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CDRT1 Gene

protein-coding   GIFtS: 41
GCID: GC17M015470

CMT1A Duplicated Region Transcript 1

(Previous names: F-box and WD repeat domain containing 10 pseudogene 1, F-box...)
(Previous symbol: FBXW10P1)
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(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
CMT1A Duplicated Region Transcript 11 2     C17ORF1A2
FBXW10P11 2     FBXW10B2
F-Box And WD Repeat Domain Containing 10 Pseudogene 11 2     SM25H22
F-Box And WD-40 Domain Protein 10 Pseudogene 11 2     Charcot-Marie-Tooth Duplicated Region Transcript 12
HREP2 3     CMT1A Duplicated Region Transcript 1 Protein2
C170RF12     C17orf13
C17ORF12     C17orf1A3

External Ids:    HGNC: 143791   Entrez Gene: 3742862   Ensembl: ENSG000002413227   OMIM: 6045965   UniProtKB: O951703   

Export aliases for CDRT1 gene to outside databases

Previous GC identifers: GC17U990245 GC17M015692 GC17M015432 GC17M015370 GC17M015476


(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 CDRT1 Gene:
Members of the F-box protein family, such as FBXW10, are characterized by an approximately 40-amino acid F-box
motif. SCF complexes, formed by SKP1 (MIM 601434), cullin (see CUL1; MIM 603034), and F-box proteins, act as
protein-ubiquitin ligases. F-box proteins interact with SKP1 through the F box, and they interact with
ubiquitination targets through other protein interaction domains (Jin et al., 2004 (PubMed 15520277)).(supplied
by OMIM, Mar 2008)

GeneCards Summary for CDRT1 Gene:
CDRT1 (CMT1A duplicated region transcript 1) is a protein-coding gene. An important paralog of this gene is ENSG00000181464.




(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_000017.10  NC_018928.2  NT_010718.17  
Regulatory elements:
   Regulatory transcription factor binding sites in the CDRT1 gene promoter:
         Max1   NF-1/L   NF-1   AP-4   PPAR-gamma1   c-Rel   CP2   IRF-7A   c-Myc   ATF6   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCDRT1 promoter sequence
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CDRT1


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

Entrez Gene cytogenetic band: 17p12   Ensembl cytogenetic band:  17p12   HGNC cytogenetic band: 17p11

CDRT1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CDRT1 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M015470:  view genomic region     (about GC identifiers)

Start:
15,468,798 bp from pter      End:
15,523,018 bp from pter
Size:
54,221 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., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: CDRT1_HUMAN, O95170 (See protein sequence)
Recommended Name: CMT1A duplicated region transcript 1 protein  
Size: 752 amino acids; 85370 Da
Miscellaneous: CDRT1 gene is located centromeric to and partially within proximal CMT1A-REP element. CMT1A-REP is
a complex binary repeat element flanking a 1.5-Mb DNA region duplicated in Charcot-Marie-Tooth disease type I
(CMT1A) or deleted in Hereditary neuropathy (HNPP)
Sequence caution: Sequence=AAD10830.1; Type=Frameshift; Positions=165;
Secondary accessions: O43848 O95611
Alternative splicing: 2 isoforms:  O95170-1   O95170-2   

Explore the universe of human proteins at neXtProt for CDRT1: NX_O95170

Explore proteomics data for CDRT1 at MOPED


See CDRT1 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins (2 alternative transcripts): 
NP_001269469.1  NP_006373.2  

ENSEMBL proteins: 
 ENSP00000468137   ENSP00000346416   ENSP00000379242   ENSP00000462959   ENSP00000463684  
 ENSP00000261644  

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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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HGNC Gene Families:
FBXW: F-boxes / WD-40 domains
WDR: WD repeat domain containing

Selected InterPro protein domains (see all 6):
 IPR019775 WD40_repeat_CS
 IPR001810 F-box_dom
 IPR001680 WD40_repeat
 IPR020472 G-protein_beta_WD-40_rep
 IPR017986 WD40_repeat_dom

Graphical View of Domain Structure for InterPro Entry O95170

ProtoNet protein and cluster: O95170

UniProtKB/Swiss-Prot: CDRT1_HUMAN, O95170
Similarity: Contains 7 WD repeats


Find genes that share domains with CDRT1           About GenesLikeMe


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, 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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Molecular Function:
     Genatlas biochemistry entry for CDRT1:
cadherin-related tumor 1

     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003674molecular_function ND--
GO:0005515protein binding ----
     
Find genes that share ontologies with CDRT1           About GenesLikeMe


Animal Models:
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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
endoplasmic reticulum1
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 CDRT1
Interactions:

    Search GeneGlobe Interaction Network for CDRT1

STRING Interaction Network Preview (showing 5 interactants - click image to see 8)

Selected Interacting proteins for CDRT1 (ENSP000003792424) via UniProtKB, MINT, STRING, and/or I2D (see all 8)
InteractantInteraction Details
GeneCardExternal ID(s)
CDC6ENSP000002097284STRING: ENSP00000209728
PSMD8ENSP000002150714STRING: ENSP00000215071
PSMD2ENSP000003101294STRING: ENSP00000310129
ATP6V1AENSP000002733984STRING: ENSP00000273398
DDI1ENSP000003028054STRING: ENSP00000302805
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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
   Browse drugs & compounds from Enzo Life Sciences
  Browse compounds at ApexBio 

Browse Tocris compounds for CDRT1



(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 CDRT1 gene (2 alternative transcripts): 
NM_001282540.1  NM_006382.3  

Unigene Clusters for CDRT1:

CMT1A duplicated region transcript 1
Hs.548021  [show with all ESTs], Hs.632233  [show with all ESTs]
Unigene Representative Sequences: AF337810, NM_006382
7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000472534 ENST00000354433(uc010vvy.2 uc010vvz.2 uc010cos.1)
ENST00000395906(uc002gov.4 uc002gou.2) ENST00000583965 ENST00000571263
ENST00000475944 ENST00000261644
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Additional mRNA sequence: 

BC143291.1 BC171723.1 U43383.1 U65652.1 

4 DOTS entries:

DT.40127954  DT.95313553  DT.40122744  DT.100689099 

13 AceView cDNA sequences:

CF994774 BM712658 AK057407 CB989113 NM_006382 U65652 U43383 AW891009 
BI461612 BF327447 BG721464 CF593769 AW062475 

GeneLoc Exon Structure


(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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CDRT1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
CDRT1 Expression
About this image

CDRT1 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

CDRT1 Protein Expression

SOURCE GeneReport for Unigene clusters: Hs.548021 Hs.632233

UniProtKB/Swiss-Prot: CDRT1_HUMAN, O95170
Tissue specificity: Expressed in pancreas, heart and skeletal muscle

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In Situ
Assay Products:
 

 
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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 animals and fungi.

Orthologs for CDRT1 gene from Selected species (see all 8)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
oppossum
(Monodelphis domestica)
Mammalia --
Uncharacterized protein
35(a)
1 → many
2(262685122-262866237)
chicken
(Gallus gallus)
Aves --
Uncharacterized protein
23(a)
1 → many
18(2210821-2221821)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
27(a)
1 → many
2(106145348-106170865)
zebrafish
(Danio rerio)
Actinopterygii fbxw106
F-box and WD repeat domain containing 10
22(a)
1 → many
12(37124733-37135125) ENSDARG00000086484
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PRP466
Member of the NineTeen Complex (NTC) that contains...
16(a)
1 → many
XVI(266180-267535) YPL151C


ENSEMBL Gene Tree for CDRT1 (if available)
TreeFam Gene Tree for CDRT1 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for CDRT1 gene
ENSG000001814642  PLRG12  KATNB12  FBXW102  
2 SIMAP similar genes for CDRT1 using alignment to 7 protein entries:     CDRT1_HUMAN (see all proteins):
FBXW10    FBXW7

Find genes that share paralogs with CDRT1           About GenesLikeMe



(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 CDRT1 (see all 836)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 17 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs28561931,2
C,H--15491497(-) TTATGG/CACACG 1 -- int12Minor allele frequency- C:0.00NA 4
rs22610391,2
C,A--15491513(+) GTTACA/GGCACT 1 -- int10--------
rs28561921,2
C,F--15491532(-) GTGGCC/TGTTGT 1 -- int12Minor allele frequency- T:0.00NA 4
rs1407308981,2
--15491555(+) GTTGTC/TGGGAA 1 -- int10--------
rs26543231,2
--15491556(+) TTGTCA/GGGAAC 1 -- int10--------
rs28561911,2
C,O--15491622(-) AATGAT/AGTGCC 1 -- int12Minor allele frequency- A:0.00NA 4
rs1880559881,2
C--15491636(+) ACTCAA/TGATCA 1 -- int10--------
rs1458704641,2
--15491648(+) TAATTA/GAGTGA 1 -- int10--------
rs22610401,2
A--15491654(+) AGTGAC/TGTCTT 1 -- int10--------
rs1429730491,2
--15491655(+) GTGACA/GTCTTA 1 -- int10--------

HapMap Linkage Disequilibrium report for CDRT1 (15468798 - 15523018 bp)

Structural Variations
     Database of Genomic Variants (DGV) 1 variation for CDRT1:    About this table    
Variant IDTypeSubtypePubMed ID
nsv457695CNV Gain19166990

Site Specific Mutation Identification with PCR Assays
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DNA2.0 Custom Variant and Variant Library Synthesis for CDRT1

(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: 604596    OMIM disorders: --


Find genes that share disorders with CDRT1           About GenesLikeMe


Export disorders for CDRT1 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 CDRT1 gene integrated from 10 sources:
(articles sorted by number of sources associating them with CDRT1)
    Utopia: connect your pdf to the dynamic
world of online information

  1. The 1.4-Mb CMT1A duplication/HNPP deletion genomic region reveals unique genome architectural features and provides insights into the recent evolution of new genes. (PubMed id 11381029)1, 2, 3 Inoue K.... Birren B. (Genome Res. 2001)
  2. Genomic structure and physical mapping of C17orf1: a gene associated with the proximal element of the CMT1A-REP binary repeat. (PubMed id 9787083)1, 2, 3 Kennerson M.L.... Nicholson G.A. (Genomics 1998)
  3. The Charcot-Marie-Tooth binary repeat contains a gene transcribed from the opposite strand of a partially duplicated region of the COX10 gene. (PubMed id 9403059)1, 2 Kennerson M.L....Nicholson G.A. (Genomics 1997)
  4. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PubMed id 16625196)2 Zody M.C.... Nusbaum C. (Nature 2006)
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1 Ota T.... Sugano S. (Nat. Genet. 2004)
  6. Systematic analysis and nomenclature of mammalian F-box proteins. (PubMed id 15520277)1 Jin J....Harper J.W. (Genes Dev. 2004)
  7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (Proc. Natl. Acad. Sci. U.S.A. 2002)
  8. Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. (PubMed id 10737800)1 Dias Neto E....Simpson A.J.G. (Proc. Natl. Acad. Sci. U.S.A. 2000)
  9. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)
  10. Single test for two hereditary neuropathies, CMT1A and HNPP. (PubMed id 7586531)1 Kennerson M.L....Nicholson G.A. (Clin. Chem. 1995)

(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: 374286 HGNC: 14379 AceView: CDRT1 Ensembl:ENSG00000241322 euGenes: HUgn374286
ECgene: CDRT1 H-InvDB: CDRT1

(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 CDRT1 Pharmacogenomics, SNPs, Pathways

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for CDRT1 gene:
Search GeneIP for patents involving CDRT1

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, LSBio, eBioscience, 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 inGenious Targeting Laboratory, genOway)
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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

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