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TARBP1 Gene

protein-coding   GIFtS: 53

GC01M232593
TAR (HIV-1) RNA binding protein 1
(Previous name: Tar (HIV-1) RNA binding protein 1 )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
Services    
(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc , and/or 7Ensembl, 8miRBase)
About This Section

Aliases
EC 2.1.1.- 3
FLJ30482 2
OTTHUMP00000036048 2
TRM3 1, 2, 3
TRP-185 1, 2, 3
TRP185 2, 3, 5
Descriptions
TAR (HIV) RNA binding protein 1 2
TAR (HIV) RNA-binding protein 1 2
TAR (HIV-1) RNA binding protein 1 1, 2
TAR RNA binding protein 1 2
TAR RNA loop binding protein 2
TAR RNA-binding protein 1 3
TAR RNA-binding protein of 185 kDa 3
External Ids
HGNC: 115681
Entrez Gene: 68942
UniProtKB: Q133953
Ensembl: ENSG000000595887
Search outside databases for aliases for TARBP1 gene

Previous GC identifers: GC01M232786 GC01M230099 GC01M230902 GC01M231611 GC01M230833

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

EntrezGene summary for TARBP1:
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]

UniProtKB/Swiss-Prot: TARB1_HUMAN, Q13395
Function: Probable S-adenosyl-L-methionine-dependent methyltransferase which methylates RNA
molecules such as tRNAs. In case of infection by HIV-1, it binds to the loop region of TAR RNA, a
region also bound by RNA polymerase II. Binding of TARBP1 and RNA polymerase II to HIV-1 TAR RNA
is mutually exclusive, suggesting that TARBP1 may function alone or in conjunction with HIV-1 Tat
to disengage RNA polymerase II from HIV-1 TAR RNA. May act by methylating HIV-1 TAR RNA

Gene Wiki entry for TARBP1

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
About This Section

Genomic View:
UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 1q42.3   Ensembl cytogenetic band:  1q42.2   HGNC cytogenetic band: 1q42.2

TARBP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)

GeneLoc gene densities for chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M232593:     (about GC identifiers)

Start:
232,593,682 bp from pter
End:
232,681,472 bp from pter
Size:
87,791 bases
Orientation:
minus strand
RefSeq DNA sequence:
NC_000001.9  NT_004559.13  
(According to 1UniProtKB, and/or Ensembl, Phosphorylation sites according to 2Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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UniProtKB/Swiss-Prot: TARB1_HUMAN, Q13395 (See protein sequence)
Recommended Name: Probable methyltransferase TARBP1  
Size: 1621 amino acids; 181675 Da
Subunit: Monomer and homodimer
PDB structures from and Proteopedia :
2HA8 (3D)    
Secondary accessions: Q9H581

REFSEQ proteins: NP_005637.3  

ENSEMBL proteins: 
ENSP00000040877 


Human Recombinant Proteins 
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Recombinant Proteins from Abcam (TARBP1)
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                Browse Origene for full length recombinant human proteins expressed in human HEK293 cells 

1 Gene Ontology (GO) cellular component term (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0005634 nucleus TAS8846792
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Antibodies for TARBP1: 
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Sigma-Aldrich Antibodies for TARBP1
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Antibodies from Abcam (TARBP1), each with their AbpromiseSM
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Search Novus for antibodies for TARBP1

Assays for TARBP1: 
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Browse Kits and Assays available from Millipore
Browse R&D Systems for biochemical assays
Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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1 InterPro domain/family:
 IPR001537 SpoU_MeTrfase


   GeneDecks  TARBP1 for the domains selected above  
About GeneDecksing

Graphical View of Domain Structure for InterPro Entry Q13395

ProtoNet protein and cluster: Q13395

1 Blocks protein family: IPB001537 tRNA/rRNA methyltransferase (SpoU)

UniProtKB/Swiss-Prot: TARB1_HUMAN, Q13395
Similarity: Belongs to the RNA methyltransferase trmH family

(According to MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (TARBP1)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (TARBP1)
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_005646

              Applied Biosystems Silencer® siRNAs for TARBP1

              Sigma-Aldrich siRNA for TARBP1  
                     Sigma-Aldrich shRNA for TARBP1  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Clones:Browse Clone Ranger at Invitrogen for clones
Browse Clones for the Expression of Recombinant Proteins Available from Millipore
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_005646
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_005646
                                 untagged cDNA clone in CMV expression vector: NM_005646 

Primers: Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers
              OriGene genome-wide validated SYBR primer pairs: NM_005646

UniProtKB/Swiss-Prot: TARB1_HUMAN, Q13395
Function: Probable S-adenosyl-L-methionine-dependent methyltransferase which methylates RNA
molecules such as tRNAs. In case of infection by HIV-1, it binds to the loop region of TAR RNA, a
region also bound by RNA polymerase II. Binding of TARBP1 and RNA polymerase II to HIV-1 TAR RNA
is mutually exclusive, suggesting that TARBP1 may function alone or in conjunction with HIV-1 Tat
to disengage RNA polymerase II from HIV-1 TAR RNA. May act by methylating HIV-1 TAR RNA
Enzyme Number (IUBMB): EC 2.1.1.- 

4 Gene Ontology (GO) molecular function terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0003723 RNA binding TAS8846792
GO:0005488 binding IEA--
GO:0008173 RNA methyltransferase activity IEA--
GO:0016740 transferase activity IEA--
About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to 1UniProtKB, 2MINT, and/or 3STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
About This Section



3 Interacting proteins for TARBP1 (ENSP000000408773) via UniProtKB, MINT, and/or STRING
InteractantInteraction Details
GeneCardExternal ID(s)
EEF1AL3ENSP000003300543STRING (score=.842)
CCT4ENSP000002338363STRING (score=.788)
TATENSP000003482343STRING (score=.754)
About this table

2 Gene Ontology (GO) biological process terms (links to tree view):

GO IDQualified GO termEvidencePubMed IDs
GO:0006357 regulation of transcription from RNA polymerase II promoter TAS8846792
GO:0006396 RNA processing IEA--
About this table
(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences
Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for TARBP1

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib.
RNA:
Invitrogen RNAi Products for gene knock-down (TARBP1)
Browse for Gene Knock-down Tools from Millipore
Abnova Chimera RNAi Products for Gene knock-down (TARBP1)
              OriGene 29mer shRNA kit in GFP-retroviral vector: NM_005646

              Sigma-Aldrich siRNA for TARBP1  
                     Sigma-Aldrich shRNA for TARBP1  
                     Explore Sigma-Aldrich super-pooled esiRNAs  

Applied Biosystems Silencer® siRNAs: 

NM_005646  

REFSEQ mRNAs for TARBP1 gene: 

NM_005646.3   

Applied Biosystems TaqMan ® Gene Expression Assays: 

NM_005646  

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_005646
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_005646
                                 untagged cDNA clone in CMV expression vector: NM_005646 

Additional cDNA sequence: 

AK055044.1 BC016023.1 U38847.1 

12 DOTS entries:

DT.455861  DT.92427259  DT.95082796  DT.100785828  DT.102822591  DT.121402880  DT.92427256  DT.100748122 
DT.101962808  DT.417658  DT.99998840  DT.92030521 

24/191 AceView cDNA sequences (see all 191 ):

AI538671 AI354872 W05319 CD557271 BM989347 BM970587 CD656493 BM475098 
AI623992 AU125388 BU186332 BM855317 F09534 BX110268 BC016023 AA319787 
N75005 AW151935 CB133843 AI312769 AA367148 AL699826 AI538735 F11887 

highest scoring ESTs for TARBP1:

U38847 AA128016 AA173121 AA173224 AA300785 AA313376 AA314923 AA319787 AA322879 AA323115 

Unigene Cluster for TARBP1:

TAR (HIV-1) RNA binding protein 1
Hs.498115  [show with all ESTs]
Unigene Representative Sequence: U38847


GeneLoc Exon Structure

5/7 Alternative Splicing Database (ASD) splice patterns (SP) for TARBP1 (see all 7 )

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23a · 23b · 23c ^ 24 ^
SP1:                                                                                                                                                  -     -   
SP2:                                                                                                                                                            
SP3:                                                                                                                                                  -     -   
SP4:                                                                                                                                                            
SP5:                                                                                                                                                            

ExUns: 25a · 25b ^ 26 ^ 27 ^ 28 ^ 29 ^ 30a · 30b ^ 31 ^ 32a · 32b ^ 33a · 33b · 33c · 33d
SP1:  -                 -     -                             -                                 
SP2:                          -                             -                                 
SP3:  -                                                                                       
SP4:                    -     -     -                                                         
SP5:                                                  -     -                                 

About this scheme

ECgene alternative splicing isoforms for TARBP1

1 Ensembl transcript including schematic representation:
ENST00000040877  
(Experimental results according to 1GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to 2GeneAnnot , 3GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
About This Section

TARBP1 expression in normal and diseased human tissues

 Applied Biosystems TaqMan ® Gene Expression Assays for TARBP1

1 / 2 / 3

3 probe-sets matching TARBP1 gene


Affymetrix
probe-set
Array  GeneAnnot data GeneNote data GeneTide data
# genes Sensitivity Specificity Correlation Length Gb_Accession Consensus Uniqueness Score Rank

39779_at2, 3 U95-A 1 1.00 1.00 1.00 1.00 U38847 1.00 1.00 1.00 1

202813_at2, 3 U133-A 1 1.00 1.00 -- -- NM_005646 0.60 1.00 0.82 1

202813_at2 U133Plus2 1 1.00 1.00 -- -- -- -- -- -- --
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Data from (Publications) and GNF BioGPS
    About these images
About these images

CGAP SAGE TAG: TGCCTTAAAC

SOURCE GeneReport for Unigene cluster: Hs.498115

Expression variation in blood from EXPOLDB for TARBP1

(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD and/or 5MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
About This Section


Orthologs for TARBP1 gene from 5/8 species (see all 8 )
Organism Gene Locus Description Human
Similarity
NCBI accessions
chimpanzee
(Pan troglodytes)
TARBP11   -- TAR (HIV-1) RNA binding protein 1 99.14(n)
98.89(a)
457830  XM_514281.2  XP_514281.2 
cow
(Bos taurus)
TARBP11   -- TAR (HIV-1) RNA binding protein 1 86.54(n)
84.99(a)
535018  XM_614988.3  XP_614988.3 
chicken
(Gallus gallus)
TARBP11   -- Tar (HIV-1) RNA binding protein 1 71.14(n)
68.79(a)
421517  XM_419559.2  XP_419559.2 
zebrafish
(Danio rerio)
LOC5663031   -- similar to TAR RNA binding protein 1 54.34(n)
48.91(a)
566303  XM_001921839.1  XP_001921874.1 
worm
(Caenorhabditis elegans)
T14B4.13 II(6736844-6741332) rRNA methylase 47(a)   --
About this table        Species with no ortholog for TARBP1

ENSEMBL Gene Tree for TARBP1
(Paralogs according to 1HomoloGene
and 2Ensembl, Pseudogenes according to 3Pseudogene.org)
About This Section

  --
(According to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
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10/635 NCBI SNPs in TARBP1 are shown (see all 635 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay)  (see all 209)
ABGenomic DataTranscription DataAllele Frequencies
SNP IDValidChr 1 posSequenceRecsAA
Chg
TypeMoreRecsAllele
freq
PopTotal
sample
More
------------
rs49202461,2
A,C,F,H232649274(+) GGTACT/CAAACT 1 G/S mis1 ese313Minor allele frequency- C:0.27EU EA WA NA 1328
rs75248221,2
A,C,F,H232593491(+) CCAAAC/TGTGTT 1 -- ng514Minor allele frequency- T:0.43EU EA WA 414
rs49202561,2
A,C,F,H232683145(+) TAAACG/AGCAAA 1 -- ng314Minor allele frequency- A:0.36EU EA WA 418
rs22738721,2
C,F,H,O232639648(+) CACTAC/TTTAGC 1 N/S mis112Minor allele frequency- N:0.00EU EA WA NA 1048
rs22756541,2
C,F,H232596069(-) AGTCAA/GTTAGT 1 I/V mis113Minor allele frequency- G:0.02EA EU WA 2754
rs109104391,2
C,F,H232668053(+) AAGCGC/TATCCA 1 A/T mis19Minor allele frequency- T:0.03EU EA WA NA 912
rs121354271,2
C,F,H232631574(+) AAAACA/TAACTG 1 F/L mis18Minor allele frequency- T:0.02EU EA WA 840
rs38206021,2
C,F,H232630083(-) CAATAC/TACTGA 1 T/I mis1 ese38Minor allele frequency- T:0.00EU EA WA 836
--
rs124028351,2
A,C232593355(+) GTGGGC/GGGCGT 1 -- ng510--------
rs5166261,2
A,F232681641(-) AACCCA/GAGGGA 1 -- ng31 tfbs33Minor allele frequency- G:0.25NA 202
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HapMap Linkage Disequilibrium images for TARBP1 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, Novoseek, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

OMIM: 605052

1 Novoseek disease relationship for TARBP1 gene

Disease   Score   Articles   PubMed IDs for Articles with Shared Sentences (# sentences)
immunodeficiency 55.43 4 17360756 (2), 8626763 (1), 9230068 (1)
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(Possibly Related Articles in Doctor's Guide)
About This Section

  --

(in PubMed. Associations of this gene to articles via 1Novoseek, 2HGNC, 3Entrez Gene, 4UniProtKB/Swiss-Prot, 5UniProtKB/TrEMBL, 6GAD, and/or 7PharmGKB)
About This Section

10/34 PubMed articles for TARBP1 gene (see all 34 ):
(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Free Text  

  Query String
PubMed
OMIM
NCBI Bookshelf
  (Note: In FireFox, select the above section and copy using Ctrl-C)
(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, and/or H-InvDB)
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Entrez Gene: 6894 HGNC: 11568 AceView: TARBP1 Ensembl:ENSG00000059588 euGenes: HUgn6894
ECgene: TARBP1 H-InvDB: TARBP1
(According to HUGE)
About This Section

  --
(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

  --
(Available from WIS Yeda, Salk, Tufts)
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  --
(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
About This Section



Products for TARBP1:
 TaqMan ® Gene Expression Assays
 TaqMan ® Genotyping Assays
  Free SNP selection tool



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