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Nanog Nanog homeobox [ Mus musculus (house mouse) ]

Gene ID: 71950, updated on 28-May-2016
Official Symbol
Nanogprovided by MGI
Official Full Name
Nanog homeoboxprovided by MGI
Primary source
MGI:MGI:1919200
See related
Ensembl:ENSMUSG00000012396 Vega:OTTMUSG00000023511
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
ENK; 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]
Orthologs
Location:
6; 6 F2
Exon count:
7
Annotation release Status Assembly Chr Location
105 current GRCm38.p3 (GCF_000001635.23) 6 NC_000072.6 (122706483..122714633)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 6 NC_000072.5 (122657586..122663796)

Chromosome 6 - NC_000072.6Genomic Context describing neighboring genes Neighboring gene predicted gene 8460 Neighboring gene predicted pseudogene 10224 Neighboring gene solute carrier family 2 (facilitated glucose transporter), member 3 Neighboring gene uridine-cytidine kinase 1 pseudogene Neighboring gene forkhead box J2 Neighboring gene microRNA 7231

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • PluriNetWork, organism-specific biosystem (from WikiPathways)
    PluriNetWork, organism-specific biosystemThe aim of the PluriNetWork is to give an overview of specific mechanisms associated with pluripotency in mouse. Each node represents a gene and its corresponding protein product. As stated, we inten...
  • Proteoglycans in cancer, organism-specific biosystem (from KEGG)
    Proteoglycans in cancer, organism-specific biosystemMany proteoglycans (PGs) in the tumor microenvironment have been shown to be key macromolecules that contribute to biology of various types of cancer including proliferation, adhesion, angiogenesis a...
  • Proteoglycans in cancer, conserved biosystem (from KEGG)
    Proteoglycans in cancer, conserved biosystemMany proteoglycans (PGs) in the tumor microenvironment have been shown to be key macromolecules that contribute to biology of various types of cancer including proliferation, adhesion, angiogenesis a...
  • Signaling pathways regulating pluripotency of stem cells, organism-specific biosystem (from KEGG)
    Signaling pathways regulating pluripotency of stem cells, organism-specific biosystemPluripotent stem cells (PSCs) are basic cells with an indefinite self-renewal capacity and the potential to generate all the cell types of the three germinal layers. The types of PSCs known to date i...
  • Signaling pathways regulating pluripotency of stem cells, conserved biosystem (from KEGG)
    Signaling pathways regulating pluripotency of stem cells, conserved biosystemPluripotent stem cells (PSCs) are basic cells with an indefinite self-renewal capacity and the potential to generate all the cell types of the three germinal layers. The types of PSCs known to date i...
  • Wnt Signaling Pathway and Pluripotency, organism-specific biosystem (from WikiPathways)
    Wnt Signaling Pathway and Pluripotency, organism-specific biosystemThis pathway was adapted from several resources and is designed to provide a theoretical frame-work for examining Wnt signaling and interacting components in the context of embryonic stem-cell pluri...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA binding ISO
Inferred from Sequence Orthology
more info
 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
enhancer sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription corepressor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription factor activity, sequence-specific DNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription factor activity, sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
transcription regulatory region DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
cell proliferation ISO
Inferred from Sequence Orthology
more info
 
embryo development IMP
Inferred from Mutant Phenotype
more info
PubMed 
endodermal cell fate specification ISO
Inferred from Sequence Orthology
more info
PubMed 
mesodermal cell fate commitment IGI
Inferred from Genetic Interaction
more info
PubMed 
multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
negative regulation of BMP signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell fate commitment IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of cell fate commitment IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of endodermal cell fate specification TAS
Traceable Author Statement
more info
PubMed 
negative regulation of transcription from RNA polymerase II promoter IGI
Inferred from Genetic Interaction
more info
PubMed 
negative regulation of transcription from RNA polymerase II promoter IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription from RNA polymerase II promoter ISO
Inferred from Sequence Orthology
more info
 
positive regulation of cell proliferation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of mitotic cell cycle IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription from RNA polymerase II promoter IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription from RNA polymerase II promoter ISO
Inferred from Sequence Orthology
more info
PubMed 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of cell differentiation ISO
Inferred from Sequence Orthology
more info
 
regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
regulation of stem cell population maintenance IGI
Inferred from Genetic Interaction
more info
PubMed 
regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
response to organic substance IDA
Inferred from Direct Assay
more info
PubMed 
response to retinoic acid IDA
Inferred from Direct Assay
more info
PubMed 
somatic stem cell population maintenance ISO
Inferred from Sequence Orthology
more info
 
stem cell differentiation IDA
Inferred from Direct Assay
more info
PubMed 
stem cell differentiation IMP
Inferred from Mutant Phenotype
more info
PubMed 
stem cell division IDA
Inferred from Direct Assay
more info
PubMed 
stem cell population maintenance IDA
Inferred from Direct Assay
more info
PubMed 
stem cell population maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleolus ISO
Inferred from Sequence Orthology
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus ISO
Inferred from Sequence Orthology
more info
 
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

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_001289828.1NP_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
    Q80Z64
    UniProtKB/TrEMBL
    B7ZN41
    Conserved Domains (1) summary
    cd00086
    Location:98155
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
  2. NM_001289830.1NP_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
    Q80Z64
    Related
    ENSMUSP00000108199, OTTMUSP00000027614, ENSMUST00000112580, OTTMUST00000057271
    Conserved Domains (1) summary
    cd00086
    Location:73130
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
  3. NM_001289831.1NP_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
    Q80Z64
    Related
    ENSMUSP00000108200, OTTMUSP00000027615, ENSMUST00000112581, OTTMUST00000057272
    Conserved Domains (1) summary
    cd00086
    Location:73130
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
  4. NM_028016.3NP_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
    Q80Z64
    UniProtKB/TrEMBL
    A2RS90, B7ZN41
    Related
    ENSMUSP00000012540, OTTMUSP00000027613, ENSMUST00000012540, OTTMUST00000057270
    Conserved Domains (1) summary
    cd00086
    Location:98155
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 105 details...

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

Reference GRCm38.p3 C57BL/6J

Genomic

  1. NC_000072.6 Reference GRCm38.p3 C57BL/6J

    Range
    122706483..122714633
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006506651.2XP_006506714.1  

    See identical proteins and their annotated locations for XP_006506714.1

    UniProtKB/Swiss-Prot
    Q80Z64
    UniProtKB/TrEMBL
    A2RS90
    Conserved Domains (1) summary
    cd00086
    Location:98155
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
  2. XM_011241471.1XP_011239773.1  

    Conserved Domains (1) summary
    cd00086
    Location:109166
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
  3. XM_011241472.1XP_011239774.1  

    Conserved Domains (1) summary
    cd00086
    Location:109166
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
  4. XM_011241473.1XP_011239775.1  

    Conserved Domains (1) summary
    cd00086
    Location:90147
    homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

Alternate Mm_Celera

Genomic

  1. AC_000028.1 Alternate Mm_Celera

    Range
    124507713..124515165
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)