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Aliases & Descriptions for TARDBP
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc
, and/or 7Ensembl,
8miRBase) About This Section
|
| Aliases |
|---|
| ALS10 2, 5 | | OTTHUMP00000002171 2 | | TDP-43 1, 2, 3 | | TDP43 3, 5 |
| | | Descriptions |
|---|
| TAR DNA binding protein 2 | | TAR DNA-binding protein-43 2 |
|
| | Search outside databases for aliases for TARDBP genePrevious GC identifers: GC01P011033 GC01P010916 GC01P010682 GC01P010782 |
Summaries for TARDBP(According to Entrez Gene,
Wikipedia's
Gene Wiki,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
| EntrezGene summary for TARDBP: 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 is a transcriptional repressor that binds to chromosomally integrated TAR DNA and represses HIV-1 transcription. In addition, this protein regulates alternate splicing of the CFTR gene. A similar pseudogene is present on chromosome 20. [provided by RefSeq] UniProtKB/Swiss-Prot: TADBP_HUMAN, Q13148Function: DNA and RNA-binding protein which regulates transcription and splicing. Involved in the regulation of CFTR splicing. It promotes CFTR exon 9 skipping by binding to the UG repeated motifs in the polymorphic region near the 3'-splice site of this exon. The resulting aberrant splicing is associated with pathological features typical of cystic fibrosis. May also be involved in microRNA biogenesis, apoptosis and cell division. Can repress HIV-1 transcription by binding to the HIV-1 long terminal repeatGene Wiki entry for TARDBP |
Genomic Location for TARDBP
(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
Transcription factor binding sites upstream to the TARDBP gene 
Entrez Gene cytogenetic band: 1p36.22 Ensembl cytogenetic band: 1p36.22 HGNC cytogenetic band: 1p36.22TARDBP 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 GC01P011006:
(about GC identifiers)
Start:
|
10,995,266 bp from pter |
End:
|
11,008,136 bp from pter |
Size:
|
12,871 bases |
Orientation:
|
plus strand |
RefSeq DNA sequence:- NC_000001.9 NT_021937.18
| Proteins for TARDBP
(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)
About This Section
| UniProtKB/Swiss-Prot: TADBP_HUMAN, Q13148 (See
protein sequence)Recommended Name: TAR DNA-binding protein 43 Size: 414 amino acids; 44740 Da
Subunit: Binds specifically to pyrimidine-rich motifs of TAR DNA and to single stranded TG repeated sequences. Binds to RNA, specifically to UG repeated sequences with a minimun of six contiguous repeats
Subcellular location: Nucleus. Note=Eliminated from nuclei of ubiquitinated inclusion-bearing neurons in FTLDU
PDB structure from and Proteopedia :1WF0 (3D)
 2CQG (3D)
 
Secondary accessions: Q6FI92 Q96DJ0Post-translational modifications:
Hyperphosphorylated in hippocampus, neocortex, and spinal cord from individuals affected with ALS and FTLDU1
Ubiquitinated in hippocampus, neocortex, and spinal cord from individuals affected with ALS and FTLDU1
Cleaved to generate C-terminal fragments in hippocampus, neocortex, and spinal cord from individuals affected with ALS and FTLDU1
View phosphorylation sites using PhosphoSite2
REFSEQ proteins: NP_031401.1
ENSEMBL proteins: ENSP00000240185 ENSP00000313129 ENSP00000323691
Human Recombinant Proteins               OriGene Purified Recombinant Human Protein: TARDBP 
1 Gene Ontology (GO) cellular component term (links to tree view): About this table
Antibodies for TARDBP: Assays for TARDBP: | Protein
Domains/ Families for TARDBP(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
| - Graphical View of Domain Structure for InterPro Entry Q13148
ProtoNet protein and cluster: Q13148 1 Blocks protein family: IPB000504 RNA-binding region RNP-1 (RNA recognition motif)
UniProtKB/Swiss-Prot: TADBP_HUMAN, Q13148Similarity: Contains 2 RRM (RNA recognition motif) domains | Gene Function for TARDBP
(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
|               OriGene 29mer shRNA kit in GFP-retroviral vector: NM_007375
Applied Biosystems Silencer® siRNAs for TARDBP
Sigma-Aldrich siRNA for TARDBP  Sigma-Aldrich shRNA for TARDBP  Explore Sigma-Aldrich super-pooled esiRNAs 
              OriGene GFP tagged cDNA clone in CMV expression vector: NM_007375                                  Myc/DDK tagged cDNA clone in CMV expression vector: NM_007375                                  untagged cDNA clones in CMV expression vector (see all 2): NM_007375 
Primers: Browse
Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers               OriGene genome-wide validated SYBR primer pairs: NM_007375
UniProtKB/Swiss-Prot: TADBP_HUMAN, Q13148Function: DNA and RNA-binding protein which regulates transcription and splicing. Involved in the regulation of CFTR splicing. It promotes CFTR exon 9 skipping by binding to the UG repeated motifs in the polymorphic region near the 3'-splice site of this exon. The resulting aberrant splicing is associated with pathological features typical of cystic fibrosis. May also be involved in microRNA biogenesis, apoptosis and cell division. Can repress HIV-1 transcription by binding to the HIV-1 long terminal repeat5 Gene Ontology (GO) molecular function terms (links to tree view): About this table | Pathways & Interactions for TARDBP
(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
|
5/14 Interacting proteins for TARDBP (Q131481 ENSP000002401853) via UniProtKB, MINT, and/or STRING (see all 14
)About this table
5/6 Gene Ontology (GO) biological process terms (links to tree view) (see all 6
): About this table
|
Drugs & Compounds for TARDBP(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 Tocris compounds for TARDBP 1 Novoseek chemical compound relationship for TARDBP gene
About this table
|
Transcripts for TARDBP(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
|               OriGene 29mer shRNA kit in GFP-retroviral vector: NM_007375
Sigma-Aldrich siRNA for TARDBP  Sigma-Aldrich shRNA for TARDBP  Explore Sigma-Aldrich super-pooled esiRNAs 
Applied Biosystems Silencer® siRNAs: NM_007375 REFSEQ mRNAs for TARDBP gene: NM_007375.3
Applied Biosystems TaqMan ® Gene Expression Assays: NM_007375               OriGene GFP tagged cDNA clone in CMV expression vector: NM_007375                                  Myc/DDK tagged cDNA clone in CMV expression vector: NM_007375                                  untagged cDNA clones in CMV expression vector (see all 2): NM_007375  Additional cDNA sequence: AF311304.1 AK222754.1 AK295920.1 AK299454.1 AK312416.1 AL050265.1 BC001487.2 BC059955.1 BC071657.1 BC095435.1 CR533534.1 EF434181.1 EF434182.1 EF434183.1 U23731.1 24/35 DOTS entries (see all 35
): DT.419641 DT.100882432 DT.100882435 DT.100882440 DT.121392100 DT.100882442 DT.97860226 DT.100032539 DT.91786971 DT.97856390 DT.100882434 DT.100882437 DT.91884354 DT.100038829 DT.100882443 DT.121392045 DT.100882429 DT.121392089 DT.40107291 DT.451822 DT.95143799 DT.105463 DT.121392036 DT.121392078 24/668 AceView cDNA sequences (see all 668
):AI619451 AA367737 AL555909 CB144506 AA130324 BM765019 AI553677 AW070804 BU631375 BX342082 BQ229966 AU106011 BU521437 AU127433 AU128519 BF056843 BF221552 BF223379 BU684769 AI633034 BX422262 AV703589 BE466367 BU552536
highest scoring ESTs for TARDBP:AI143794 AI933665 AL050265 AA013401 AA025965 AA042859 AA044410 AA081839 AA125745 AA130325 Unigene Cluster for TARDBP: TAR DNA binding protein Hs.300624 [show with all ESTs]Unigene Representative Sequence: NM_007375
GeneLoc Exon Structure
3 Ensembl transcripts including schematic representations: ENST00000240185
ENST00000315091
ENST00000323644
|
Expression for TARDBP
(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
| TARDBP expression in normal and diseased human tissues
Applied Biosystems TaqMan ® Gene Expression Assays for TARDBP
1 / 2 / 3 9 probe-sets matching TARDBP gene Data from
(Publications) and GNF BioGPS About these images About these images
CGAP SAGE TAG: CAGATTCAGA
SOURCE GeneReport for Unigene cluster: Hs.300624
Expression variation in blood from EXPOLDB for TARDBP UniProtKB/Swiss-Prot: TADBP_HUMAN, Q13148Tissue specificity: Ubiquitously expressed. In particular, expression is high in pancreas, placenta, lung, genital tract and spleen |
Orthologs for TARDBP
(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 TARDBP gene from 5/11 species (see all 11
)
About this table Species with no ortholog for TARDBP
ENSEMBL Gene Tree for TARDBP | Paralogs for TARDBP(Paralogs according to 1HomoloGene and 2Ensembl, Pseudogenes according to 3Pseudogene.org) About This Section
| Paralogs for TARDBP gene
- DAZAP12
Pseudogenes
- 5 related pseudogenes
|
SNPs/Variants for TARDBP(According to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE, and
UniProtKB,
Linkage Disequilibrium by HapMap,
Genotyping Reagents from
Applied Biosystems)
About This Section
|
HapMap Linkage Disequilibrium images for TARDBP (up to first 250kb)
|
Disorders & Mutations for TARDBP
(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: 605078 disorders: 612069 UniProtKB/Swiss-Prot: TADBP_HUMAN, Q13148
Defects in TARDBP are a cause of amyotrophic lateral sclerosis type 10 (ALS10) [MIM:612069]. ALS is a neurodegenerative disorder affecting upper and lower motor neurons and resulting in fatal paralysis. Sensory abnormalities are absent. Death usually occurs within 2 to 5 years. The etiology of ALS is likely to be multifactorial, involving both genetic and environmental factors. TARDBP is the primary component of ubiquitin-positive inclusion bodies found in ALS and in frontotemporal lobar degeneration with ubiquitin-positive inclusions (FTLDU)10 Novoseek disease relationships for TARDBP gene
| Disease |
Score |
Articles |
PubMed IDs for Articles with Shared Sentences (# sentences) |
| frontotemporal dementia |
95.47 |
79 |
18989115 (3), 18087705 (2), 18535185 (2), 19350673 (2) (see all 49) |
| amyotrophic lateral sclerosis |
89.93 |
89 |
18989115 (4), 18396105 (2), 18802454 (2), 19104447 (2) (see all 46) |
| motor neuron disease |
81.98 |
11 |
18087705 (2), 18288693 (1), 17492294 (1), 18755042 (1) (see all 8) |
| inclusion body myopathy |
79.92 |
2 |
18796596 (2) |
| neurodegenerative diseases |
72.75 |
20 |
18802454 (2), 18929508 (2), 18288693 (1), 18549326 (1) (see all 10) |
| picks disease |
71.43 |
2 |
18091558 (1), 18607609 (1) |
| neurodegeneration |
70.95 |
25 |
18396105 (2), 17898224 (2), 18634762 (1), 18802454 (1) (see all 12) |
| dementia |
60.77 |
9 |
19112176 (1), 17653732 (1), 18505686 (1), 19329383 (1) |
| alzheimers disease |
51.29 |
14 |
18634762 (2), 18592255 (2), 18929508 (1), 17653732 (1) (see all 9) |
| neurofibrillary tangles |
33.32 |
1 |
18592255 (1) |
About this table
GeneTests: TARDBP Amyotrophic Lateral Sclerosis Human Gene Mutation Database: TARDBP Human Genome Epidemiology Navigator: TARDBP (9 documents)
|
Medical News for TARDBP(Possibly Related Articles in
Doctor's Guide)
About This Section
| -- |
Publications for TARDBP (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
| 10/146 PubMed articles for TARDBP gene (see all 146
):- Cloning and characterization of a novel cellular protein, TDP-43, that binds to human immunodeficiency virus type 1 TAR DNA sequence motifs. (PubMed id 7745706)1, 2, 3, 4 Ou S.-H.I.... Gaynor R.B. (1995)
- TARDBP mutations in amyotrophic lateral sclerosis with TDP-43 neuropathology: a genetic and histopathological analysis. (PubMed id 18396105)1, 3, 4 Van Deerlin V.M....Yu C.E. (2008)
- TDP-43 mutations in familial and sporadic amyotrophic lateral sclerosis. (PubMed id 18309045)1, 3, 4 Sreedharan J....Shaw C.E. (2008)
- TARDBP mutations in individuals with sporadic and familial amyotrophic lateral sclerosis. (PubMed id 18372902)3, 4 Kabashi E....Rouleau G.A. (2008)
- Ubiquitinated TDP-43 in frontotemporal lobar degeneration and amyotrophic lateral sclerosis. (PubMed id 17023659)3, 4 Neumann M....Lee V.M. (2006)
- The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)3, 4 Gregory S.G.... Bentley D.R. (2006)
- Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)3, 4 Olsen J.V....Mann M. (2006)
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)3, 4 Gerhard D.S....Malek J. (2004)
- Characterization and functional implications of the RNA binding properties of nuclear factor TDP-43, a novel splicing regulator of CFTR exon 9. (PubMed id 11470789)3, 4 Buratti E. and Baralle F.E. (2001)
- Nuclear factor TDP-43 and SR proteins promote in vitro and in vivo CFTR exon 9 skipping. (PubMed id 11285240)3, 4 Buratti E.... Baralle F.E. (2001)
|
Search for TARDBP
(in PubMed,
OMIM, and NCBI Bookshelf) About This Section
|
|
Genome Databases showing TARDBP
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
and/or
H-InvDB)
About This Section
|
| Other Databases showing TARDBP
(According to HUGE)
About This Section
| -- |
Specialized Databases showing TARDBP(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
|
| About This Section
| --
| Services for TARDBP(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 TARDBP:

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| Antibodies & Assays for TARDBP  (tdp43) |
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GeneCards Homepage - Last full update: 2 Jul 2009
Incremental update: 13 Oct 2009
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