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    NANOG Nanog homeobox [ Homo sapiens (human) ]

    Gene ID: 79923, updated on 9-Dec-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See NANOG in Genome Data Viewer
    Location:
    12p13.31
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (7789402..7799146)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (7803995..7813735)
    RS_2024_09 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

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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
    located_in 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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001297698.2NP_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:95151
      HOX; Homeodomain
    2. NM_024865.4NP_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:95151
      HOX; Homeodomain
      COG5576
      Location:74191
      COG5576; Homeodomain-containing transcription factor [Transcription]

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    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)