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

Gene ID: 9238, updated on 3-Nov-2024

Summary

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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, Nov 2024]
Expression
Ubiquitous expression in testis (RPKM 18.2), duodenum (RPKM 14.9) and 25 other tissues See more
Orthologs
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Genomic context

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See TBRG4 in Genome Data Viewer
Location:
7p13
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (45100100..45111697, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (45260901..45272500, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (45139699..45151296, complement)

Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102723334 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18162 Neighboring gene CCM2 scaffold protein Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18163 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:45112087-45112746 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:45112747-45113406 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_99227 Neighboring gene NAC alpha domain containing Neighboring gene ReSE screen-validated silencer GRCh37_chr7:45143162-45143329 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:45151068-45151823 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18164 Neighboring gene small nucleolar RNA, H/ACA box 5A Neighboring gene small nucleolar RNA, H/ACA box 5C Neighboring gene small nucleolar RNA, H/ACA box 5B Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:45163452-45164277 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:45173420-45173920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:45217100-45217600 Neighboring gene receptor activity modifying protein 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:45230075-45230721 Neighboring gene uncharacterized LOC124901623 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25971

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. High expression of TBRG4 in relation to unfavorable outcome and cell ferroptosis in hepatocellular carcinoma. Tao S, et al. BMC Cancer, 2024 Feb 12. PMID 38347489, Free PMC Article
  2. Mitochondrial protein, TBRG4, modulates KSHV and EBV reactivation from latency. Zhang H, et al. PLoS Pathog, 2022 Nov. PMID 36417478, Free PMC Article
  3. Expression quantitative trait loci of genes predicting outcome are associated with survival of multiple myeloma patients. Macauda A, et al. Int J Cancer, 2021 Jul 15. PMID 33675538, Free PMC Article
  4. The FASTK family proteins fine-tune mitochondrial RNA processing. Ohkubo A, et al. PLoS Genet, 2021 Nov. PMID 34748562, Free PMC Article
  5. SLERT Regulates DDX21 Rings Associated with Pol I Transcription. Xing YH, et al. Cell, 2017 May 4. PMID 28475895

See all (77) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. Mitochondrial protein, TBRG4, modulates KSHV and EBV reactivation from latency.
    Title: Mitochondrial protein, TBRG4, modulates KSHV and EBV reactivation from latency.
  3. The FASTK family proteins fine-tune mitochondrial RNA processing.
    Title: The FASTK family proteins fine-tune mitochondrial RNA processing.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. Observational study of gene-disease association. (HuGE Navigator)
    Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
  10. 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)

Genotypes

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

Homology

Clone Names

  • KIAA0948

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA 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 HTP PubMed 
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)

  1. 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

  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

  3. 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

  4. 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

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

  1. NC_000007.14 Reference GRCh38.p14 Primary Assembly

    Range
    45100100..45111697 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060931.1 Alternate T2T-CHM13v2.0

    Range
    45260901..45272500 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q969Z0.1 GenPept UniProtKB/Swiss-Prot:Q969Z0

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