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TARBP2 TARBP2, RISC loading complex RNA binding subunit [ Homo sapiens (human) ]

Gene ID: 6895, updated on 6-Jan-2019

Summary

Official Symbol
TARBP2provided by HGNC
Official Full Name
TARBP2, RISC loading complex RNA binding subunitprovided by HGNC
Primary source
HGNC:HGNC:11569
See related
Ensembl:ENSG00000139546 MIM:605053
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
LOQS; TRBP; TRBP1; TRBP2
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. The protein encoded by this gene binds between the bulge and the loop of the HIV-1 TAR RNA regulatory element and activates HIV-1 gene expression in synergy with the viral Tat protein. Alternative splicing results in multiple transcript variants encoding different isoforms. This gene also has a pseudogene. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in placenta (RPKM 7.8), testis (RPKM 6.1) and 25 other tissues See more
Orthologs

Genomic context

See TARBP2 in Genome Data Viewer
Location:
12q13.13
Exon count:
11
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 12 NC_000012.12 (53500921..53506431)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (53893557..53900215)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene proline rich 13 Neighboring gene poly(rC) binding protein 2 Neighboring gene PCBP2 overlapping transcript 1 Neighboring gene mitogen-activated protein kinase kinase kinase 12 Neighboring gene uncharacterized LOC100652999 Neighboring gene neuropeptide FF-amide peptide precursor Neighboring gene activating transcription factor 7

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Gag-Pol gag-pol The binding of HIV-1 TAR and RRE to TRBP displaces small interfering (si) RNAs from binding to TRBP, but RNA interference is restored when HIV-1 Rev or GagPol are coexpressed in cells PubMed
Rev rev The binding of HIV-1 TAR and RRE to TRBP displaces small interfering (si) RNAs from binding to TRBP, but RNA interference is restored when HIV-1 Rev or GagPol are coexpressed in cells PubMed
rev HIV-1 Rev binds TRBP/PACT complex and the binding requires the arginine rich motif (residues 35-50) of HIV-1 Rev PubMed
Tat tat HIV-1 Tat binds TRBP/PACT complex and the binding requires the arginine rich motif (residues 48-58) of HIV-1 Tat PubMed
tat TRBP2 binds to HIV-1 TAR RNA and synergizes with HIV-1 Tat to activate the HIV-1 LTR promoter PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Gene Silencing by RNA, organism-specific biosystem (from REACTOME)
    Gene Silencing by RNA, organism-specific biosystemIn this module, the biology of various types of regulatory non-coding RNAs are described. Currently, biogenesis and functions of small interfering RNAs (siRNAs) and microRNAs are annotated.
  • MicroRNA (miRNA) biogenesis, organism-specific biosystem (from REACTOME)
    MicroRNA (miRNA) biogenesis, organism-specific biosystemBiogenesis of microRNAs (miRNAs) can be summarized in five steps (reviewed in Ketting 2011, Nowotny and Yang 2009, Kim et al. 2009, Chua et al. 2009, Hannon and He 2004):1. Transcription. miRNA trans...
  • Small interfering RNA (siRNA) biogenesis, organism-specific biosystem (from REACTOME)
    Small interfering RNA (siRNA) biogenesis, organism-specific biosystemSmall interfering RNAs (siRNAs) are 21-25 nucleotide single-stranded RNAs produced by cleavage of longer double-stranded RNAs by the enzyme DICER1 within the RISC loading complex containing DICER1, a...
  • miRNA Biogenesis, organism-specific biosystem (from WikiPathways)
    miRNA Biogenesis, organism-specific biosystemmicroRNA biogenesis + an example of a miRBase entry. As an example immature hsa-mir-146a is shown

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
double-stranded RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enzyme binding IPI
Inferred from Physical Interaction
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
miRNA binding IEA
Inferred from Electronic Annotation
more info
 
pre-mRNA binding TAS
Traceable Author Statement
more info
PubMed 
pre-miRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
contributes_to pre-miRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein N-terminus binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IPI
Inferred from Physical Interaction
more info
PubMed 
siRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
miRNA loading onto RISC involved in gene silencing by miRNA IDA
Inferred from Direct Assay
more info
PubMed 
miRNA metabolic process TAS
Traceable Author Statement
more info
 
multicellular organism growth IEA
Inferred from Electronic Annotation
more info
 
negative regulation of defense response to virus by host IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of protein kinase activity TAS
Traceable Author Statement
more info
PubMed 
neural precursor cell proliferation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of muscle cell differentiation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of translation IEA
Inferred from Electronic Annotation
more info
 
positive regulation of viral genome replication IDA
Inferred from Direct Assay
more info
PubMed 
pre-miRNA processing IDA
Inferred from Direct Assay
more info
PubMed 
production of miRNAs involved in gene silencing by miRNA IDA
Inferred from Direct Assay
more info
PubMed 
production of siRNA involved in RNA interference IDA
Inferred from Direct Assay
more info
PubMed 
production of siRNA involved in RNA interference TAS
Traceable Author Statement
more info
 
regulation of production of miRNAs involved in gene silencing by miRNA IEA
Inferred from Electronic Annotation
more info
 
regulation of production of siRNA involved in RNA interference IEA
Inferred from Electronic Annotation
more info
 
regulation of viral transcription IDA
Inferred from Direct Assay
more info
PubMed 
siRNA loading onto RISC involved in RNA interference IDA
Inferred from Direct Assay
more info
PubMed 
single fertilization IEA
Inferred from Electronic Annotation
more info
 
skeletal muscle tissue regeneration IEA
Inferred from Electronic Annotation
more info
 
spermatid development IEA
Inferred from Electronic Annotation
more info
 
targeting of mRNA for destruction involved in RNA interference IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
RISC complex IEA
Inferred from Electronic Annotation
more info
 
RISC-loading complex IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
micro-ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 
nuclear body IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
perinuclear region of cytoplasm IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
RISC-loading complex subunit TARBP2
Names
TAR (HIV) RNA-binding protein 2
TAR (HIV) RNA-binding protein TRBP1
TAR (HIV-1) RNA binding protein 2
TAR RNA binding protein 2
trans-activation responsive RNA-binding protein

NCBI Reference Sequences (RefSeq)

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_004178.4NP_004169.3  RISC-loading complex subunit TARBP2 isoform b

    See identical proteins and their annotated locations for NP_004169.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an internal segment in the 5' region, and uses a downstream AUG codon for translation, as compared to variant 1. The encoded isoform (b) thus has a shorter N-terminus, as compared to isoform a.
    Source sequence(s)
    BC002419, M60801
    Consensus CDS
    CCDS41791.1
    UniProtKB/Swiss-Prot
    Q15633
    Related
    ENSP00000416077.2, ENST00000456234.6
    Conserved Domains (2) summary
    smart00358
    Location:1058
    DSRM; Double-stranded RNA binding motif
    cd00048
    Location:138201
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
  2. NM_134323.1NP_599150.1  RISC-loading complex subunit TARBP2 isoform a

    See identical proteins and their annotated locations for NP_599150.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) is the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    BC002419, BC005860
    Consensus CDS
    CCDS8861.1
    UniProtKB/Swiss-Prot
    Q15633
    Related
    ENSP00000266987.2, ENST00000266987.6
    Conserved Domains (2) summary
    smart00358
    Location:3179
    DSRM; Double-stranded RNA binding motif
    cd00048
    Location:159222
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
  3. NM_134324.2NP_599151.2  RISC-loading complex subunit TARBP2 isoform b

    See identical proteins and their annotated locations for NP_599151.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) has an alternate 5' exon and uses a downstream AUG codon for translation, as compared to variant 1. The encoded isoform (b) thus has a shorter N-terminus, as compared to isoform a.
    Source sequence(s)
    AC023509, BC002419, BI771121
    Consensus CDS
    CCDS41791.1
    UniProtKB/Swiss-Prot
    Q15633
    Related
    ENSP00000377885.2, ENST00000394357.6
    Conserved Domains (2) summary
    smart00358
    Location:1058
    DSRM; Double-stranded RNA binding motif
    cd00048
    Location:138201
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p12 Primary Assembly

    Range
    53500921..53506431
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005269117.1XP_005269174.1  RISC-loading complex subunit TARBP2 isoform X3

    Conserved Domains (2) summary
    smart00358
    Location:3179
    DSRM; Double-stranded RNA binding motif
    cd00048
    Location:159215
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
  2. XM_017019911.2XP_016875400.1  RISC-loading complex subunit TARBP2 isoform X5

    UniProtKB/TrEMBL
    A0A024RB49
    Conserved Domains (1) summary
    cd00048
    Location:1578
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
  3. XM_005269120.5XP_005269177.1  RISC-loading complex subunit TARBP2 isoform X5

    See identical proteins and their annotated locations for XP_005269177.1

    UniProtKB/TrEMBL
    A0A024RB49
    Conserved Domains (1) summary
    cd00048
    Location:1578
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
  4. XM_006719581.1XP_006719644.1  RISC-loading complex subunit TARBP2 isoform X2

    Conserved Domains (1) summary
    cd00048
    Location:60123
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
  5. XM_005269114.1XP_005269171.1  RISC-loading complex subunit TARBP2 isoform X1

    See identical proteins and their annotated locations for XP_005269171.1

    UniProtKB/Swiss-Prot
    Q15633
    Conserved Domains (2) summary
    smart00358
    Location:1058
    DSRM; Double-stranded RNA binding motif
    cd00048
    Location:138201
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
  6. XM_017019910.1XP_016875399.1  RISC-loading complex subunit TARBP2 isoform X4

    Related
    ENSP00000447767.1, ENST00000550407.1
  7. XM_005269115.2XP_005269172.1  RISC-loading complex subunit TARBP2 isoform X1

    See identical proteins and their annotated locations for XP_005269172.1

    UniProtKB/Swiss-Prot
    Q15633
    Conserved Domains (2) summary
    smart00358
    Location:1058
    DSRM; Double-stranded RNA binding motif
    cd00048
    Location:138201
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
  8. XM_005269122.4XP_005269179.1  RISC-loading complex subunit TARBP2 isoform X5

    See identical proteins and their annotated locations for XP_005269179.1

    UniProtKB/TrEMBL
    A0A024RB49
    Conserved Domains (1) summary
    cd00048
    Location:1578
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
  9. XM_011538712.3XP_011537014.1  RISC-loading complex subunit TARBP2 isoform X5

    See identical proteins and their annotated locations for XP_011537014.1

    UniProtKB/TrEMBL
    A0A024RB49
    Conserved Domains (1) summary
    cd00048
    Location:1578
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...

RNA

  1. XR_944695.2 RNA Sequence

    Related
    ENST00000549572.5
  2. XR_001748860.2 RNA Sequence

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