Nanog Nanog homeobox [Mus musculus (house mouse)] - Gene

Summary

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

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_000072.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
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.
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.
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.
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.
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.
Phosphorylation of NANOG by casein kinase I regulates embryonic stem cell self-renewal.
Title: Phosphorylation of NANOG by casein kinase I regulates embryonic stem cell self-renewal.

Submit: New GeneRIF Correction See all GeneRIFs (204)

Variation

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Alleles

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

Gene trapped (2)
Targeted (7) 1 citation
Endonuclease-mediated (3)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Nanog (e-PCR), detects polymorphism
- UniSTS:516864

NoName (e-PCR)
- UniSTS:492058

D9Mit34.1 (e-PCR), detects polymorphism
- UniSTS:131903

Nanog (e-PCR), detects polymorphism
- UniSTS:474698

NoName (e-PCR)
- UniSTS:548460

Nanog (e-PCR), detects polymorphism
- UniSTS:498798

Nanog (e-PCR), detects polymorphism
- UniSTS:547697

Nanog (e-PCR), detects polymorphism
- UniSTS:256431

Enk-pending (e-PCR), detects polymorphism
- UniSTS:256432

Nanog (e-PCR), detects polymorphism
- UniSTS:502744

Nanog (e-PCR), detects polymorphism
- UniSTS:548072

Nanog (e-PCR), detects polymorphism
- UniSTS:546538

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
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
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 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 DNA-templated transcription	IEA Inferred from Electronic Annotation more info
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 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 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	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

Component	Evidence Code	Pubs
part_of 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)

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
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
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
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