Human Gene NDRG1 (ENST00000323851.13_7) from GENCODE V47lift37
  Description: N-myc downstream regulated 1, transcript variant 2 (from RefSeq NM_006096.4)
Gencode Transcript: ENST00000323851.13_7
Gencode Gene: ENSG00000104419.17_21
Transcript (Including UTRs)
   Position: hg19 chr8:134,249,418-134,309,495 Size: 60,078 Total Exon Count: 16 Strand: -
Coding Region
   Position: hg19 chr8:134,251,121-134,296,554 Size: 45,434 Coding Exon Count: 15 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:134,249,418-134,309,495)mRNA (may differ from genome)Protein (394 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NDRG1_HUMAN
DESCRIPTION: RecName: Full=Protein NDRG1; AltName: Full=Differentiation-related gene 1 protein; Short=DRG-1; AltName: Full=N-myc downstream-regulated gene 1 protein; AltName: Full=Nickel-specific induction protein Cap43; AltName: Full=Reducing agents and tunicamycin-responsive protein; Short=RTP; AltName: Full=Rit42;
FUNCTION: Stress-responsive protein involved in hormone responses, cell growth, and differentiation. Acts as a tumor suppressor in many cell types. Necessary but not sufficient for p53/TP53- mediated caspase activation and apoptosis. Has a role in cell trafficking, notably of the Schwann cell, and is necessary for the maintenance and development of the peripheral nerve myelin sheath. Required for vesicular recycling of CDH1 and TF. May also function in lipid trafficking. Protects cells from spindle disruption damage. Functions in p53/TP53-dependent mitotic spindle checkpoint. Regulates microtubule dynamics and maintains euploidy.
SUBUNIT: Interacts with RAB4A (membrane-bound form); the interaction involves NDRG1 in vesicular recycling of CDH1.
INTERACTION: P27824:CANX; NbExp=2; IntAct=EBI-716486, EBI-355947; P12956:XRCC6; NbExp=2; IntAct=EBI-716486, EBI-353208;
SUBCELLULAR LOCATION: Cytoplasm, cytosol. Cytoplasm, cytoskeleton, centrosome. Nucleus. Cell membrane. Note=Mainly cytoplasmic but differentially localized to other regions. Associates with the plasma membrane in intestinal epithelia and lactating mammary gland. Translocated to the nucleus in a p53/TP53-dependent manner. In prostate epithelium and placental chorion, located in both the cytoplasm and in the nucleus. No nuclear localization in colon epithelium cells. In intestinal mucosa, prostate and renal cortex, located predominantly adjacent to adherens junctions. Cytoplasmic with granular staining in proximal tubular cells of the kidney and salivary gland ducts. Recruits to the membrane of recycling/sorting and late endosomes via binding to phosphatidylinositol 4-phosphate. Associates with microtubules. Colocalizes with TUBG1 in the centrosome. Cytoplasmic location increased with hypoxia. Phosphorylated form found associated with centromeres during S-phase of mitosis and with the plasma membrane.
TISSUE SPECIFICITY: Ubiquitous; expressed most prominently in placental membranes and prostate, kidney, small intestine, and ovary tissues. Also expressed in heart, brain, skeletal muscle, lung, liver and pancreas. Low levels in peripheral blood leukocytes and in tissues of the immune system. Expressed mainly in epithelial cells. Also found in Schwann cells of peripheral neurons. Reduced expression in adenocarcinomas compared to normal tissues. In colon, prostate and placental membranes, the cells that border the lumen show the highest expression.
INDUCTION: By homocysteine, 2-mercaptoethanol, tunicamycin in endothelial cells. Induced approximately 20-fold during in vitro differentiation of the colon carcinoma cell lines HT29-D4 and Caco-2. Induced by oxidative stress in colon cancers. Decreased expression in colon adenomas and adenocarcinomas. Induced by nickel compounds in all tested cell lines. The primary signal for its induction is an elevation of free intracellular calcium ion caused by nickel ion exposure. Okadaic acid, a serine/threonine phosphatase inhibitor, induced its expression more rapidly and more efficiently than nickel.
PTM: Under stress conditions, phosphorylated in the C-terminal on many serine and threonine residues. Phosphorylated in vitro by PKA. Phosphorylation enhanced by increased intracellular cAMP levels. Homocysteine induces dephosphorylation. Phosphorylation by SGK1 is cell cycle dependent.
DISEASE: Defects in NDRG1 are the cause of Charcot-Marie-Tooth disease type 4D (CMT4D) [MIM:601455]; also known as hereditary motor and sensory neuropathy Lom type (HMSNL). CMT4D is a recessive form of Charcot-Marie-Tooth disease, the most common inherited disorder of the peripheral nervous system. Charcot- Marie-Tooth disease is classified in two main groups on the basis of electrophysiologic properties and histopathology: primary peripheral demyelinating neuropathy and primary peripheral axonal neuropathy. Demyelinating CMT neuropathies are characterized by severely reduced nerve conduction velocities (less than 38 m/sec), segmental demyelination and remyelination with onion bulb formations on nerve biopsy, slowly progressive distal muscle atrophy and weakness, absent deep tendon reflexes, and hollow feet. By convention, autosomal recessive forms of demyelinating Charcot-Marie-Tooth disease are designated CMT4.
SIMILARITY: Belongs to the NDRG family.
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/NDRG1";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: NDRG1
Diseases sorted by gene-association score: charcot-marie-tooth disease, type 4d* (1378), congenital hypomyelination neuropathy* (400), neuropathy, congenital hypomyelinating* (196), transitional papilloma (9), neuropathy, hereditary motor and sensory, russe type (8), charcot-marie-tooth disease (8), central neurocytoma (8), hereditary neuropathies (8), motor peripheral neuropathy (6), tooth disease (5), sensory peripheral neuropathy (5), charcot-marie-tooth disease, type 1d (5), hereditary motor and sensory neuropathy, type iic (5), charcot-marie-tooth disease, type 2e (4), charcot-marie-tooth disease, type 1c (4)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 309.84 RPKM in Nerve - Tibial
Total median expression: 4099.76 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -53.30137-0.389 Picture PostScript Text
3' UTR -595.601703-0.350 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR004142 - Ndr

Pfam Domains:
PF03096 - Ndr family
PF12697 - Alpha/beta hydrolase family

SCOP Domains:
52467 - DHS-like NAD/FAD-binding domain
53474 - alpha/beta-Hydrolases

ModBase Predicted Comparative 3D Structure on Q92597
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008017 microtubule binding
GO:0017137 Rab GTPase binding
GO:0043015 gamma-tubulin binding
GO:0045296 cadherin binding

Biological Process:
GO:0008285 negative regulation of cell proliferation
GO:0010038 response to metal ion
GO:0030330 DNA damage response, signal transduction by p53 class mediator
GO:0032287 peripheral nervous system myelin maintenance
GO:0042127 regulation of cell proliferation
GO:0042981 regulation of apoptotic process
GO:0045576 mast cell activation
GO:0071456 cellular response to hypoxia
GO:0090232 positive regulation of spindle checkpoint

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0005874 microtubule
GO:0005886 plasma membrane
GO:0005913 cell-cell adherens junction
GO:0015630 microtubule cytoskeleton
GO:0016020 membrane
GO:0043209 myelin sheath
GO:0048471 perinuclear region of cytoplasm
GO:0055038 recycling endosome membrane
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  LF210295 - JP 2014500723-A/17798: Polycomb-Associated Non-Coding RNAs.
D87953 - Homo sapiens mRNA for RTP, complete cds.
LF214025 - JP 2014500723-A/21528: Polycomb-Associated Non-Coding RNAs.
AK095649 - Homo sapiens cDNA FLJ38330 fis, clone FCBBF3025280, highly similar to NDRG1 PROTEIN.
AF039944 - Homo sapiens TARG1 mRNA, 3' untranslated region.
AX229879 - Sequence 5 from Patent WO0162959.
BC006260 - Homo sapiens N-myc downstream regulated 1, mRNA (cDNA clone IMAGE:3946764), with apparent retained intron.
AK026383 - Homo sapiens cDNA: FLJ22730 fis, clone HSI15793, highly similar to AF004162 Homo sapiens nickel-specific induction protein (Cap43) mRNA.
AF004162 - Homo sapiens nickel-specific induction protein (Cap43) mRNA, complete cds.
X92845 - H.sapiens mRNA for Drg1 protein.
BC003175 - Homo sapiens N-myc downstream regulated 1, mRNA (cDNA clone MGC:4412 IMAGE:2957847), complete cds.
AK130985 - Homo sapiens cDNA FLJ27475 fis, clone DMC07108.
AK091269 - Homo sapiens cDNA FLJ33950 fis, clone CTONG2018413.
AX746885 - Sequence 410 from Patent EP1308459.
AK129867 - Homo sapiens cDNA FLJ26357 fis, clone HRT05043, highly similar to NDRG1 PROTEIN.
AK124709 - Homo sapiens cDNA FLJ42719 fis, clone BRAMY3010492, highly similar to Protein NDRG1.
AK091147 - Homo sapiens cDNA FLJ33828 fis, clone CTONG2003599, highly similar to Protein NDRG1.
AK096562 - Homo sapiens cDNA FLJ39243 fis, clone OCBBF2008283, highly similar to Protein NDRG1.
AK126924 - Homo sapiens cDNA FLJ44977 fis, clone BRAWH3002513, highly similar to Protein NDRG1.
JD245342 - Sequence 226366 from Patent EP1572962.
JD331707 - Sequence 312731 from Patent EP1572962.
JD382577 - Sequence 363601 from Patent EP1572962.
LF336988 - JP 2014500723-A/144491: Polycomb-Associated Non-Coding RNAs.
JD225767 - Sequence 206791 from Patent EP1572962.
JD518137 - Sequence 499161 from Patent EP1572962.
LF336989 - JP 2014500723-A/144492: Polycomb-Associated Non-Coding RNAs.
JD423612 - Sequence 404636 from Patent EP1572962.
JD459390 - Sequence 440414 from Patent EP1572962.
JD400277 - Sequence 381301 from Patent EP1572962.
JD204308 - Sequence 185332 from Patent EP1572962.
JD476248 - Sequence 457272 from Patent EP1572962.
LF336990 - JP 2014500723-A/144493: Polycomb-Associated Non-Coding RNAs.
JD193279 - Sequence 174303 from Patent EP1572962.
JD530481 - Sequence 511505 from Patent EP1572962.
LF336991 - JP 2014500723-A/144494: Polycomb-Associated Non-Coding RNAs.
JD145801 - Sequence 126825 from Patent EP1572962.
JD138946 - Sequence 119970 from Patent EP1572962.
JD183520 - Sequence 164544 from Patent EP1572962.
LF336992 - JP 2014500723-A/144495: Polycomb-Associated Non-Coding RNAs.
JD225110 - Sequence 206134 from Patent EP1572962.
AK299636 - Homo sapiens cDNA FLJ53648 complete cds, highly similar to Protein NDRG1.
JD140183 - Sequence 121207 from Patent EP1572962.
JD043277 - Sequence 24301 from Patent EP1572962.
JD525807 - Sequence 506831 from Patent EP1572962.
AK298236 - Homo sapiens cDNA FLJ53637 complete cds, highly similar to Protein NDRG1.
JD437293 - Sequence 418317 from Patent EP1572962.
JD497581 - Sequence 478605 from Patent EP1572962.
AK296794 - Homo sapiens cDNA FLJ55222 complete cds, highly similar to Protein NDRG1.
AK223542 - Homo sapiens mRNA for N-myc downstream regulated gene 1 variant, clone: FCC125F02.
JD399497 - Sequence 380521 from Patent EP1572962.
AY277597 - Homo sapiens transformation-related protein 14 (TRG14) mRNA, complete cds.
DQ892952 - Synthetic construct clone IMAGE:100005582; FLH191116.01X; RZPDo839H0876D N-myc downstream regulated gene 1 (NDRG1) gene, encodes complete protein.
KJ902098 - Synthetic construct Homo sapiens clone ccsbBroadEn_11492 NDRG1 gene, encodes complete protein.
KJ893025 - Synthetic construct Homo sapiens clone ccsbBroadEn_02419 NDRG1 gene, encodes complete protein.
DQ896199 - Synthetic construct Homo sapiens clone IMAGE:100010659; FLH191112.01L; RZPDo839H0866D N-myc downstream regulated gene 1 (NDRG1) gene, encodes complete protein.
AB529085 - Synthetic construct DNA, clone: pF1KB4166, Homo sapiens NDRG1 gene for N-myc downstream regulated 1, without stop codon, in Flexi system.
CR456842 - Homo sapiens full open reading frame cDNA clone RZPDo834C1011D for gene NDRG1, N-myc downstream regulated gene 1; complete cds, incl. stopcodon.
AK308117 - Homo sapiens cDNA, FLJ98065.
AF147402 - Homo sapiens full length insert cDNA clone YN54B03.
CU678420 - Synthetic construct Homo sapiens gateway clone IMAGE:100017172 5' read NDRG1 mRNA.
BX648361 - Homo sapiens mRNA; cDNA DKFZp686B09185 (from clone DKFZp686B09185).
AK307829 - Homo sapiens cDNA, FLJ97777.
AK297342 - Homo sapiens cDNA FLJ59927 complete cds, moderately similar to Protein NDRG1.
LF336996 - JP 2014500723-A/144499: Polycomb-Associated Non-Coding RNAs.
AF230380 - Homo sapiens N-myc downsteam regulated gene 1 (NDRG1) mRNA, partial cds.
LF212607 - JP 2014500723-A/20110: Polycomb-Associated Non-Coding RNAs.
JD256419 - Sequence 237443 from Patent EP1572962.
JD408865 - Sequence 389889 from Patent EP1572962.
JD391997 - Sequence 373021 from Patent EP1572962.
MA449602 - JP 2018138019-A/21528: Polycomb-Associated Non-Coding RNAs.
MA445872 - JP 2018138019-A/17798: Polycomb-Associated Non-Coding RNAs.
MA572565 - JP 2018138019-A/144491: Polycomb-Associated Non-Coding RNAs.
MA572566 - JP 2018138019-A/144492: Polycomb-Associated Non-Coding RNAs.
MA572567 - JP 2018138019-A/144493: Polycomb-Associated Non-Coding RNAs.
MA572568 - JP 2018138019-A/144494: Polycomb-Associated Non-Coding RNAs.
MA572569 - JP 2018138019-A/144495: Polycomb-Associated Non-Coding RNAs.
MA572573 - JP 2018138019-A/144499: Polycomb-Associated Non-Coding RNAs.
MA448184 - JP 2018138019-A/20110: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q92597 (Reactome details) participates in the following event(s):

R-HSA-6803205 TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain
R-HSA-5633008 TP53 Regulates Transcription of Cell Death Genes
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-212436 Generic Transcription Pathway
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B3KR80, B7Z446, CAP43, DRG1, ENST00000323851.1, ENST00000323851.10, ENST00000323851.11, ENST00000323851.12, ENST00000323851.2, ENST00000323851.3, ENST00000323851.4, ENST00000323851.5, ENST00000323851.6, ENST00000323851.7, ENST00000323851.8, ENST00000323851.9, NDRG1_HUMAN, NM_006096, O15207, Q6IBG2, Q92597, Q9NYR6, Q9UK29, RTP, uc317rnv.1, uc317rnv.2
UCSC ID: ENST00000323851.13_7
RefSeq Accession: NM_006096.4
Protein: Q92597 (aka NDRG1_HUMAN or NDR1_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene NDRG1:
cmt (Charcot-Marie-Tooth Hereditary Neuropathy Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.