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CDRT4 Gene

protein-coding   GIFtS: 38
GCID: GC17M015351

CMT1A Duplicated Region Transcript 4

  See 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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
CMT1A Duplicated Region Transcript 41 2
CMT1A Duplicated Region Transcript 4 Protein2

External Ids:    HGNC: 143831   Entrez Gene: 2840402   Ensembl: ENSG000002397047   UniProtKB: Q8N9R63   
ORGUL members:         

Export aliases for CDRT4 gene to outside databases

Previous GC identifers: GC17U990288 GC17M015281 GC17M015340 GC17M015344


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for CDRT4 Gene:
CDRT4 (CMT1A duplicated region transcript 4) is a protein-coding gene. Diseases associated with CDRT4 include pulmonary function.


(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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Regulatory elements:
   Regulatory transcription factor binding sites in the CDRT4 gene promoter:
         c-Fos   AP-1   JunB   Fra-1   FosB   HSF1 (long)   HNF-3beta   JunD   HSF1short   c-Jun   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidCDRT4 promoter sequence
   Search Chromatin IP Primers for CDRT4

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat CDRT4


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

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

CDRT4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
CDRT4 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M015351:  view genomic region     (about GC identifiers)

Start:
15,339,332 bp from pter      End:
15,406,922 bp from pter
Size:
67,591 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, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: CDRT4_HUMAN, Q8N9R6 (See protein sequence)
Recommended Name: CMT1A duplicated region transcript 4 protein  
Size: 151 amino acids; 17514 Da
Secondary accessions: A8MSL9 Q8IZ19

Explore the universe of human proteins at neXtProt for CDRT4: NX_Q8N9R6

Explore proteomics data for CDRT4 at MOPED


See CDRT4 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001191406.1  
ENSEMBL proteins: 
 ENSP00000310031   ENSP00000452374  

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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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ProtoNet protein and cluster: Q8N9R6


(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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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     Gene Ontology (GO): 2 molecular function terms:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0003677DNA binding ----
GO:0003899DNA-directed RNA polymerase activity ----
     
CDRT4 for ontologies           About GeneDecksing


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miRNA
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miRTarBase miRNAs that target CDRT4:
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Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CDRT4


(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
nucleus3
cytosol1
golgi apparatus1
mitochondrion1

(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 CDRT4
Interactions:

    Search GeneGlobe Interaction Network for CDRT4

STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

1 Interacting protein for CDRT4 (ENSP000003100314) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
UBCENSP000003448184STRING: ENSP00000344818
About this table

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006351transcription, DNA-templated ----

CDRT4 for ontologies           About GeneDecksing



(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 CDRT4



(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,
Conferences by KenesGroup, 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, Primers from OriGene, and/or QIAGEN )
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REFSEQ mRNAs for CDRT4 gene (2 alternative transcripts): 
NM_173622.3  NM_001204477.1  

4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000312177(uc002gop.2) ENST00000519354 ENST00000520956 ENST00000524205

miRNA
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Selected qRT-PCR Assays for microRNAs that regulate CDRT4 (see all 15):
hsa-miR-647 hsa-miR-3660 hsa-miR-516b* hsa-miR-548s hsa-miR-1205 hsa-miR-29b-1* hsa-miR-519e* hsa-miR-27b*
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Selected AceView cDNA sequences (see all 174):

AA877968 AA746000 CA428237 BQ180889 BF434193 D81958 AI342069 AW303919 
AI659095 T16750 CA446264 AA565398 AA057498 AI205524 AW025663 AI348190 
AW297656 Z39202 BM541393 BX478671 AK172733 BM712217 AV702789 CA308727 

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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CDRT4 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CAAATGTTTT
CDRT4 Expression
About this image

CDRT4 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

CDRT4 Protein Expression

UniProtKB/Swiss-Prot: CDRT4_HUMAN, Q8N9R6
Tissue specificity: Expressed in fetal skeletal muscle and kidney

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In Situ
Assay Products:
 

 
Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for CDRT4

(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 human and mouse.

Orthologs for CDRT4 gene from Selected species (see all 6)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Cdrt41 , 5 CMT1A duplicated region transcript 41, 5 63.18(n)1
50.75(a)1
  11 (38.84 cM)5
663381  NM_025496.11  NP_079772.11 
 629511935 


ENSEMBL Gene Tree for CDRT4 (if available)
TreeFam Gene Tree for CDRT4 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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(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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2 SNPs for CDRT4    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 17 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs29547591,2,4
----see VAR_0381202 mis40--------
rs37443321,2,4
----see VAR_0381192 mis40--------

HapMap Linkage Disequilibrium report for CDRT4 (15339332 - 15406922 bp)

Structural Variations
     Database of Genomic Variants (DGV) 7 variations for CDRT4:    About this table    
Variant IDTypeSubtypePubMed ID
esv2346287CNV Deletion18987734
esv4023CNV Deletion18987735
esv2715698CNV Deletion23290073
esv2715700CNV Deletion23290073
esv2715699CNV Deletion23290073
nsv1992CNV Insertion18451855
nsv907703CNV Gain21882294

Site Specific Mutation Identification with PCR Assays
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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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1 disease for CDRT4:    About MalaCards
pulmonary function


CDRT4 for disorders           About GeneDecksing

Genetic Association Database (GAD): CDRT4

Export disorders for CDRT4 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 CDRT4 gene integrated from 10 sources:
(articles sorted by number of sources associating them with CDRT4)
    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. Framingham Heart Study genome-wide association: results for pulmonary function measures. (PubMed id 17903307)1, 4 Wilk J.B....O'Connor G.T. (BMC Med. Genet. 2007)
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
  4. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
  5. 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)
  6. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 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. Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)1 Bonaldo M.F.... Soares M.B. (Genome Res. 1996)

(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: 284040 HGNC: 14383 AceView: LOC201158 Ensembl:ENSG00000239704 euGenes: HUgn284040
ECgene: CDRT4 H-InvDB: CDRT4

(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 CDRT4 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 CDRT4 gene:
Search GeneIP for patents involving CDRT4

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, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, 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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