Nanog (Nanog homeobox) - Rat Genome Database

Name: Nanog
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Nanog (Nanog homeobox) Chinchilla lanigera

Analyze

Symbol:

Nanog

Name:

Nanog homeobox

RGD ID:

8988473

Description:

ENCODES a protein that exhibits chromatin binding (ortholog); DNA binding (ortholog); DNA-binding transcription activator activity, RNA polymerase II-specific (ortholog); INVOLVED IN BMP signaling pathway (ortholog); cell dedifferentiation (ortholog); cell differentiation (ortholog); PARTICIPATES IN DNA modification pathway; ASSOCIATED WITH colon cancer (ortholog); developmental and epileptic encephalopathy 21 (ortholog); Germ Cell and Embryonal Neoplasms (ortholog); FOUND IN chromatin (ortholog); condensed chromosome (ortholog); intracellular membrane-bounded organelle (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

homeobox protein NANOG

RGD Orthologs

Alliance Orthologs

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	NANOG (Nanog homeobox)	NCBI	Ortholog
Mus musculus (house mouse):	Nanog (Nanog homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Nanog (Nanog homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	NANOG (Nanog homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	NANOG (Nanog homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Nanog (Nanog homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	NANOG (Nanog homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	NANOG (Nanog homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Nanog (Nanog homeobox)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

ChiLan1.0 - Chinchilla ChiLan1.0 Assembly

Position:

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0	NW_004955413	6,561,323 - 6,565,770 (+)	NCBI	ChiLan1.0	ChiLan1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

colon cancer (ISO)

developmental and epileptic encephalopathy 21 (ISO)

Germ Cell and Embryonal Neoplasms (ISO)

Hyperphosphatemic Familial Tumoral Calcinosis 1 (ISO)

Klippel-Feil syndrome 3 (ISO)

lymphoproliferative syndrome 2 (ISO)

Neoplastic Cell Transformation (ISO)

Parkinson's disease (ISO)

peroxisome biogenesis disorder 2B (ISO)

Temtamy syndrome (ISO)

teratoma (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

BMP signaling pathway (ISO)

cell dedifferentiation (ISO)

cell differentiation (ISO)

cellular response to erythropoietin (ISO)

cellular response to rapamycin (ISO)

embryonic pattern specification (ISO)

endodermal cell fate specification (ISO)

gene expression (ISO)

gonad development (ISO)

mesodermal cell fate commitment (ISO)

multidimensional cell growth (ISO)

negative regulation of BMP signaling pathway (ISO)

negative regulation of cell fate commitment (ISO)

negative regulation of stem cell differentiation (ISO)

negative regulation of transcription by RNA polymerase II (ISO)

positive regulation of cell population proliferation (ISO)

positive regulation of DNA-templated transcription (ISO)

positive regulation of mitotic cell cycle (ISO)

positive regulation of stem cell proliferation (ISO)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of cell differentiation (ISO)

regulation of DNA-templated transcription (ISO)

regulation of gene expression (ISO)

regulation of stem cell division (ISO)

response to organic cyclic compound (ISO)

response to retinoic acid (ISO)

somatic stem cell population maintenance (ISO)

stem cell differentiation (ISO)

stem cell division (ISO)

stem cell population maintenance (ISO)

tissue regeneration (ISO)

Cellular Component

chromatin (ISO)

condensed chromosome (ISO)

intracellular membrane-bounded organelle (ISO)

nucleolus (ISO)

nucleoplasm (ISO)

nucleus (ISO)

Molecular Function

chromatin binding (ISO)

DNA binding (ISO)

DNA-binding transcription activator activity, RNA polymerase II-specific (ISO)

DNA-binding transcription factor activity (ISO)

DNA-binding transcription repressor activity, RNA polymerase II-specific (ISO)

identical protein binding (ISO)

lysine-acetylated histone binding (ISO)

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (ISO)

RNA polymerase II sequence-specific DNA-binding transcription factor recruiting activity (ISO)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (ISO)

sequence-specific DNA binding (ISO)

sequence-specific double-stranded DNA binding (ISO)

transcription cis-regulatory region binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

DNA modification pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Transitive Annotation Pipeline	Automated assignment of GO, PW and RDO ISO annotations across species

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Nanog
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0	NW_004955413	6,561,323 - 6,565,770 (+)	NCBI	ChiLan1.0	ChiLan1.0

NANOG
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	12	7,789,402 - 7,799,146 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	12	7,787,794 - 7,799,146 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	12	7,941,998 - 7,951,742 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	12	7,833,262 - 7,839,922 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	12	7,833,261 - 7,839,922	NCBI
Celera	12	9,520,085 - 9,526,744 (+)	NCBI		Celera
Cytogenetic Map	12	p13.31	NCBI
HuRef	12	7,755,619 - 7,762,294 (+)	NCBI		HuRef
CHM1_1	12	7,941,303 - 7,947,961 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	12	7,803,995 - 7,813,735 (+)	NCBI		T2T-CHM13v2.0

Nanog
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	122,684,448 - 122,691,592 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	122,684,448 - 122,691,592 (+)	Ensembl		GRCm39 Ensembl
GRCm38	6	122,707,489 - 122,714,633 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	122,707,489 - 122,714,633 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	122,657,586 - 122,663,796 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	6	122,673,114 - 122,680,252 (+)	NCBI		MGSCv36	mm8
Celera	6	124,507,792 - 124,514,310 (+)	NCBI		Celera
Cytogenetic Map	6	F1	NCBI
cM Map	6	57.8	NCBI

Nanog
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	157,615,687 - 157,623,061 (+)	NCBI		GRCr8
mRatBN7.2	4	155,943,737 - 155,951,116 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	155,943,737 - 155,951,116 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	4	162,211,480 - 162,218,867 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	186,563,349 - 186,570,736 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	156,639,759 - 156,647,147 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	155,531,906 - 155,539,268 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	155,531,906 - 155,539,268 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	222,552,995 - 222,560,653 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	159,190,786 - 159,198,160 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	4	159,438,699 - 159,441,754 (+)	NCBI
Celera	4	144,763,722 - 144,771,060 (+)	NCBI		Celera
Cytogenetic Map	4	q42	NCBI

NANOG
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	10	13,347,790 - 13,354,739 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	12	13,344,549 - 13,351,498 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	12	7,913,037 - 7,919,715 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	12	8,070,877 - 8,077,556 (+)	NCBI	panpan1.1	PanPan1.1	panPan2

NANOG
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	27	37,262,558 - 37,266,449 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	27	9,348,312 - 9,354,207 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	27	37,614,640 - 37,620,732 (+)	NCBI		ROS_Cfam_1.0
UMICH_Zoey_3.1	27	37,494,510 - 37,500,598 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	27	37,530,317 - 37,536,638 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	27	8,831,817 - 8,837,819 (-)	NCBI		UU_Cfam_GSD_1.0

Nanog
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024404945	98,997,260 - 99,003,117 (+)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936892	181,834 - 187,691 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

NANOG
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	5	62,932,382 - 62,939,082 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	5	62,931,642 - 62,939,086 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	5	65,798,046 - 65,843,373 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

NANOG
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	11	7,813,309 - 7,820,009 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666063	363,373 - 369,814 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Nanog
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624860	5,026,203 - 5,037,219 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_005379613	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AGCD01013754	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBDF01115089	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

XM_005379613 ⟹ XP_005379670

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955413	6,561,323 - 6,565,770 (+)	NCBI

Sequence:

show sequence

ATGAACATGGAGAACAATAGCCAGTCAGCCTCTCCCCTCCCTTCCTCCGGGGACCTGCTCACTC
AGGCAACCCCCGACTCCTCCACCAGCCCCTGCGTCACCAGCCCCTGCGTCGCCCTGCCTGGCTC
CCTGGAGTCCTCGGGCAGGAAGGAGGAGGCGGCGAAGGTCCCGGCGAAGAAGCAGAAGGTACGC
ACGGTCTTCTCACAGACGCAGCTGTGCGTGCTCAACGACCGCTTCCAGAGGCAGAAGTACCTCA
GCCTGCAGCAGATGCAGGAGCTCTCCAGCCTCCTGAACCTCAGCTACAAGCAGGTTAAGACCTG
GTTCCAAAATCAGAGAATGAAATGTAAGAGGTGGCAGAAAAGCAACTGGCCGAAGAGCAGCGCC
GGTGCATCTCAGACGGGCCCGGCCTCTGCTGAGTACCCAGGCTCCAACTACACCCAGGGCTGCA
TGGTGAACACATCCGGGAACTTTCCCGTGTGGGGCAACCAGACCTGGAACAGCCCAACGTGGAG
CAGCCAGTCATGGAGCAACCACTCCTGGAACACGCAGACCTGGAACACACAGACCTGGAACGCG
CAGACCTGGAACACGCAGACCTGGTACCCCCAAGGCTGGAACTCCTTCCCTGCTGGCGGTGAGG
AGTCGCTGCAGCCCTGCCTGCCCTTGCCGCAGAATTTCTCCGCCAGTGACTTGGAGGCCACCCT
GGAAGCAGCTGGGGACGGCCACAAGTACTTCAACACCCCCCAGGCCCTGGATCTGTTCCTGAAT
TATGCCATGAACCTGCAGCCTGAAGATCTATGAAAGCGAGGTTCCCTCCCTCCCGCACAGGGTT
TTGCTGTTGGTTTTAGGGTGGTGCTGGATTTCTCGGGGTCCCGGTTCTCACTGGGCCTGTTGTG
ACGACGCGGGGTGTGGGCAGGACTGGAGACGGAAGGAGGAGGCTGTAGTGACCTCGTGTGCTGC
AGGCAGGCAGTGTCTGGGTATCAAGCAGCCACCAGACACCGTCGGACCTCTGGGTGGAGAACCC
AACCTCAAGGCGGGGGGACACGGCTGTGGTGAAGCATCATTCCTGTTTGCAGGAAGTGGA

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Protein Sequences


Protein RefSeqs	XP_005379670	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCLAP00000024395.1

RefSeq Acc Id:

XP_005379670 ⟸ XM_005379613

- UniProtKB:

A0A8C2W530 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MNMENNSQSASPLPSSGDLLTQATPDSSTSPCVTSPCVALPGSLESSGRKEEAAKVPAKKQKVR
TVFSQTQLCVLNDRFQRQKYLSLQQMQELSSLLNLSYKQVKTWFQNQRMKCKRWQKSNWPKSSA
GASQTGPASAEYPGSNYTQGCMVNTSGNFPVWGNQTWNSPTWSSQSWSNHSWNTQTWNTQTWNA
QTWNTQTWYPQGWNSFPAGGEESLQPCLPLPQNFSASDLEATLEAAGDGHKYFNTPQALDLFLN
YAMNLQPEDL

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Protein Domains

Homeobox

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCLAG00000016751	UniProtKB/TrEMBL
Ensembl Transcript	ENSCLAT00000024630.1	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/TrEMBL
NCBI Gene	Nanog	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN	UniProtKB/TrEMBL
	HOMEOBOX PROTEIN NANOG	UniProtKB/TrEMBL
Pfam	Homeodomain	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/TrEMBL
UniProt	A0A8C2W530	ENTREZGENE, UniProtKB/TrEMBL

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

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