TRIM46 tripartite motif containing 46 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TRIM46provided by HGNC
Official Full Name: tripartite motif containing 46provided by HGNC
Primary source: HGNC:HGNC:19019
See related: Ensembl:ENSG00000163462 MIM:600986; AllianceGenome:HGNC:19019
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: GENEY; TRIFIC
Summary: This gene encodes a protein of the tripartite motif (TRIM) family. The TRIM motif includes zinc-binding domains, a RING finger region, a B-box motif and a coiled-coil domain. TRIM46 is reported to be involved in the proliferation of multiple types of cancer cells including lung and breast cancer. It has also been shown to control neuronal polarity and axon specification by forming uniform microtubule bundles in the axon. [provided by RefSeq, May 2022]
Annotation information: Note: This gene has been reviewed for its involvement in coronavirus biology, and is locus in the vicinity of disease-associated variant(s).
Expression: Broad expression in brain (RPKM 2.5), testis (RPKM 0.9) and 14 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q22

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (155173849..155184971)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (154313465..154324587)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (155146325..155157447)

Chromosome 1 - NC_000001.11 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?

TRIM46 upregulates Wnt/beta-catenin signaling by inhibiting Axin1 to mediate hypoxia-induced epithelial-mesenchymal transition in HK2 cells.
Title: TRIM46 upregulates Wnt/β-catenin signaling by inhibiting Axin1 to mediate hypoxia-induced epithelial-mesenchymal transition in HK2 cells.
TRIM46 activates AKT/HK2 signaling by modifying PHLPP2 ubiquitylation to promote glycolysis and chemoresistance of lung cancer cells.
Title: TRIM46 activates AKT/HK2 signaling by modifying PHLPP2 ubiquitylation to promote glycolysis and chemoresistance of lung cancer cells.
SNP rs4971059 predisposes to breast carcinogenesis and chemoresistance via TRIM46-mediated HDAC1 degradation.
Title: SNP rs4971059 predisposes to breast carcinogenesis and chemoresistance via TRIM46-mediated HDAC1 degradation.
Axonal TAU Sorting Requires the C-terminus of TAU but is Independent of ANKG and TRIM46 Enrichment at the AIS.
Title: Axonal TAU Sorting Requires the C-terminus of TAU but is Independent of ANKG and TRIM46 Enrichment at the AIS.

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 analyses identify 18 new loci associated with serum urate concentrations. 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

RH64529 (e-PCR)
- UniSTS:32558

RH92624 (e-PCR)
- UniSTS:86577

RH18512 (e-PCR)
- UniSTS:27981

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in anterograde synaptic vesicle transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in axonogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in microtubule bundle formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of axon extension	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron migration	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of anterograde dense core granule transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in protein localization to axon	IEA Inferred from Electronic Annotation more info
involved_in regulation of protein localization	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in axon cytoplasm	IEA Inferred from Electronic Annotation more info
located_in axon initial segment	IEA Inferred from Electronic Annotation more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
is_active_in main axon	IBA Inferred from Biological aspect of Ancestor more info
located_in main axon	ISS Inferred from Sequence or Structural Similarity more info
located_in proximal neuron projection	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: tripartite motif-containing protein 46

Names: gene Y protein; tripartite, fibronectin type-III and C-terminal SPRY motif protein

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_001256599.2 → NP_001243528.1 tripartite motif-containing protein 46 isoform 2

See identical proteins and their annotated locations for NP_001243528.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AK096158, AK128139, AK308075, DA509424, DB326530

Consensus CDS

CCDS58033.1

UniProtKB/TrEMBL

B7Z3S2

Related

ENSP00000357366.1, ENST00000368382.5

Conserved Domains (6) summary

cd00063
Location:421 → 502

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12895
Location:509 → 718

SPRY_PRY_TRIM46; PRY/SPRY domain in tripartite motif-containing protein 46 (TRIM46)

pfam00643
Location:199 → 240

zf-B_box; B-box zinc finger

cd16757
Location:4 → 38

RING-HC_TRIM46; RING finger, HC subclass, found in tripartite motif-containing protein 46 (TRIM46) and similar proteins

cl25407
Location:247 → 372

ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)

cl28410
Location:1 → 73

RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
NM_001256601.1 → NP_001243530.1 tripartite motif-containing protein 46 isoform 4

See identical proteins and their annotated locations for NP_001243530.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (4) is shorter and has a distinct N-terminus, compared to isoform 1.

Source sequence(s)

AK128139, AK309699, DB326530

Consensus CDS

CCDS72931.1

UniProtKB/TrEMBL

A0A087WUH1, B7Z3S2

Related

ENSP00000478669.1, ENST00000611379.1

Conserved Domains (6) summary

cd00063
Location:431 → 512

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12895
Location:519 → 728

SPRY_PRY_TRIM46; PRY/SPRY domain in tripartite motif-containing protein 46 (TRIM46)

pfam00643
Location:209 → 250

zf-B_box; B-box zinc finger

cd16757
Location:14 → 48

RING-HC_TRIM46; RING finger, HC subclass, found in tripartite motif-containing protein 46 (TRIM46) and similar proteins

cl25407
Location:257 → 382

ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)

cl28410
Location:8 → 83

RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
NM_001282378.2 → NP_001269307.1 tripartite motif-containing protein 46 isoform 5

Status: VALIDATED

Description

Transcript Variant: This variant (6) uses an alternate 5' exon structure and thus differs in the 5' UTR and 5' coding region compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (5) with a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AK128139, AK297318, BX283909, DA509424, DB326530

Consensus CDS

CCDS72932.1

UniProtKB/TrEMBL

B7Z4F9, F5GYK0

Related

ENSP00000440254.1, ENST00000545012.5

Conserved Domains (6) summary

smart00502
Location:144 → 269

BBC; B-Box C-terminal domain

cd00063
Location:318 → 399

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12895
Location:406 → 615

SPRY_PRY_TRIM46; PRY/SPRY domain in tripartite motif-containing protein 46 (TRIM46)

cd19786
Location:97 → 142

Bbox2_TRIM46_C-I; B-box-type 2 zinc finger found in tripartite motif-containing protein 46 (TRIM46) and similar proteins

cd19849
Location:43 → 94

Bbox1_TRIM46_C-I; B-box-type 1 zinc finger found in tripartite motif-containing protein 46 (TRIM46) and similar proteins

pfam18568
Location:247 → 296

COS; TRIM C-terminal subgroup One Signature domain
NM_001282379.2 → NP_001269308.1 tripartite motif-containing protein 46 isoform 6

See identical proteins and their annotated locations for NP_001269308.1

Status: VALIDATED

Description

Transcript Variant: This variant (8) uses an alternate 3' exon structure and thus differs in the 3' coding region and 3' UTR compared to variant 1. The encoded isoform (6) is shorter and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

AK026882, AL713999, DA509424, DB262381

Consensus CDS

CCDS60285.1

UniProtKB/TrEMBL

Q5VT61

Related

ENSP00000357369.4, ENST00000368385.8

Conserved Domains (4) summary

cd00063
Location:444 → 525

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd00162
Location:33 → 63

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 ...

pfam00643
Location:222 → 263

zf-B_box; B-box zinc finger

cl23765
Location:270 → 395

iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits
NM_001406245.1 → NP_001393174.1 tripartite motif-containing protein 46 isoform 3

Status: VALIDATED

Source sequence(s)

AC234582, AL607067, AL713999

UniProtKB/TrEMBL

B7Z3S2
NM_001406246.1 → NP_001393175.1 tripartite motif-containing protein 46 isoform 7

Status: VALIDATED

Source sequence(s)

AC234582, AL607067, AL713999

UniProtKB/TrEMBL

Q5VT61
NM_001406247.1 → NP_001393176.1 tripartite motif-containing protein 46 isoform 8

Status: VALIDATED

Source sequence(s)

AC234582, AL607067, AL713999

UniProtKB/TrEMBL

B7Z3S2
NM_001406256.1 → NP_001393185.1 tripartite motif-containing protein 46 isoform 2

Status: VALIDATED

Source sequence(s)

AC234582, AL713999

UniProtKB/TrEMBL

B7Z3S2
NM_025058.5 → NP_079334.3 tripartite motif-containing protein 46 isoform 1

See identical proteins and their annotated locations for NP_079334.3

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AK096158, AY251386, DA509424, DB262381, DB326530

Consensus CDS

CCDS1097.1

UniProtKB/Swiss-Prot

A0AVI6, B1AVQ4, Q5VT60, Q5VT62, Q6NT17, Q6NT41, Q6ZRL7, Q7Z4K8, Q9H5P2

UniProtKB/TrEMBL

B7Z3S2

Related

ENSP00000334657.4, ENST00000334634.9

Conserved Domains (6) summary

cd00063
Location:444 → 525

FN3; Fibronectin type 3 domain; One of three types of internal repeats found in the plasma protein fibronectin. Its tenth fibronectin type III repeat contains an RGD cell recognition sequence in a flexible loop between 2 strands. Approximately 2% of all ...

cd12895
Location:532 → 741

SPRY_PRY_TRIM46; PRY/SPRY domain in tripartite motif-containing protein 46 (TRIM46)

pfam00643
Location:222 → 263

zf-B_box; B-box zinc finger

cd16757
Location:27 → 61

RING-HC_TRIM46; RING finger, HC subclass, found in tripartite motif-containing protein 46 (TRIM46) and similar proteins

cl25407
Location:270 → 395

ClassIIa_HDAC_Gln-rich-N; Glutamine-rich N-terminal helical domain of various Class IIa histone deacetylases (HDAC4, HDAC5 and HDCA9)

cl28410
Location:22 → 96

RAD18; RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]

RNA

NR_046327.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (5) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK128139, BC143828, DA509424, DB326530
NR_046329.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (7) lacks an exon and includes three alternate exons, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK128139, AL713999, CN259033, DB326530

Related

ENST00000468878.1
NR_104150.3 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (9) uses an alternate, internal exon and an alternate 3' exon structure, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC234582, AL607067, AL713999
NR_176037.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC234582, AL607067, AL713999

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_000001.11 Reference GRCh38.p14 Primary Assembly

Range

155173849..155184971

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

154313465..154324587

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001256600.1: Suppressed sequence

Description

NM_001256600.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.