TRIM50 tripartite motif containing 50 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TRIM50provided by HGNC
Official Full Name: tripartite motif containing 50provided by HGNC
Primary source: HGNC:HGNC:19017
See related: Ensembl:ENSG00000146755 MIM:612548; AllianceGenome:HGNC:19017
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: TRIM50A
Summary: Enables identical protein binding activity. Predicted to be involved in innate immune response. Predicted to act upstream of or within regulation of establishment of protein localization. Located in cytosol. [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in stomach (RPKM 3.4), testis (RPKM 2.8) and 8 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7q11.23

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (73312536..73328082, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (74512695..74528253, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (72726532..72742085, complement)

Chromosome 7 - NC_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TRIM50 Inhibits Gastric Cancer Progression by Regulating the Ubiquitination and Nuclear Translocation of JUP.
Title: TRIM50 Inhibits Gastric Cancer Progression by Regulating the Ubiquitination and Nuclear Translocation of JUP.
TRIM50 acted as a tumor suppressor in hepatocarcinoma cells by directly targeting SNAIL and reversing epithelial-to-mesenchymal transition.
Title: TRIM50 suppressed hepatocarcinoma progression through directly targeting SNAIL for ubiquitous degradation.
TRIM50, via the RING domain, ubiquitinates Beclin 1 in a K63-dependent manner enhancing its binding with ULK1 and autophagy activity.
Title: TRIM50 regulates Beclin 1 proautophagic activity.
TRIM50 K372 residue competes for post-translational protein modifications such as acetylation and ubiquitination.
Title: HDAC6 mediates the acetylation of TRIM50.
When the proteasome activity is impaired, TRIM50 fails to drive its substrates to the proteasome-mediated degradation.
Title: The E3-ubiquitin ligase TRIM50 interacts with HDAC6 and p62, and promotes the sequestration and clearance of ubiquitinated proteins into the aggresome.
Encodes an E3 ubiquitin ligase; putatively involved in phenotype determination of Williams-Beuren syndrome.
Title: Williams-Beuren syndrome TRIM50 encodes an E3 ubiquitin ligase.

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 analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients. 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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
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

Component	Evidence Code	Pubs
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytosol	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase TRIM50

Names: RING-type E3 ubiquitin transferase TRIM50; tripartite motif-containing 50A; tripartite motif-containing protein 50

NP_001268379.1

EC 2.3.2.27

NP_001268380.1

EC 2.3.2.27

NP_835226.2

EC 2.3.2.27

XP_011514089.1

EC 2.3.2.27

XP_011514090.1

EC 2.3.2.27

XP_011514091.2

EC 2.3.2.27

XP_047275836.1

EC 2.3.2.27

XP_054213203.1

EC 2.3.2.27

XP_054213204.1

EC 2.3.2.27

XP_054213205.1

EC 2.3.2.27

XP_054213206.1

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_001281450.1 → NP_001268379.1 E3 ubiquitin-protein ligase TRIM50 isoform b

See identical proteins and their annotated locations for NP_001268379.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (b) is shorter than isoform a.

Source sequence(s)

AI208986, AK057366, AY081948, BC143787, HY014417

UniProtKB/TrEMBL

B7ZLG2

Conserved Domains (3) summary

cd00021
Location:90 → 125

BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.

cd13743
Location:282 → 468

SPRY_PRY_TRIM50; PRY/SPRY domain in tripartite motif-binding protein 50 (TRIM50)

cl17238
Location:16 → 56

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 ...
NM_001281451.1 → NP_001268380.1 E3 ubiquitin-protein ligase TRIM50 isoform a

See identical proteins and their annotated locations for NP_001268380.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same isoform (a).

Source sequence(s)

AI208986, AK292074, AY081948, DA045168, DA632418

Consensus CDS

CCDS34654.1

UniProtKB/Swiss-Prot

Q2M204, Q86XT3, Q86XT4

Related

ENSP00000413875.1, ENST00000453152.1

Conserved Domains (3) summary

cd00021
Location:90 → 125

BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.

cd13743
Location:283 → 469

SPRY_PRY_TRIM50; PRY/SPRY domain in tripartite motif-binding protein 50 (TRIM50)

cd16605
Location:14 → 58

RING-HC_TRIM50_like_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein TRIM50, TRIM73, TRIM74 and similar proteins
NM_178125.3 → NP_835226.2 E3 ubiquitin-protein ligase TRIM50 isoform a

See identical proteins and their annotated locations for NP_835226.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 encode the same isoform (a).

Source sequence(s)

AI208986, AK057366, AY081948, BC112154, HY014417

Consensus CDS

CCDS34654.1

UniProtKB/Swiss-Prot

Q2M204, Q86XT3, Q86XT4

Related

ENSP00000327994.2, ENST00000333149.7

Conserved Domains (3) summary

cd00021
Location:90 → 125

BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.

cd13743
Location:283 → 469

SPRY_PRY_TRIM50; PRY/SPRY domain in tripartite motif-binding protein 50 (TRIM50)

cd16605
Location:14 → 58

RING-HC_TRIM50_like_C-IV; RING finger, HC subclass, found in tripartite motif-containing protein TRIM50, TRIM73, TRIM74 and similar proteins

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_000007.14 Reference GRCh38.p14 Primary Assembly

Range

73312536..73328082 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047419880.1 → XP_047275836.1 E3 ubiquitin-protein ligase TRIM50 isoform X3
XM_011515788.3 → XP_011514090.1 E3 ubiquitin-protein ligase TRIM50 isoform X3

Conserved Domains (1) summary

cl02614
Location:74 → 260

SPRY; SPRY domain
XM_011515789.2 → XP_011514091.2 E3 ubiquitin-protein ligase TRIM50 isoform X1

UniProtKB/TrEMBL

B7ZLG2

Conserved Domains (3) summary

cd00021
Location:90 → 125

BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.

cd13743
Location:282 → 468

SPRY_PRY_TRIM50; PRY/SPRY domain in tripartite motif-binding protein 50 (TRIM50)

cl17238
Location:16 → 56

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_011515787.2 → XP_011514089.1 E3 ubiquitin-protein ligase TRIM50 isoform X2

UniProtKB/TrEMBL

I3L0H3

Conserved Domains (2) summary

cd00021
Location:90 → 125

BBOX; B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.

cl17238
Location:16 → 56

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 ...

Alternate T2T-CHM13v2.0

Genomic

NC_060931.1 Alternate T2T-CHM13v2.0

Range

74512695..74528253 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054357231.1 → XP_054213206.1 E3 ubiquitin-protein ligase TRIM50 isoform X3
XM_054357230.1 → XP_054213205.1 E3 ubiquitin-protein ligase TRIM50 isoform X3
XM_054357228.1 → XP_054213203.1 E3 ubiquitin-protein ligase TRIM50 isoform X1

UniProtKB/TrEMBL

B7ZLG2
XM_054357229.1 → XP_054213204.1 E3 ubiquitin-protein ligase TRIM50 isoform X2

UniProtKB/TrEMBL

I3L0H3