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RTDR1 Gene

protein-coding   GIFtS: 50
GCID: GC22M023401

Rhabdoid Tumor Deletion Region Gene 1

  See RTDR1-related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
Rhabdoid Tumor Deletion Region Gene 11 2
Rhabdoid Tumor Deletion Region Protein 12

External Ids:    HGNC: 134371   Entrez Gene: 271562   Ensembl: ENSG000001002187   OMIM: 6056635   UniProtKB: Q9UHP63   

Export aliases for RTDR1 gene to outside databases

Previous GC identifers: GC22M020100 GC22M021726 GC22M006369


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RTDR1 Gene:
This gene encodes a protein with no known function but with slight similarity to a yeast vacuolar protein. The
gene is located in a region deleted in pediatric rhabdoid tumors of the brain, kidney and soft tissues, but
mutations in this gene have not been associated with the disease. (provided by RefSeq, Jul 2008)

GeneCards Summary for RTDR1 Gene:
RTDR1 (rhabdoid tumor deletion region gene 1) is a protein-coding gene. Diseases associated with RTDR1 include rhabdoid cancer.




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000022.10  NC_018933.2  NT_011520.13  
Regulatory elements:
   Regulatory transcription factor binding sites in the RTDR1 gene promoter:
         TBP   AML1a   Egr-1   GCNF   Olf-1   CUTL1   c-Ets-1   GCNF-1   c-Myb   GCNF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRTDR1 promoter sequence
   Search Chromatin IP Primers for RTDR1

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RTDR1


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 22q11.2   Ensembl cytogenetic band:  22q11.22   HGNC cytogenetic band: 22q11.2

RTDR1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RTDR1 gene location

GeneLoc information about chromosome 22         GeneLoc Exon Structure

GeneLoc location for GC22M023401:  view genomic region     (about GC identifiers)

Start:
23,401,593 bp from pter      End:
23,487,208 bp from pter
Size:
85,616 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: RTDR1_HUMAN, Q9UHP6 (See protein sequence)
Recommended Name: Rhabdoid tumor deletion region protein 1  
Size: 348 amino acids; 38592 Da

Explore the universe of human proteins at neXtProt for RTDR1: NX_Q9UHP6

Explore proteomics data for RTDR1 at MOPED


See RTDR1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_055248.1  
ENSEMBL proteins: 
 ENSP00000216036   ENSP00000414155   ENSP00000406822   ENSP00000391552   ENSP00000385567  

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(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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2 InterPro protein domains:
 IPR011989 ARM-like
 IPR016024 ARM-type_fold

Graphical View of Domain Structure for InterPro Entry Q9UHP6

ProtoNet protein and cluster: Q9UHP6

1 Blocks protein domain: IPB000357 HEAT repeat


Find genes that share domains with RTDR1           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, genOway,
transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 3 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003674molecular_function ND--
GO:0005488binding ----
GO:0005515protein binding ----
     
Find genes that share ontologies with RTDR1           About GenesLikeMe


Phenotypes:
     2 GenomeRNAi human phenotypes for RTDR1:
 Decreased cell number, increas  Synthetic lethal with Ras 

Animal Models:
   genOway: Develop your customized and physiologically relevant rodent model for RTDR1

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(According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
cytosol3
nucleus2
mitochondrion1
peroxisome1

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005575cellular_component ND--

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(SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RTDR1
Interactions:

    Search GeneGlobe Interaction Network for RTDR1

STRING Interaction Network Preview (showing 2 interactants - click image to see more details)

2 Interacting proteins for RTDR1 (Q9UHP62, 3 ENSP000002160364) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
AP2M1Q96CW12, 3, ENSP000002928074MINT-67263 I2D: score=5 STRING: ENSP00000292807
SMAD4Q134853, ENSP000003415514I2D: score=3 STRING: ENSP00000341551
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Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0008150biological_process ND--

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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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Browse Small Molecules at EMD Millipore
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  Browse compounds at ApexBio 

Browse Tocris compounds for RTDR1



(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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REFSEQ mRNAs for RTDR1 gene: 
NM_014433.2  

Unigene Cluster for RTDR1:

Rhabdoid tumor deletion region gene 1
Hs.526920  [show with all ESTs]
Unigene Representative Sequence: NM_014433
5 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000216036(uc002zwt.3 uc010gtv.1) ENST00000421213 ENST00000439064
ENST00000452757 ENST00000406876
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Additional mRNA sequence: 

AF133587.1 AK299530.1 AK310327.1 BC008986.1 CR456567.1 

4 DOTS entries:

DT.306820  DT.415060  DT.40272429  DT.100728447 

Selected AceView cDNA sequences (see all 50):

AF133587 CA313610 BI769448 BQ029431 H55204 BC008986 BX113495 BQ045248 
AI147366 NM_014433 BU584048 AI142374 BX103084 CR456567 AL039764 AA705709 
BI827420 BX428600 AA932603 BF446674 AI002099 AA921936 T05755 BF791681 

GeneLoc Exon Structure

3 Alternative Splicing Database (ASD) splice patterns (SP) for RTDR1    About this scheme

ExUns: 1 ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6 ^ 7 ^ 8 ^ 9
SP1:                                -     -                           
SP2:        -                                                         
SP3:                                                                  


ECgene alternative splicing isoforms for RTDR1

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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RTDR1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GAGGTGGAGA
RTDR1 Expression
About this image

RTDR1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

RTDR1 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.526920

UniProtKB/Swiss-Prot: RTDR1_HUMAN, Q9UHP6
Tissue specificity: Expressed in adult cerebellum, spinal cord, spleen, skeletal muscle and some/5 out of 9
rhabdoid tumors. Detected in fetal brain, lung, liver and kidney

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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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This gene was present in the common ancestor of chordates.

Orthologs for RTDR1 gene from Selected species (see all 12)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Rtdr11 , 5 rhabdoid tumor deletion region gene 11, 5 72.25(n)1
64.41(a)1
  10 (38.48 cM)5
712361  NM_001163535.11  NP_001157007.11 
 749574775 
chicken
(Gallus gallus)
Aves RTDR11 rhabdoid tumor deletion region gene 1 55.75(n)
46.31(a)
  416954  XM_415246.4  XP_415246.1 
lizard
(Anolis carolinensis)
Reptilia RTDR16
rhabdoid tumor deletion region gene 1
43(a)
1 ↔ 1
AAWZ02037698(672-8224)
tropical clawed frog
(Xenopus tropicalis)
Amphibia Str.50582 Transcribed sequence with weak similarity to protein refNP_055248.1 (H.sapiens) rhabdoid tumor deletion region protein 1 [Homo sapiens] less 71.33(n)    BQ396034.1 
zebrafish
(Danio rerio)
Actinopterygii rtdr11 rhabdoid tumor deletion region gene 1 52.45(n)
46.18(a)
  553388  XM_695166.5  XP_700258.5 


ENSEMBL Gene Tree for RTDR1 (if available)
TreeFam Gene Tree for RTDR1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for RTDR1 gene

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1 Pseudogenes.org Pseudogene for RTDR1
PGOHUM00000246526


(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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Selected SNPs for RTDR1 (see all 638)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 22 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1924334161,2
--23401431(+) GGAGAC/GAGAGC 1 -- ds50010--------
rs1147829751,2
F--23401499(+) AGACCC/TGGTGC 1 -- ds50011Minor allele frequency- T:0.02WA 118
rs285051311,2
C--23401588(+) GGACCC/GGAGAT 1 -- ds50010--------
rs2001929201,2
C--23401632(+) GTGAAC/TGAAGG 1 -- ut310--------
rs1419818031,2
C,F--23401668(+) TGATGG/ACGATC 2 /A /V mis12Minor allele frequency- A:0.00NA EU 5843
rs1457716091,2
C,F--23401684(+) TGCCCG/TCTGTA 2 R syn12Minor allele frequency- T:0.01NA EU 5861
rs358816011,2
C,F--23401696(+) GGCTTC/TGGCCA 2 K E mis13Minor allele frequency- T:0.01NA WA 4726
rs1486568861,2
C,F--23401750(+) GGGCAC/TGTGCG 2 M V mis11Minor allele frequency- T:0.00NA 4552
rs342631971,2
C,F,H--23401770(+) CCTTGC/TGGCCC 2 H R mis110Minor allele frequency- T:0.01NS NA WA EU 6909
rs2010075001,2
--23401775(+) CGGCCC/TTCGGG 2 E syn10--------

HapMap Linkage Disequilibrium report for RTDR1 (23401593 - 23487208 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for RTDR1 (see all 23):    About this table    
Variant IDTypeSubtypePubMed ID
esv2724038CNV Deletion23290073
esv2666115CNV Deletion23128226
dgv824e199CNV Deletion23128226
esv2658091CNV Deletion23128226
nsv521695CNV Loss19592680
esv24055CNV Loss19812545
dgv748n67CNV Loss20364138
nsv511644CNV Loss21212237
dgv19e24CNV Loss17666407
esv29480CNV Loss19812545

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 605663    OMIM disorders: --

1 disease for RTDR1:    
About MalaCards
rhabdoid cancer

1 disease from the University of Copenhagen DISEASES database for RTDR1:
Rhabdoid cancer

Find genes that share disorders with RTDR1           About GenesLikeMe

Genetic Association Database (GAD): RTDR1

Export disorders for RTDR1 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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PubMed articles for RTDR1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with RTDR1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Isolation of genes from the rhabdoid tumor deletion region in chromosome band 22q11.2. (PubMed id 10607907)1, 2, 9 Zhou J.-Y.... Biegel J.A. (Gene 2000)
  2. Many sequence variants affecting diversity of adult human height. (PubMed id 18391951)1, 4 Gudbjartsson D.F....Stefansson K. (Nat. Genet. 2008)
  3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
  4. A genome annotation-driven approach to cloning the human ORFeome. (PubMed id 15461802)1, 2 Collins J.E.... Dunham I. (Genome Biol. 2004)
  5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1, 3 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  6. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
  7. Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. (PubMed id 22504420)1 Estrada K....Rivadeneira F. (Nat. Genet. 2012)
  8. Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (Nature 2005)
  9. High-throughput mapping of a dynamic signaling network in mammalian cells. (PubMed id 15761153)1 Barrios-Rodiles M....Wrana J.L. (Science 2005)

(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, Kegg, and/or H-InvDB)
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Entrez Gene: 27156 HGNC: 13437 AceView: RTDR1 Ensembl:ENSG00000100218 euGenes: HUgn27156
ECgene: RTDR1 H-InvDB: RTDR1

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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NameDescription
PharmGKB entry for RTDR1 Pharmacogenomics, SNPs, Pathways
ATLAS Chromosomes in Cancer entry for RTDR1 Genetics and Cytogenetics in Oncology and Haematology

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for RTDR1 gene:
Search GeneIP for patents involving RTDR1

GeneCards and IP:
Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
Advanced Cell Diagnostics, Animal models from genOway)
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 Block miRNA regulation of human, mouse, rat RTDR1 using miScript Target Protectors SeqTarget long-range PCR primers for resequencing RTDR1
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 Search Tocris compounds for RTDR1
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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

 Novus Tissue Slides
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 antibodies-online antibodies for RTDR1 (18 products)
 antibodies-online kits for RTDR1 (2 products)
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 antibodies-online proteins for RTDR1 (5 products)
       
GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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