RTDR1 Gene
protein-coding GIFtS: 49
GCID: GC22M023401
|
|
rhabdoid tumor deletion region gene 1
| |
Aliases
for RTDR1 gene
(According to
1HGNC,
2Entrez Gene,
3UniProtKB/Swiss-Prot,
4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc,
7Ensembl,
8DME,
9miRBase,
and/or 10fRNAdb)
About This Section
|
| Aliases |
|---|
| Rhabdoid Tumor Deletion Region Gene 11 2 | | Rhabdoid Tumor Deletion Region Protein 12 |
Export aliases for RTDR1 gene to outside databasesPrevious GC identifers: GC22M020100 GC22M021726 GC22M006369 |
Summaries
for RTDR1 gene(According to Entrez Gene,
Tocris Bioscience,
Wikipedia's
Gene Wiki,
PharmGKB,
UniProtKB/Swiss-Prot,
and/or
UniProtKB/TrEMBL)
About This Section
|
Entrez Gene summary for RTDR1:
This gene encodes a protein with no known function but with slight similarity to a yeast vacuolar protein. The gene islocated in a region deleted in pediatric rhabdoid tumors of the brain, kidney and soft tissues, but mutations in thisgene have not been associated with the disease. (provided by RefSeq, Jul 2008)
|
Genomic Views
for RTDR1 gene
(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 69),
Regulatory elements and Epigenetics data according to
QIAGEN,
SABiosciences, and/or
SwitchGear Genomics)
About This Section
| RefSeq DNA sequence:- NC_000022.10 NC_018933.1 NT_011520.12
Regulatory elements:
 SABiosciences 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
Search SABiosciences Chromatin IP Primers for RTDR1
Epigenetics:
| | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays 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: 22q11.2RTDR1 Gene in genomic location: bands according to Ensembl, locations according to
 (and/or Entrez Gene and/or Ensembl if different)
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 |
|
Proteins
for RTDR1 gene
(According to
1UniProtKB,
HORDE,
neXtProt,
Ensembl,
and/or Reactome,
Modification sites according to 2PhosphoSitePlus,
Specific Peptides from DME,
Protein expression images according to data from SPIRE MOPED and PaxDb,
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, and/or
Uscn,
Biochemical Assays by
EMD Millipore,
R&D Systems,
OriGene,
GenScript,
Cell Signaling Technology,
Enzo Life Sciences, and/or
Uscn,
Ontologies according to Gene
Ontology Consortium 01 Mar 2013 and
Entrez Gene,
Antibodies by
EMD Millipore,
R&D Systems,
GenScript,
Cell Signaling Technology,
OriGene,
Novus Biologicals,
Thermo Fisher Scientific,
Abcam, and/or
Uscn)
About This Section
|
UniProtKB/Swiss-Prot: RTDR1_HUMAN, Q9UHP6 (See
protein sequence)Recommended Name: Rhabdoid tumor deletion region protein 1 Size: 348 amino acids; 38592 DaExplore the universe of human proteins at neXtProt for RTDR1: NX_Q9UHP6
Post-translational modifications:
View modification sites using PhosphoSitePlus2View neXtProt modification sites for NX_Q9UHP6
RTDR1 Protein expression data from MOPED and PaxDb: About this image 
REFSEQ proteins: NP_055248.1
ENSEMBL proteins: ENSP00000216036 ENSP00000414155 ENSP00000406822 ENSP00000391552 ENSP00000385567
Human Recombinant Protein Products:
Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0005575 | cellular_component |
ND | -- |
RTDR1 for ontologies About GeneDecksing
RTDR1 Antibody Products:
Assay Products for RTDR1: |
Protein
Domains /
Families
for RTDR1 gene(According to InterPro, ProtoNet,
UniProtKB, and/or BLOCKS,
Sets of similar genes according to GeneDecks)
About This Section
|
RTDR1 for domains About GeneDecksing
2 InterPro domains/families:Graphical View of Domain Structure for InterPro Entry Q9UHP6ProtoNet protein and cluster: Q9UHP6 1 Blocks protein family: IPB000357 HEAT repeat
|
Function
for RTDR1 gene
(According to 1UniProtKB,
Genatlas,
LifeMap Discovery™,
IUBMB, and/or
2DME,
Human phenotypes from GenomeRNAi,
Animal models from MGI Mar 06 2013,
bound targets from SABiosciences,
miRNA Gene Targets from miRTarBase
shRNA from
OriGene,
RNAi from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
microRNA from QIAGEN,
Gene Editing from DNA2.0,
Clones from EMD Millipore,
OriGene,
SwitchGear Genomics,
GenScript,
Sino Biological,
DNA2.0,
and Vector BioLabs,
Cell Lines from GenScript,
LifeMap BioReagents,
In Situ Hybridization Assays from Advanced Cell Diagnostics,
Ontologies according to Gene Ontology Consortium 01 Mar 2013 via
Entrez Gene.)
About This Section
|
Clone
Products: |  | Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore | |  | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for RTDR1 (see all 6)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for RTDR1
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling 
| |  | GenScript: all cDNA clones in your preferred vector: RTDR1 (NM_014433) | |  | Browse Sino Biological Human cDNA Clones | |  | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for RTDR1 | |  | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RTDR1 |
In Situ Assay
Products: |
 | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RTDR1 |
Gene Ontology (GO): 1 molecular function term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0003674 | molecular_function |
ND | -- |
RTDR1 for ontologies About GeneDecksing
2 GenomeRNAi human phenotypes for RTDR1:
|
Pathways & Interactions
for RTDR1 gene
(Pathways according to
EMD Millipore,
R&D Systems,
Cell Signaling Technology,
KEGG,
PharmGKB,
BioSystems,
Reactome,
Tocris Bioscience,
GeneGo (Thomson Reuters),
QIAGEN,
and/or UniProtKB,
Sets of similar genes according to GeneDecks,
Interaction Networks according to
SABiosciences,
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 Mar 2013 via
Entrez Gene).
About This Section
|
Interactions:
Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks 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 I2DAbout this table
Gene Ontology (GO): 1 biological process term (GO ID links to tree view): About this table | GO ID | Qualified GO term | Evidence | PubMed IDs |
|---|
| GO:0008150 | biological_process |
ND | -- |
RTDR1 for ontologies About GeneDecksing
|
Drugs & Compounds
for RTDR1 gene(Chemical Compounds according to UniProtKB, Enzo Life Sciences,
EMD Millipore, Tocris Bioscience
HMDB,
BitterDB, and/or
Novoseek, and Drugs according to
DrugBank,
Enzo Life Sciences, and/or
PharmGKB, with drugs/clinical trials/news
search links to CenterWatch)
About This Section
|
 Browse Tocris compounds for RTDR1
Search CenterWatch for drugs/clinical trials and news about RTDR1
|
Transcripts
for RTDR1 gene(Secondary structures according to
fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene
(Build 235 Homo sapiens; Mar 10 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,
RNAi Products from
EMD Millipore,
siRNAs from
OriGene,
QIAGEN,
shRNA from
OriGene,
microRNA from QIAGEN,
Tagged/untagged cDNA clones from
OriGene,
SwitchGear Genomics,
GenScript,
DNA2.0,
Vector BioLabs,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN
)
About This Section
|
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_0144335 Ensembl transcripts including schematic representations, and UCSC links where relevant: ENST00000216036(uc002zwt.3 uc010gtv.1) ENST00000421213 ENST00000439064
ENST00000452757 ENST00000406876
Clone
Products: | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for RTDR1 (see all 6)
OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for RTDR1
OriGene custom cloning services – gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling
| | | GenScript: all cDNA clones in your preferred vector: RTDR1 (NM_014433) | | | DNA2.0 Custom Codon Optimized Gene
Synthesis Service for RTDR1 | | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RTDR1 |
Additional cDNA sequence: AF133587.1 AK299530.1 AK310327.1 BC008986.1 CR456567.1 7 DOTS entries: DT.306820 DT.415060 DT.100728447 DT.100773110 DT.40272429 DT.100680712 DT.100691246 24/50 AceView cDNA sequences (see all 50): H55204 AF133587 BX113495 BC008986 BQ029431 NM_014433 AI147366 BI769448 CA313610 BQ045248 BF446674 AI002099 AA932603 AI918482 BX103084 R98617 BX428613 AA921936 T05755 AA705709 AI142374 BU584048 CD674905 BF794172
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
|
Expression
for RTDR1 gene
(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™,
plus additional links to
Genevestigator, and/or
SOURCE, and/or
BioGPS, and/or
UniProtKB,
PCR Arrays from
SABiosciences,
Primers from
OriGene,
SABiosciences, and/or
QIAGEN,
In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section
| RTDR1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: GAGGTGGAGA
About this image
See RTDR1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for RTDR1
SOURCE GeneReport for Unigene cluster: Hs.526920
UniProtKB/Swiss-Prot: RTDR1_HUMAN, Q9UHP6Tissue specificity: Expressed in adult cerebellum, spinal cord, spleen, skeletal muscle and some/5 out of 9 rhabdoidtumors. Detected in fetal brain, lung, liver and kidney
SABiosciences Custom PCR Arrays for RTDR1
Primer
Products: | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for RTDR1
Browse OriGene validated miRNA SYBR primer pairs
| | | SABiosciences RT2 qPCR Primer Assay in human, mouse / rat RTDR1 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RTDR1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RTDR1 | In Situ
Assay Products: |
| Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RTDR1 |
Orthologs
for RTDR1 gene
(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)
About This Section
|
This gene was present in the common ancestor of chordates.
Orthologs for RTDR1 gene from 5/17 species (see all 17) 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
64.71(a)1 |
|
10 (38.48 cM)5
712361 NM_027730.11 NP_082006.11
749574775 |
chicken
(Gallus gallus) |
Aves |
RTDR11 |
rhabdoid tumor deletion region gene 1 |
55.75(n)
46.02(a) |
|
416954 XM_415246.3 XP_415246.1 |
lizard
(Anolis carolinensis) |
Reptilia |
RTDR16 |
-- |
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 |
52.35(n)
46.18(a) |
|
553388 XM_695166.4 XP_700258.4 |
ENSEMBL Gene Tree for RTDR1 (if available)
TreeFam Gene Tree for RTDR1 (if available) |
Paralogs
for RTDR1 gene(Paralogs according to
1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
| Paralogs for RTDR1 gene
RTDR1 for paralogs About GeneDecksing
1 Pseudogenes.org Pseudogene for RTDR1
PGOHUM00000246526
|
Genomic Variants
for RTDR1 gene(SNPs/Variants according to the
1NCBI SNP Database,
2Ensembl,
3PupaSUITE,
UniProtKB, 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) and the Locus Specific Mutation
Databases (LSDB), Blood group antigen gene mutations by BGMUT,
Resequencing Primers from QIAGEN,
Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section
|
| Genomic Data | Transcription Related Data | Allele Frequencies | | SNP ID | Valid | Clinical
significance | Chr 22 pos | Sequence | # | AA
Chg | Type | More | # | Allele
freq | Pop | Total
sample | More |
|---|
HapMap Linkage Disequilibrium report for RTDR1 (23401593 - 23487208 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV): 6 variations for RTDR1
2 CNVs: 48008 59064
4 Indels: 67850 73775 11199 11198 | SABiosciences Cancer Mutation PCR Assays |
| | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing RTDR1 |
|
Disorders
/ Diseases
for RTDR1 gene
(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.)
About This Section
|
RTDR1 for disorders About GeneDecksing
OMIM gene information: 605663
OMIM disorders: --
2  diseases for RTDR1: About MalaCardsrhabdoid tumors rhabdoid cancer
Export disorders for RTDR1 gene to outside databases
|
Publications
for RTDR1 gene (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)
About This Section
|
PubMed articles for RTDR1 gene integrated from 9 sources:
(articles sorted by number of sources associating them with RTDR1) | |  | Utopia: connect your pdf to the dynamic
world of online information |
- Isolation of genes from the rhabdoid tumor deletion region in chromosome band 22q11.2. (PubMed id 10607907)1, 2, 3, 9 Zhou J.-Y.... Biegel J.A. (2000)
- A genome annotation-driven approach to cloning the human ORFeome. (PubMed id 15461802)1, 2 Collins J.E.... Dunham I. (2004)
- 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. (2004)
- 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. (2002)
- Many sequence variants affecting diversity of adult human height. (PubMed id 18391951)1 Gudbjartsson D.F....Stefansson K. (2008)
- Towards a proteome-scale map of the human protein-protein interaction network. (PubMed id 16189514)1 Rual J.F....Vidal M. (2005)
- High-throughput mapping of a dynamic signaling network in mammalian cells. (PubMed id 15761153)1 Barrios-Rodiles M....Wrana J.L. (2005)
|
External Searches for RTDR1 gene
(in PubMed,
OMIM, and NCBI Bookshelf)
About This Section
|
|
Genome Databases showing RTDR1 gene
(According to
Entrez Gene,
HGNC,
AceView,
euGenes,
Ensembl,
miRBase,
ECgene,
Kegg,
and/or
H-InvDB)
About This Section
|
|
Other Databases showing RTDR1 gene
(According to HUGE)
About This Section
| -- |
Specialized Databases showing RTDR1 gene(According to PharmGKB,
ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
|
|
About This Section
| 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
|
Products
for RTDR1 gene(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or
Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section
|
 | |
 | |
 |
| | |  | Browse OriGene Antibodies | | OriGene shRNA RFP for RTDR1 | | | OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for RTDR1 | | OriGene genome-wide validated SYBR primer pairs in human, mouse, rat for RTDR1 | | | OriGene Protein Over-expression Lysate for RTDR1 | | Browse OriGene Fluorogenic Cell Assay Kits | | | OriGene siRNA for RTDR1 | | Browse 3'-UTR reporter clones for miRNA target validation | | | OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for RTDR1 | | OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for RTDR1 | | | Browse OriGene GFP tagged cDNA clones in CMV expression vector | | Browse OriGene MicroRNA Expression Plasmids | | | Browse OriGene basic RS shRNAs | | Browse OriGene validated miRNA SYBR primer pairs | | | OriGene Purified Protein for RTDR1 | | OriGene custom cloning services - gene synthesis, subcloning, mutagenesis,
variant library, vector shuttling | | | OriGene Custom Antibody Services for RTDR1 | | OriGene Custom Protein Services for RTDR1 | | | OriGene Custom Immunoassay Development | | |
| |
 |
 |
| | | QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat RTDR1 | | | QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing RTDR1 | | | QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RTDR1 | | | QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat RTDR1 | | | QIAGEN QuantiFast Probe-based Assays in human, mouse, rat RTDR1 | | | QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat RTDR1 |
| |
 |  |  |  | |
| | | | Search Tocris compounds for RTDR1 |
| |  |  |  |  | | | | |
 |
 |
 |
 | | | RTDR1 Proteins, Antibodies, CLIAs, and ELISAs |
| | | | | Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RTDR1 |
|  |  |  | | | | Search ThermoFisher Antibodies for RTDR1 |
| | | Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat RTDR1 |
|
|
|
|
