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Nanog Nanog homeobox [ Mus musculus (house mouse) ]

Gene ID: 71950, updated on 16-Oct-2021

Summary

Official Symbol
Nanogprovided by MGI
Official Full Name
Nanog homeoboxprovided by MGI
Primary source
MGI:MGI:1919200
See related
Ensembl:ENSMUSG00000012396
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; 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
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Genomic context

See Nanog in Genome Data Viewer
Location:
6; 6 F1
Exon count:
5
Annotation release Status Assembly Chr Location
109 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)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 6 NC_000072.5 (122657586..122663796)

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

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
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
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 cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables identical protein binding IPI
Inferred from Physical Interaction
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
involved_in cell dedifferentiation IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within embryo development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within 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 
acts_upstream_of_or_within gonad development IEP
Inferred from Expression Pattern
more info
PubMed 
acts_upstream_of_or_within mesodermal cell fate commitment IGI
Inferred from Genetic Interaction
more info
PubMed 
acts_upstream_of_or_within multicellular organism development 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 differentiation 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 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
 
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 positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
involved_in positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
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
PubMed 
involved_in regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within response to organic substance IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within response to retinoic acid 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 
acts_upstream_of_or_within stem cell population maintenance IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within 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 
acts_upstream_of_or_within stem cell population maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in stem cell population maintenance IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
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
 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 

General protein information

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_001289828.1NP_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
    smart00389
    Location:96152
    HOX; Homeodomain
  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
    ENSMUSP00000108199.2, ENSMUST00000112580.8
    Conserved Domains (1) summary
    smart00389
    Location:71127
    HOX; Homeodomain
  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
    ENSMUSP00000108200.2, ENSMUST00000112581.8
    Conserved Domains (1) summary
    smart00389
    Location:71127
    HOX; Homeodomain
  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
    ENSMUSP00000012540.4, ENSMUST00000012540.5
    Conserved Domains (1) summary
    smart00389
    Location:96152
    HOX; Homeodomain

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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)
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