TRIM47 tripartite motif containing 47 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TRIM47provided by HGNC
Official Full Name: tripartite motif containing 47provided by HGNC
Primary source: HGNC:HGNC:19020
See related: Ensembl:ENSG00000132481 MIM:611041
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: GOA; RNF100
Expression: Ubiquitous expression in brain (RPKM 11.4), kidney (RPKM 8.9) and 24 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 17q25.1

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
109.20200522	current	GRCh38.p13 (GCF_000001405.39)	17	NC_000017.11 (75874164..75878599, complement)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	17	NC_000017.10 (73870242..73874683, complement)

Chromosome 17 - NC_000017.11 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
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?

our study has shown the biological and clinical significance of TRIM47 in colorectal cancer. TRIM47 exerts an inhibitory effect on SMAD4 by ubiquitylating and degrading SMAD4, thereby promoting tumor growth and progression.
Title: TRIM47 is up-regulated in colorectal cancer, promoting ubiquitination and degradation of SMAD4.
Study shows that protein and gene expression level of TRIM47 are up-regulated in prostate neoplasm.
Title: Increased Expression of Tripartite Motif (TRIM) 47 Is a Negative Prognostic Predictor in Human Prostate Cancer.
High TRIM47 expression is associated with non-small cell lung carcinoma.
Title: TRIM47 overexpression is a poor prognostic factor and contributes to carcinogenesis in non-small cell lung carcinoma.
These results suggest that rs1055129 in TRIM47 is not associated with leukoaraiosis (LA) risk in the Chinese population. However, the association of rs1055129 (TRIM47) with LA before Bonferroni correction and Sidak correction is worth highlighting.
Title: Analysis of genetic polymorphisms associated with leukoaraiosis in the southern Chinese population: A case-control study.

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

NHGRI GWAS Catalog

Description
Genome-wide association studies of cerebral white matter lesion burden: the CHARGE consortium. NHGRI GWA Catalog NHGRI GWA 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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Homology

Homologs of the TRIM47 gene: The TRIM47 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, and chicken.
Orthologs from Annotation Pipeline: 228 organisms have orthologs with human gene TRIM47
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
ubiquitin-protein transferase activity	IDA Inferred from Direct Assay more info	PubMed
zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
protein ubiquitination	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
cytosol	IDA Inferred from Direct Assay more info
nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: E3 ubiquitin-protein ligase TRIM47

Names: RING finger protein 100; gene overexpressed in astrocytoma protein; tripartite motif-containing protein 47

NP_258411.2

EC 2.3.2.27

XP_005257844.1

EC 2.3.2.27

XP_005257845.1

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_033452.3 → NP_258411.2 E3 ubiquitin-protein ligase TRIM47

See identical proteins and their annotated locations for NP_258411.2

Status: VALIDATED

Source sequence(s)

AC087289, AY026763, BG385464

Consensus CDS

CCDS32737.1

UniProtKB/Swiss-Prot

Q96LD4

Related

ENSP00000254816.1, ENST00000254816.6

Conserved Domains (3) summary

pfam00643
Location:178 → 217

zf-B_box; B-box zinc finger

cd15808
Location:421 → 626

SPRY_PRY_TRIM47; PRY/SPRY domain in tripartite motif-containing protein 47 (TRIM47), also known as RING finger protein 100 (RNF100) or Gene overexpressed in astrocytoma protein (GOA)

cl17238
Location:9 → 57

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: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000017.11 Reference GRCh38.p13 Primary Assembly

Range

75874164..75878599 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005257787.4 → XP_005257844.1 E3 ubiquitin-protein ligase TRIM47 isoform X1

See identical proteins and their annotated locations for XP_005257844.1

UniProtKB/Swiss-Prot

Q96LD4

Conserved Domains (1) summary

cd15808
Location:183 → 388

SPRY_PRY_TRIM47; PRY/SPRY domain in tripartite motif-containing protein 47 (TRIM47), also known as RING finger protein 100 (RNF100) or Gene overexpressed in astrocytoma protein (GOA)
XM_005257788.5 → XP_005257845.1 E3 ubiquitin-protein ligase TRIM47 isoform X1

See identical proteins and their annotated locations for XP_005257845.1

UniProtKB/Swiss-Prot

Q96LD4

Conserved Domains (1) summary

cd15808
Location:183 → 388

SPRY_PRY_TRIM47; PRY/SPRY domain in tripartite motif-containing protein 47 (TRIM47), also known as RING finger protein 100 (RNF100) or Gene overexpressed in astrocytoma protein (GOA)