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TARBP1 TAR (HIV-1) RNA binding protein 1 [ Homo sapiens (human) ]

Gene ID: 6894, updated on 2-Nov-2024

Summary

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Official Symbol
TARBP1provided by HGNC
Official Full Name
TAR (HIV-1) RNA binding protein 1provided by HGNC
Primary source
HGNC:HGNC:11568
See related
Ensembl:ENSG00000059588 MIM:605052; AllianceGenome:HGNC:11568
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
TRM3; TRMT3; TRP185; TRP-185
Summary
HIV-1, the causative agent of acquired immunodeficiency syndrome (AIDS), contains an RNA genome that produces a chromosomally integrated DNA during the replicative cycle. Activation of HIV-1 gene expression by the transactivator Tat is dependent on an RNA regulatory element (TAR) located downstream of the transcription initiation site. This element forms a stable stem-loop structure and can be bound by either the protein encoded by this gene or by RNA polymerase II. This protein may act to disengage RNA polymerase II from TAR during transcriptional elongation. Alternatively spliced transcripts of this gene may exist, but their full-length natures have not been determined. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in lymph node (RPKM 7.3), prostate (RPKM 6.2) and 25 other tissues See more
Orthologs
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Genomic context

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See TARBP1 in Genome Data Viewer
Location:
1q42.2
Exon count:
34
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (234391313..234479179, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (233781469..233869581, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (234527059..234614925, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2747 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2748 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2749 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2750 Neighboring gene ribosomal protein S15 pseudogene 2 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:234508390-234509214 Neighboring gene COA6 antisense RNA 1 Neighboring gene cytochrome c oxidase assembly factor 6 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1969 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1970 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1971 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2752 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2753 Neighboring gene Sharpr-MPRA regulatory region 12347 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2754 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2755 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2756 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:234657990-234658756 Neighboring gene Sharpr-MPRA regulatory region 10256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2759 Neighboring gene Sharpr-MPRA regulatory region 14716 Neighboring gene long intergenic non-protein coding RNA 1354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:234675813-234676316 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:234677690-234678190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:234678191-234678691 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:234689060-234689267 Neighboring gene Sharpr-MPRA regulatory region 4208 Neighboring gene uncharacterized LOC107985465

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. Crystal structure of the methyltransferase domain of human TARBP1. Wu H, et al. Proteins, 2008 Jul. PMID 18412263
  2. Expression of protein TARBP1 in human hepatocellular carcinoma and its prognostic significance. Ye J, et al. Int J Clin Exp Pathol, 2015. PMID 26464651, Free PMC Article
  3. DNA methylation associated with persistent ADHD suggests TARBP1 as novel candidate. Weiß AL, et al. Neuropharmacology, 2021 Feb 15. PMID 33137342
  4. Two distinct nuclear transcription factors recognize loop and bulge residues of the HIV-1 TAR RNA hairpin. Sheline CT, et al. Genes Dev, 1991 Dec. PMID 1752441
  5. tat regulates binding of the human immunodeficiency virus trans-activating region RNA loop-binding protein TRP-185. Wu F, et al. Genes Dev, 1991 Nov. PMID 1936997

See all (51) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. DNA methylation associated with persistent ADHD suggests TARBP1 as novel candidate.
    Title: DNA methylation associated with persistent ADHD suggests TARBP1 as novel candidate.
  2. TARBP1 is up-regulated in hepatocellular carcinoma, and the expression of TARBP1 was associated with the pathological grading and clinical stage.
    Title: Expression of protein TARBP1 in human hepatocellular carcinoma and its prognostic significance.
  3. TARBP1 is positively regulated by MIR10A and MIR21 which are upregulated in heavy drinkers following psychological stress.
    Title: Stress-related alcohol consumption in heavy drinkers correlates with expression of miR-10a, miR-21, and components of the TAR-RNA-binding protein-associated complex.
  4. DGCR8, AGO1, AGO2, PACT, and TARBP1 expression levels were significantly higher in the epithelial skin cancer groups than the healthy controls (P > 0.05).
    Title: Expression levels of the microRNA maturing microprocessor complex component DGCR8 and the RNA-induced silencing complex (RISC) components argonaute-1, argonaute-2, PACT, TARBP1, and TARBP2 in epithelial skin cancer.
  5. 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.
  6. Binding of Dicer to TRBPs is critical for RNAi function.
    Title: Characterization of the TRBP domain required for dicer interaction and function in RNA interference.
  7. The crystal structure of methyltransferase domain of human TARBP1 protein in complex with S-adenosyl-L-homocysteine (AdoHcy) at 1.6-A resolution, is reported.
    Title: Crystal structure of the methyltransferase domain of human TARBP1.
  8. induces induction of HIV-1 long terminal repeat by human and murine cyclin T1 and requires Sp1.
    Title: Tat and trans-activation-responsive (TAR) RNA-independent induction of HIV-1 long terminal repeat by human and murine cyclin T1 requires Sp1.
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
Genetic correlates of brain aging on MRI and cognitive test measures: a genome-wide association and linkage analysis in the Framingham Study.
EBI GWAS Catalog

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
Tat tat HIV-1 Tat downregulates TAR (HIV) RNA binding protein 1 in HEK 293T cells PubMed
tat HIV-1 Tat regulates the binding of TRP-185 to HIV-1 TAR RNA, which in turn regulates the binding of RNA polymerase II to TAR RNA 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

  • FLJ30482

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IEA
Inferred from Electronic Annotation
more info
  
enables tRNA (guanine) methyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in regulation of transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
involved_in tRNA methylation IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in nucleus TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
probable methyltransferase TARBP1
Names
TAR (HIV) RNA-binding protein 1
TAR RNA loop binding protein
TAR RNA-binding protein 1
TAR RNA-binding protein of 185 kDa
tRNA methyltransferase 3 homolog

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_005646.4 → NP_005637.3  probable methyltransferase TARBP1

    See identical proteins and their annotated locations for NP_005637.3

    Status: REVIEWED

    Source sequence(s)
    AL136124, AL355472, U38847
    Consensus CDS
    CCDS1601.1
    UniProtKB/Swiss-Prot
    Q13395, Q9H581
    Related
    ENSP00000040877.1, ENST00000040877.2
    Conserved Domains (1) summary
    pfam00588
    Location:1464 → 1606
    SpoU_methylase; SpoU rRNA Methylase family

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_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    234391313..234479179 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047429060.1 → XP_047285016.1  probable methyltransferase TARBP1 isoform X3

  2. XM_005273234.4 → XP_005273291.1  probable methyltransferase TARBP1 isoform X1

    Conserved Domains (1) summary
    pfam00588
    Location:1463 → 1605
    SpoU_methylase; SpoU rRNA Methylase family

  3. XM_011544263.3 → XP_011542565.1  probable methyltransferase TARBP1 isoform X2

    Conserved Domains (1) summary
    pfam00588
    Location:1440 → 1582
    SpoU_methylase; SpoU rRNA Methylase family

  4. XM_047429080.1 → XP_047285036.1  probable methyltransferase TARBP1 isoform X11

  5. XM_047429097.1 → XP_047285053.1  probable methyltransferase TARBP1 isoform X14

  6. XM_017002196.2 → XP_016857685.1  probable methyltransferase TARBP1 isoform X12

  7. XM_047429061.1 → XP_047285017.1  probable methyltransferase TARBP1 isoform X4

  8. XM_047429073.1 → XP_047285029.1  probable methyltransferase TARBP1 isoform X8

  9. XM_047429068.1 → XP_047285024.1  probable methyltransferase TARBP1 isoform X6

  10. XM_047429072.1 → XP_047285028.1  probable methyltransferase TARBP1 isoform X7

  11. XM_047429067.1 → XP_047285023.1  probable methyltransferase TARBP1 isoform X5

  12. XM_047429091.1 → XP_047285047.1  probable methyltransferase TARBP1 isoform X13

  13. XM_047429079.1 → XP_047285035.1  probable methyltransferase TARBP1 isoform X10

  14. XM_017002194.3 → XP_016857683.1  probable methyltransferase TARBP1 isoform X9

RNA

  1. XR_007063103.1 RNA Sequence

  2. XR_949157.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    233781469..233869581 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054338500.1 → XP_054194475.1  probable methyltransferase TARBP1 isoform X3

  2. XM_054338498.1 → XP_054194473.1  probable methyltransferase TARBP1 isoform X1

  3. XM_054338499.1 → XP_054194474.1  probable methyltransferase TARBP1 isoform X2

  4. XM_054338508.1 → XP_054194483.1  probable methyltransferase TARBP1 isoform X11

  5. XM_054338511.1 → XP_054194486.1  probable methyltransferase TARBP1 isoform X14

  6. XM_054338509.1 → XP_054194484.1  probable methyltransferase TARBP1 isoform X12

  7. XM_054338501.1 → XP_054194476.1  probable methyltransferase TARBP1 isoform X4

  8. XM_054338505.1 → XP_054194480.1  probable methyltransferase TARBP1 isoform X8

  9. XM_054338503.1 → XP_054194478.1  probable methyltransferase TARBP1 isoform X6

  10. XM_054338504.1 → XP_054194479.1  probable methyltransferase TARBP1 isoform X7

  11. XM_054338502.1 → XP_054194477.1  probable methyltransferase TARBP1 isoform X5

  12. XM_054338510.1 → XP_054194485.1  probable methyltransferase TARBP1 isoform X13

  13. XM_054338507.1 → XP_054194482.1  probable methyltransferase TARBP1 isoform X10

  14. XM_054338506.1 → XP_054194481.1  probable methyltransferase TARBP1 isoform X9

RNA

  1. XR_008486157.1 RNA Sequence

  2. XR_008486158.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13395.1 GenPept UniProtKB/Swiss-Prot:Q13395

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