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    Nanog Nanog homeobox [ Mus musculus (house mouse) ]

    Gene ID: 71950, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Nanogprovided by MGI
    Official Full Name
    Nanog homeoboxprovided by MGI
    Primary source
    MGI:MGI:1919200
    See related
    Ensembl:ENSMUSG00000012396 AllianceGenome:MGI:1919200
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    ENK; Stm1; ecat4; 2410002E02Rik
    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. Several 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
    human all
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    Genomic context

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    See Nanog in Genome Data Viewer
    Location:
    6 F1; 6 57.8 cM
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 6 NC_000072.7 (122684448..122691592)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 6 NC_000072.6 (122707489..122714633)

    Chromosome 6 - NC_000072.7Genomic Context describing neighboring genes Neighboring gene Nanog 5' regulatory region Neighboring gene predicted gene 10420 Neighboring gene predicted pseudogene 10224 Neighboring gene solute carrier family 2 (facilitated glucose transporter), member 3 Neighboring gene Nanog +60 enhancer Neighboring gene uridine-cytidine kinase 1 pseudogene Neighboring gene STARR-positive B cell enhancer ABC_E3679 Neighboring gene STARR-positive B cell enhancer ABC_E283 Neighboring gene predicted gene 5112

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. Identification and regulation of a stage-specific stem cell niche enriched by Nanog-positive spermatogonial stem cells in the mouse testis. Ventelä S, et al. Stem Cells, 2012 May. PMID 22388986
    2. Nanog retrotransposed genes with functionally conserved open reading frames. Robertson M, et al. Mamm Genome, 2006 Jul. PMID 16845474
    3. Reprogramming of mouse fibroblasts into induced pluripotent stem cells with Nanog. Moon JH, et al. Biochem Biophys Res Commun, 2013 Feb 15. PMID 23333380
    4. Chromatin decondensation and nuclear softening accompany Nanog downregulation in embryonic stem cells. Chalut KJ, et al. Biophys J, 2012 Nov 21. PMID 23200040, Free PMC Article
    5. OCT4/SOX2-independent Nanog autorepression modulates heterogeneous Nanog gene expression in mouse ES cells. Navarro P, et al. EMBO J, 2012 Dec 12. PMID 23178592, Free PMC Article

    See all (508) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The transcription factor OCT6 promotes the dissolution of the naive pluripotent state by repressing Nanog and activating a formative state gene regulatory network.
      Title: The transcription factor OCT6 promotes the dissolution of the naïve pluripotent state by repressing Nanog and activating a formative state gene regulatory network.
    2. Single-molecule tracking of Nanog and Oct4 in living mouse embryonic stem cells uncovers a feedback mechanism of pluripotency maintenance.
      Title: Single-molecule tracking of Nanog and Oct4 in living mouse embryonic stem cells uncovers a feedback mechanism of pluripotency maintenance.
    3. Embryonic stem cell ERK, AKT, plus STAT3 response dynamics combinatorics are heterogeneous but NANOG state independent.
      Title: Embryonic stem cell ERK, AKT, plus STAT3 response dynamics combinatorics are heterogeneous but NANOG state independent.
    4. Epigenetic regulation of pluripotency inducer genes NANOG and SOX2 in human prostate cancer.
      Title: Epigenetic regulation of pluripotency inducer genes NANOG and SOX2 in human prostate cancer.
    5. Trim28 citrullination maintains mouse embryonic stem cell pluripotency via regulating Nanog and Klf4 transcription.
      Title: Trim28 citrullination maintains mouse embryonic stem cell pluripotency via regulating Nanog and Klf4 transcription.
    6. H3K9 tri-methylation at Nanog times differentiation commitment and enables the acquisition of primitive endoderm fate.
      Title: H3K9 tri-methylation at Nanog times differentiation commitment and enables the acquisition of primitive endoderm fate.
    7. LC3B upregulation by NANOG promotes immune resistance and stem-like property through hyperactivation of EGFR signaling in immune-refractory tumor cells.
      Title: LC3B upregulation by NANOG promotes immune resistance and stem-like property through hyperactivation of EGFR signaling in immune-refractory tumor cells.
    8. Long noncoding RNA lnc-NAP sponges mmu-miR-139-5p to modulate Nanog functions in mouse ESCs and embryos.
      Title: Long noncoding RNA lnc-NAP sponges mmu-miR-139-5p to modulate Nanog functions in mouse ESCs and embryos.
    9. Genome editing demonstrates that the -5 kb Nanog enhancer regulates Nanog expression by modulating RNAPII initiation and/or recruitment.
      Title: Genome editing demonstrates that the -5 kb Nanog enhancer regulates Nanog expression by modulating RNAPII initiation and/or recruitment.
    10. Effect of Nanog overexpression on the metastatic potential of a mouse melanoma cell line B16-BL6.
      Title: Effect of Nanog overexpression on the metastatic potential of a mouse melanoma cell line B16-BL6.
    Submit: New GeneRIF Correction See all GeneRIFs (205)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (3) 
    • Gene trapped (2) 
    • Targeted (8)  1 citation

    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 MGI

    Function Evidence Code Pubs
    enables DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables DNA-binding transcription repressor activity, RNA polymerase II-specific IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables lysine-acetylated histone binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables sequence-specific DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables sequence-specific double-stranded DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription cis-regulatory region binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables transcription cis-regulatory region binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables transcription factor binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    acts_upstream_of BMP signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cell dedifferentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in cellular response to erythropoietin IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cellular response to rapamycin IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within embryo development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in embryonic pattern specification IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within endodermal cell fate specification ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    involved_in gene expression IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in gonad development IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of mesodermal cell fate commitment IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of mesodermal cell fate commitment IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within mesodermal cell fate commitment IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in multidimensional cell growth IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within negative regulation of BMP signaling pathway IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of cell fate commitment IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of cell fate commitment IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in negative regulation of endodermal cell fate specification TAS
    Traceable Author Statement
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of stem cell differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of DNA-templated transcription IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of cell population proliferation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of mitotic cell cycle IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    involved_in regulation of stem cell division IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within response to retinoic acid IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within somatic stem cell population maintenance IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within somatic stem cell population maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of stem cell differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within stem cell differentiation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_or_within stem cell differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within stem cell division IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in stem cell population maintenance IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in stem cell population maintenance IEP
    Inferred from Expression Pattern
    more info
    		 PubMed 
    acts_upstream_of_or_within stem cell population maintenance IGI
    Inferred from Genetic Interaction
    more info
    		 PubMed 
    involved_in stem cell population maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in tissue regeneration IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in chromatin IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    NOT located_in condensed chromosome IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    homeobox protein NANOG
    Names
    ES cell-associated protein 4
    early embryo specific expression NK family
    early embryo specific expression NK-type homeobox protein
    homeobox transcription factor Nanog

    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_001289828.1 → NP_001276757.1  homeobox protein NANOG isoform 2

      See identical proteins and their annotated locations for NP_001276757.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. It encodes isoform 2, which is shorter than isoform 1.
      Source sequence(s)
      AK167259, AY455282, AY455285, BC144995, BY382803
      UniProtKB/Swiss-Prot
      Q5TM83
      UniProtKB/TrEMBL
      B7ZN41
      Conserved Domains (1) summary
      smart00389
      Location:96 → 152
      HOX; Homeodomain

    2. NM_001289830.1 → NP_001276759.1  homeobox protein NANOG isoform 3

      See identical proteins and their annotated locations for NP_001276759.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3, also known as Nanog1b) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. Variants 3 and 4 encode the same isoform (3), which has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK167259, AY455282, AY455285, BY382803
      Consensus CDS
      CCDS80607.1
      UniProtKB/Swiss-Prot
      Q5TM83
      Related
      ENSMUSP00000108199.2, ENSMUST00000112580.8
      Conserved Domains (1) summary
      smart00389
      Location:71 → 127
      HOX; Homeodomain

    3. NM_001289831.1 → NP_001276760.1  homeobox protein NANOG isoform 3

      See identical proteins and their annotated locations for NP_001276760.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4, also known as Nanog1a) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon, compared to variant 1. Variants 3 and 4 encode the same isoform (3), which has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AK167259, AY455282, BY382803
      Consensus CDS
      CCDS80607.1
      UniProtKB/Swiss-Prot
      Q5TM83
      Related
      ENSMUSP00000108200.2, ENSMUST00000112581.8
      Conserved Domains (1) summary
      smart00389
      Location:71 → 127
      HOX; Homeodomain

    4. NM_028016.3 → NP_082292.1  homeobox protein NANOG isoform 1

      See identical proteins and their annotated locations for NP_082292.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AK167259, AY455285, BC144995, BY382803
      Consensus CDS
      CCDS39623.1
      UniProtKB/Swiss-Prot
      Q5TM83, Q6SMR1, Q7TN85, Q80Z64
      UniProtKB/TrEMBL
      A2RS90
      Related
      ENSMUSP00000012540.4, ENSMUST00000012540.5
      Conserved Domains (1) summary
      smart00389
      Location:96 → 152
      HOX; Homeodomain

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000072.7 Reference GRCm39 C57BL/6J

      Range
      122684448..122691592
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5TM83.1 GenPept UniProtKB/Swiss-Prot:Q5TM83
    Q80Z64.1 GenPept UniProtKB/Swiss-Prot:Q80Z64

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
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