Human Gene NANOG (ENST00000229307.9) from GENCODE V44
  Description: Homo sapiens Nanog homeobox (NANOG), transcript variant 1, mRNA. (from RefSeq NM_024865)
RefSeq Summary (NM_024865): The protein encoded by this gene is a DNA binding homeobox transcription factor involved in embryonic stem (ES) cell proliferation, renewal, and pluripotency. The encoded protein can block ES cell differentiation and can also autorepress its own expression in differentiating cells. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2015].
Gencode Transcript: ENST00000229307.9
Gencode Gene: ENSG00000111704.11
Transcript (Including UTRs)
   Position: hg38 chr12:7,789,402-7,799,146 Size: 9,745 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg38 chr12:7,789,615-7,795,095 Size: 5,481 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:7,789,402-7,799,146)mRNA (may differ from genome)Protein (305 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: NANOG_HUMAN
DESCRIPTION: RecName: Full=Homeobox protein NANOG; AltName: Full=Homeobox transcription factor Nanog; Short=hNanog;
FUNCTION: Transcription regulator involved in inner cell mass and embryonic stem (ES) cells proliferation and self-renewal. Imposes pluripotency on ES cells and prevents their differentiation towards extraembryonic endoderm and trophectoderm lineages. Blocks bone morphogenetic protein-induced mesoderm differentiation of ES cells by physically interacting with SMAD1 and interfering with the recruitment of coactivators to the active SMAD transcriptional complexes. Acts as a transcriptional activator or repressor. Binds optimally to the DNA consensus sequence 5'-TAAT[GT][GT]-3' or 5'- [CG][GA][CG]C[GC]ATTAN[GC]-3'. Able to autorepress its expression in differentiating (ES) cells: binds to its own promoter following interaction with ZNF281/ZFP281, leading to recruitment of the NuRD complex and subsequent repression of expression. When overexpressed, promotes cells to enter into S phase and proliferation.
SUBUNIT: Interacts with SMAD1 and SALL4. Interacts with ZNF281/ZFP281 (By similarity).
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed in testicular carcinoma and derived germ cell tumors (at protein level). Expressed in fetal gonads, ovary and testis. Also expressed in ovary teratocarcinoma cell line and testicular embryonic carcinoma. Not expressed in many somatic organs and oocytes.
DEVELOPMENTAL STAGE: Expressed in embryonic stem (ES) and carcinoma (EC) cells. Expressed in inner cell mass (ICM) of the blastocyst and gonocytes between 14 and 19 weeks of gestation (at protein level). Not expressed in oocytes, unfertilized oocytes, 2- 16 cell embryos and early morula (at protein level). Expressed in embryonic stem cells (ES). Expression decreases with ES differentiation.
MISCELLANEOUS: Exists an other tandem duplicated non-processed pseudogene (NANOGP1) and 10 other NANOG-related nucleotide sequences located on different chromosomes, all of which are processed pseudogenes lacking introns (NANOGP2 to NANOGP11); except NANOGP8 which is a retrogene.
SIMILARITY: Belongs to the Nanog homeobox family.
SIMILARITY: Contains 1 homeobox DNA-binding domain.
WEB RESOURCE: Name=Wikipedia; Note=Nanog entry; URL="http://en.wikipedia.org/wiki/Nanog";

-  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: NANOG
Diseases sorted by gene-association score: teratocarcinoma (7), germ cell and embryonal cancer (2), ovarian embryonal carcinoma (2), venous hemangioma (2), extragonadal seminoma (1), n syndrome (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 0.38 RPKM in Testis
Total median expression: 2.34 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 -44.20213-0.208 Picture PostScript Text
3' UTR -1537.904051-0.380 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
IPR017970 - Homeobox_CS
IPR001356 - Homeodomain
IPR009057 - Homeodomain-like

Pfam Domains:
PF00046 - Homeobox domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2KT0 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q9H9S0
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001228 transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA binding
GO:0003714 transcription corepressor activity
GO:0005515 protein binding
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding

Biological Process:
GO:0001714 endodermal cell fate specification
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006366 transcription from RNA polymerase II promoter
GO:0007275 multicellular organism development
GO:0008283 cell proliferation
GO:0010468 regulation of gene expression
GO:0019221 cytokine-mediated signaling pathway
GO:0019827 stem cell population maintenance
GO:0030154 cell differentiation
GO:0035019 somatic stem cell population maintenance
GO:0045595 regulation of cell differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:1903507 negative regulation of nucleic acid-templated transcription

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  AB093576 - Homo sapiens mRNA for homeobox transcription factor Nanog, complete cds.
AK022643 - Homo sapiens cDNA FLJ12581 fis, clone NT2RM4001140, weakly similar to HOMEOBOX PROTEIN MSH-D.
JD500863 - Sequence 481887 from Patent EP1572962.
AK290896 - Homo sapiens cDNA FLJ78395 complete cds, highly similar to Homo sapiens Nanog homeobox (NANOG), mRNA.
BC098275 - Homo sapiens Nanog homeobox pseudogene 8, mRNA (cDNA clone IMAGE:40004923).
BC099704 - Homo sapiens Nanog homeobox pseudogene 8, mRNA (cDNA clone IMAGE:40004920).
BC069807 - Homo sapiens Nanog homeobox pseudogene 8, mRNA (cDNA clone IMAGE:7262621).
JD101724 - Sequence 82748 from Patent EP1572962.
BC160187 - Synthetic construct Homo sapiens clone IMAGE:100064219, MGC:193302 Nanog homeobox (NANOG) mRNA, encodes complete protein.
AY230262 - Homo sapiens NANOG mRNA, partial cds.
AY578089 - Homo sapiens homeobox transcription factor Nanog-delta 48 mRNA, complete cds.
JD308569 - Sequence 289593 from Patent EP1572962.
JD526509 - Sequence 507533 from Patent EP1572962.
JD530845 - Sequence 511869 from Patent EP1572962.
JD530844 - Sequence 511868 from Patent EP1572962.
JD521534 - Sequence 502558 from Patent EP1572962.
JD402469 - Sequence 383493 from Patent EP1572962.
JD538990 - Sequence 520014 from Patent EP1572962.
JD085652 - Sequence 66676 from Patent EP1572962.
JD070105 - Sequence 51129 from Patent EP1572962.
JD070104 - Sequence 51128 from Patent EP1572962.
JD397731 - Sequence 378755 from Patent EP1572962.
JD203793 - Sequence 184817 from Patent EP1572962.
JD318202 - Sequence 299226 from Patent EP1572962.
JD322109 - Sequence 303133 from Patent EP1572962.
JD152118 - Sequence 133142 from Patent EP1572962.
JD476957 - Sequence 457981 from Patent EP1572962.
JD476956 - Sequence 457980 from Patent EP1572962.
JD416475 - Sequence 397499 from Patent EP1572962.
JD416476 - Sequence 397500 from Patent EP1572962.
JD371986 - Sequence 353010 from Patent EP1572962.
JD505831 - Sequence 486855 from Patent EP1572962.
JD087239 - Sequence 68263 from Patent EP1572962.
JD063198 - Sequence 44222 from Patent EP1572962.
JD565599 - Sequence 546623 from Patent EP1572962.
JD257449 - Sequence 238473 from Patent EP1572962.
JD295629 - Sequence 276653 from Patent EP1572962.
JD295169 - Sequence 276193 from Patent EP1572962.
JD562924 - Sequence 543948 from Patent EP1572962.
JD254679 - Sequence 235703 from Patent EP1572962.
JD075157 - Sequence 56181 from Patent EP1572962.
JD441772 - Sequence 422796 from Patent EP1572962.
JD329863 - Sequence 310887 from Patent EP1572962.
JD179138 - Sequence 160162 from Patent EP1572962.
JD179139 - Sequence 160163 from Patent EP1572962.
JD074887 - Sequence 55911 from Patent EP1572962.

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

Protein Q9H9S0 (Reactome details) participates in the following event(s):

R-HSA-480204 POU5F1 (OCT4), SOX2, NANOG, KLF4, PBX1, SMAD2 bind the NANOG promoter
R-HSA-480685 POU5F1 (OCT4), SOX2, NANOG bind the SOX2 promoter
R-HSA-1112609 POU5F1 (OCT4), SOX2, NANOG, ZSCAN10, PRDM14, SMAD2, FOXP1-ES bind the POU5F1 (OCT4) promoter
R-HSA-2972948 POU5F1 (OCT4), SOX2, NANOG bind the GSC promoter
R-HSA-2972949 POU5F1 (OCT4), SOX2, NANOG bind the EOMES promoter
R-HSA-2972952 POU5F1 (OCT4), NANOG bind the GATA6 promoter
R-HSA-2972956 POU5F1 (OCT4), SOX2, NANOG bind the STAT3 promoter
R-HSA-2972960 POU5F1 (OCT4), SOX2, NANOG bind the FGF2 promoter
R-HSA-2972962 POU5F1 (OCT4), SOX2, NANOG bind the TDGF1 promoter
R-HSA-2972964 POU5F1 (OCT4), SOX2, NANOG bind the FOXD3 promoter
R-HSA-2972965 POU5F1 (OCT4), SOX2, NANOG bind the TSC22D1 promoter
R-HSA-2972966 POU5F1 (OCT4), SOX2, NANOG bind the HHEX promoter
R-HSA-2972967 POU5F1 (OCT4), SOX2, NANOG bind the EPHA1 promoter
R-HSA-2972975 POU5F1 (OCT4), SOX2, NANOG Bind the SALL1 Promoter
R-HSA-2972977 POU5F1 (OCT4), SOX2, NANOG bind the DKK1 promoter
R-HSA-2972978 POU5F1 (OCT4), SOX2, NANOG bind the ZIC3 promoter
R-HSA-2972979 POU5F1 (OCT4), NANOG bind the CDX2 promoter
R-HSA-6800120 POU5F1 (OCT4), SOX2, NANOG bind DPPA4 gene
R-HSA-452723 Transcriptional regulation of pluripotent stem cells
R-HSA-2892245 POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiation
R-HSA-2892247 POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation
R-HSA-6785807 Interleukin-4 and 13 signaling
R-HSA-1266738 Developmental Biology
R-HSA-449147 Signaling by Interleukins
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: D3DUU4, ENST00000229307.1, ENST00000229307.2, ENST00000229307.3, ENST00000229307.4, ENST00000229307.5, ENST00000229307.6, ENST00000229307.7, ENST00000229307.8, NANOG_HUMAN, NM_024865, Q2TTG0, Q6JZS5, Q9H9S0, uc009zfy.1, uc009zfy.2, uc009zfy.3
UCSC ID: ENST00000229307.9
RefSeq Accession: NM_024865
Protein: Q9H9S0 (aka NANOG_HUMAN)
CCDS: CCDS31736.1

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