TBRG4 transforming growth factor beta regulator 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: TBRG4provided by HGNC
Official Full Name: transforming growth factor beta regulator 4provided by HGNC
Primary source: HGNC:HGNC:17443
See related: Ensembl:ENSG00000136270 MIM:611325; AllianceGenome:HGNC:17443
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: CPR2; FASTKD4
Summary: Enables RNA binding activity. Involved in mitochondrial mRNA processing and regulation of mitochondrial mRNA stability. Located in mitochondrial matrix. [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in testis (RPKM 18.2), duodenum (RPKM 14.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 7p13

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	7	NC_000007.14 (45100100..45111697, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	7	NC_060931.1 (45260901..45272500, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	7	NC_000007.13 (45139699..45151296, complement)

Chromosome 7 - NC_000007.14 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?

High expression of TBRG4 in relation to unfavorable outcome and cell ferroptosis in hepatocellular carcinoma.
Title: High expression of TBRG4 in relation to unfavorable outcome and cell ferroptosis in hepatocellular carcinoma.
Mitochondrial protein, TBRG4, modulates KSHV and EBV reactivation from latency.
Title: Mitochondrial protein, TBRG4, modulates KSHV and EBV reactivation from latency.
The FASTK family proteins fine-tune mitochondrial RNA processing.
Title: The FASTK family proteins fine-tune mitochondrial RNA processing.
Expression quantitative trait loci of genes predicting outcome are associated with survival of multiple myeloma patients.
Title: Expression quantitative trait loci of genes predicting outcome are associated with survival of multiple myeloma patients.
TBRG4 silencing promotes progression of squamous cell carcinoma via regulation of CAV-1 expression and ROS formation.
Title: TBRG4 silencing promotes progression of squamous cell carcinoma via regulation of CAV-1 expression and ROS formation.
Despite the fact that proteins of the FASTK family FASTKD1-5 share the same domains, they exhibit various-sometimes opposing-functions in almost all steps of mitochondrial RNA metabolism.
Title: The FASTK family of proteins: emerging regulators of mitochondrial RNA biology.
Disruption of FASTKD4 reduces the level of ND3 and of other mature mRNAs including ND5 and CYB, and causes accumulation of ND5-CYB precursor RNA. Disrupting FASTKD1 and FASTKD4 decreases ND3 mRNA like depleting FASTKD4 alone, indicating that FASTKD4 loss is epistatic. RAP domain of FASTKD4 has a nuclease fold with a conserved aspartate at the putative active site, mutation of which abolishes its function.
Title: FASTKD1 and FASTKD4 have opposite effects on expression of specific mitochondrial RNAs, depending upon their endonuclease-like RAP domain.
SLERT is 694 nucleotides & contains SNORA5A & SNORA5C at its ends; it is produced from the human TBRG4 locus via skipping of exons 4 and 5 that leads to both SNORA5A & SNORA5C embedded within one intron, thereby producing SLERT from this alternatively spliced intron; results reveal an important control of ribosome biogenesis by SLERT lncRNA & its regulatory role in DDX21 ring-shaped arrangements acting on Pol I complexes.
Title: SLERT Regulates DDX21 Rings Associated with Pol I Transcription.
Observational study of gene-disease association. (HuGE Navigator)
Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

Submit: New GeneRIF Correction See all GeneRIFs (11)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vpu	vpu	HIV-1 Vpu is identified to have a physical interaction with transforming growth factor beta regulator 4 (TBRG4) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G54021 (e-PCR)
- UniSTS:109403

RH66403 (e-PCR)
- UniSTS:9838

SHGC-67307 (e-PCR)
- UniSTS:89991

D15S1390 (e-PCR)
- UniSTS:474340

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in mRNA metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mitochondrial RNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in mitochondrial mRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell population proliferation	TAS Traceable Author Statement more info	PubMed
involved_in regulation of cell cycle	TAS Traceable Author Statement more info	PubMed
involved_in regulation of mitochondrial mRNA stability	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of mitochondrial mRNA stability	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
is_active_in mitochondrial matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in mitochondrial matrix	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial matrix	TAS Traceable Author Statement more info
located_in mitochondrion	IDA Inferred from Direct Assay more info	PubMed
is_active_in ribonucleoprotein granule	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: FAST kinase domain-containing protein 4

Names: FAST kinase domains 4; H_TD2522F11.8; cell cycle progression protein 2; cell cycle progression restoration protein 2; protein TBRG4

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_001261834.2 → NP_001248763.1 FAST kinase domain-containing protein 4 isoform 3

See identical proteins and their annotated locations for NP_001248763.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) uses an alternate splice site in the 5' region and initiates translation at an upstream, in-frame start codon, compared to variant 1. The encoded isoform (3) has a longer N-terminus, compared to isoform 1.

Source sequence(s)

AK298155, AK300489, BM150942

UniProtKB/TrEMBL

B4DU42

Conserved Domains (3) summary

smart00952
Location:574 → 631

RAP; This domain is found in various eukaryotic species, particularly in apicomplexans

pfam06743
Location:381 → 447

FAST_1; FAST kinase-like protein, subdomain 1

pfam08368
Location:465 → 546

FAST_2; FAST kinase-like protein, subdomain 2
NM_004749.4 → NP_004740.2 FAST kinase domain-containing protein 4 isoform 1

See identical proteins and their annotated locations for NP_004740.2

Status: VALIDATED

Description

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

Source sequence(s)

BC017235, BM150942, DA980367

Consensus CDS

CCDS5501.1

UniProtKB/Swiss-Prot

A4D2L2, A4D2L3, D3DVL5, D3DVL6, O14710, Q53GI8, Q8NDM4, Q969Z0, Q9BUC6, Q9Y2F6

Related

ENSP00000258770.3, ENST00000258770.8

Conserved Domains (3) summary

smart00952
Location:563 → 620

RAP; This domain is found in various eukaryotic species, particularly in apicomplexans

pfam06743
Location:370 → 436

FAST_1; FAST kinase-like protein, subdomain 1

pfam08368
Location:454 → 535

FAST_2; FAST kinase-like protein, subdomain 2
NM_030900.4 → NP_112162.1 FAST kinase domain-containing protein 4 isoform 2

See identical proteins and their annotated locations for NP_112162.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks two consecutive exons in the coding region, but maintains the reading frame, compared to variant 1. Variants 2 and 3 encode the same isoform (2), which is shorter than isoform 1.

Source sequence(s)

AB023165, AK222943, BM150942, DA980367

Consensus CDS

CCDS5502.1

UniProtKB/TrEMBL

B3KM73

Related

ENSP00000354992.3, ENST00000361278.7

Conserved Domains (3) summary

smart00952
Location:453 → 510

RAP; This domain is found in various eukaryotic species, particularly in apicomplexans

pfam06743
Location:260 → 326

FAST_1; FAST kinase-like protein, subdomain 1

pfam08368
Location:344 → 425

FAST_2; FAST kinase-like protein, subdomain 2
NM_199122.3 → NP_954573.1 FAST kinase domain-containing protein 4 isoform 2

See identical proteins and their annotated locations for NP_954573.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and lacks two consecutive exons in the coding region, but maintains the reading frame, compared to variant 1. Variants 2 and 3 encode the same isoform (2), which is shorter than isoform 1.

Source sequence(s)

AK001281, BM150942

Consensus CDS

CCDS5502.1

UniProtKB/TrEMBL

B3KM73

Related

ENSP00000379016.4, ENST00000395655.8

Conserved Domains (3) summary

smart00952
Location:453 → 510

RAP; This domain is found in various eukaryotic species, particularly in apicomplexans

pfam06743
Location:260 → 326

FAST_1; FAST kinase-like protein, subdomain 1

pfam08368
Location:344 → 425

FAST_2; FAST kinase-like protein, subdomain 2