteins

cl00034
Location:66 → 108

Bbox_SF; B-box-type zinc finger superfamily