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

    Gene ID: 6894, updated on 28-Oct-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
    mouse all
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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)

    Genotypes

    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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    NEW Try the new Transcript table

    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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