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    NANOG Nanog homeobox [ Homo sapiens (human) ]

    Gene ID: 79923, updated on 5-Mar-2024

    Summary

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    Official Symbol
    NANOGprovided by HGNC
    Official Full Name
    Nanog homeoboxprovided by HGNC
    Primary source
    HGNC:HGNC:20857
    See related
    Ensembl:ENSG00000111704 MIM:607937; AllianceGenome:HGNC:20857
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    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]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
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    Genomic context

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    Location:
    12p13.31
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (7789402..7799146)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (7803995..7813735)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (7941998..7951742)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene MPRA-validated peak1561 silencer Neighboring gene C-type lectin domain family 4 member C Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5920 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5921 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5922 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7918923-7919522 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7919523-7920122 Neighboring gene ReSE screen-validated silencer GRCh37_chr12:7924892-7925059 Neighboring gene NANOG neighbor homeobox Neighboring gene NANOG 5' regulatory region Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr12:7950942-7951507 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7951508-7952074 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7954393-7954894 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:7957389-7957910 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:7957911-7958430 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4204 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:7960397-7960896 Neighboring gene solute carrier family 2 member 14 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7978921-7979457 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:7986285-7986785 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7991923-7992596 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:7994866-7995750 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr12:8003712-8004911 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8012389-8013184 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:8013185-8013979 Neighboring gene MPRA-validated peak1563 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:8016225-8016726 Neighboring gene ribosomal protein S20 pseudogene 29 Neighboring gene myosin light chain 9 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Novel Roles of Nanog in Cancer Cells and Their Extracellular Vesicles. Saito M. Cells, 2022 Dec 1. PMID 36497144, Free PMC Article
    2. NANOG regulates epithelial-mesenchymal transition via AMPK/mTOR signalling pathway in ovarian cancer SKOV-3 and A2780 cells. Yun H, et al. J Cell Mol Med, 2022 Oct. PMID 36114703, Free PMC Article
    3. NANOG confers resistance to complement-dependent cytotoxicity in immune-edited tumor cells through up-regulating CD59. Son SW, et al. Sci Rep, 2022 May 23. PMID 35606403, Free PMC Article
    4. NANOG prion-like assembly mediates DNA bridging to facilitate chromatin reorganization and activation of pluripotency. Choi KJ, et al. Nat Cell Biol, 2022 May. PMID 35484250, Free PMC Article
    5. Nanog, as a key cancer stem cell marker in tumor progression. Vasefifar P, et al. Gene, 2022 Jun 15. PMID 35337852

    See all (337) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinicopathologic Impact of NANOG, ZEB1, and EpCAM Biomarkers on Prognosis of Serous Ovarian Carcinoma.
      Title: Clinicopathologic Impact of NANOG, ZEB1, and EpCAM Biomarkers on Prognosis of Serous Ovarian Carcinoma.
    2. High NANOG expression correlates with worse patients' survival in esophageal adenocarcinoma.
      Title: High NANOG expression correlates with worse patients' survival in esophageal adenocarcinoma.
    3. Prognostic Implications of CD24, SOX2, and Nanog Expression in Invasive Urothelial Carcinoma.
      Title: Prognostic Implications of CD24, SOX2, and Nanog Expression in Invasive Urothelial Carcinoma.
    4. SOX9 and HMGB3 co-operatively transactivate NANOG and promote prostate cancer progression.
      Title: SOX9 and HMGB3 co-operatively transactivate NANOG and promote prostate cancer progression.
    5. Immunoexpression of stem cell markers SOX-2, NANOG AND OCT4 in ameloblastoma.
      Title: Immunoexpression of stem cell markers SOX-2, NANOG AND OCT4 in ameloblastoma.
    6. Niche stiffness sustains cancer stemness via TAZ and NANOG phase separation.
      Title: Niche stiffness sustains cancer stemness via TAZ and NANOG phase separation.
    7. NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naive pluripotent stem cells.
      Title: NANOGP1, a tandem duplicate of NANOG, exhibits partial functional conservation in human naïve pluripotent stem cells.
    8. Novel Roles of Nanog in Cancer Cells and Their Extracellular Vesicles.
      Title: Novel Roles of Nanog in Cancer Cells and Their Extracellular Vesicles.
    9. NANOG regulates epithelial-mesenchymal transition via AMPK/mTOR signalling pathway in ovarian cancer SKOV-3 and A2780 cells.
      Title: NANOG regulates epithelial-mesenchymal transition via AMPK/mTOR signalling pathway in ovarian cancer SKOV-3 and A2780 cells.
    10. Altered immunoexpression of SOX2, OCT4 and Nanog in the normal-appearing oral mucosa of tobacco users.
      Title: Altered immunoexpression of SOX2, OCT4 and Nanog in the normal-appearing oral mucosa of tobacco users.
    Submit: New GeneRIF Correction See all GeneRIFs (309)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
    Inferred from Sequence Alignment
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell differentiation IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within endodermal cell fate specification IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of stem cell proliferation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in somatic stem cell population maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in stem cell population maintenance IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    involved_in stem cell population maintenance ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of chromatin ISA
    Inferred from Sequence Alignment
    more info
    		  
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus IC
    Inferred by Curator
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    homeobox protein NANOG
    Names
    homeobox transcription factor Nanog
    homeobox transcription factor Nanog-delta 48

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001297698.2 → NP_001284627.1  homeobox protein NANOG isoform 2

      See identical proteins and their annotated locations for NP_001284627.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC006517, AI656990, AY578089, DC425336
      Consensus CDS
      CCDS73436.1
      UniProtKB/TrEMBL
      A8K4D1
      Related
      ENSP00000435288.1, ENST00000526286.1
      Conserved Domains (1) summary
      smart00389
      Location:95 → 151
      HOX; Homeodomain

    2. NM_024865.4 → NP_079141.2  homeobox protein NANOG isoform 1

      See identical proteins and their annotated locations for NP_079141.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC006517, AI656990, AK290896, DC425336
      Consensus CDS
      CCDS31736.1
      UniProtKB/Swiss-Prot
      D3DUU4, Q2TTG0, Q6JZS5, Q9H9S0
      UniProtKB/TrEMBL
      A8K4D1
      Related
      ENSP00000229307.4, ENST00000229307.9
      Conserved Domains (2) summary
      smart00389
      Location:95 → 151
      HOX; Homeodomain
      COG5576
      Location:74 → 191
      COG5576; Homeodomain-containing transcription factor [Transcription]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      7789402..7799146
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      7803995..7813735
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H9S0.2 GenPept UniProtKB/Swiss-Prot:Q9H9S0

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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