Nr6a1 nuclear receptor subfamily 6, group A, member 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Nr6a1provided by MGI
Official Full Name: nuclear receptor subfamily 6, group A, member 1provided by MGI
Primary source: MGI:MGI:1352459
See related: Ensembl:ENSMUSG00000063972 AllianceGenome:MGI:1352459
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: RTR; Gcnf; NCNF; 1700113M01Rik
Summary: Enables DNA-binding transcription activator activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and protein homodimerization activity. Involved in positive regulation of transcription by RNA polymerase II. Acts upstream of or within gamete generation and negative regulation of transcription by RNA polymerase II. Part of transcription regulator complex. Is expressed in several structures, including early conceptus; embryo ectoderm; genitourinary system; nervous system; and retina. Orthologous to human NR6A1 (nuclear receptor subfamily 6 group A member 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in testis adult (RPKM 28.1), placenta adult (RPKM 4.6) and 5 other tissues See more
Orthologs: human all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 2 B; 2 24.42 cM

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (38613381..38816464, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (38723369..38926461, complement)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Hippocampal NR6A1 impairs CREB-BDNF signaling and leads to the development of depression-like behaviors in mice.
Title: Hippocampal NR6A1 impairs CREB-BDNF signaling and leads to the development of depression-like behaviors in mice.
Here, the authors present the first structure of mouse GCNF DNA-binding domain in complex with the Oct4 DR0. The overall structure revealed two molecules bound in a head-to-tail fashion on opposite sides of the DNA at a DR0 motif located within the Oct4 promoter.
Title: A Structural Investigation into Oct4 Regulation by Orphan Nuclear Receptors, Germ Cell Nuclear Factor (GCNF), and Liver Receptor Homolog-1 (LRH-1).
Inactivation of the Gcnf gene in vivo leads to loss of repression of Oct4 expression in both male and female gonads.
Title: Germ cell nuclear factor regulates gametogenesis in developing gonads.
These results reveal that GCNF plays a key role in regulating activation of cyclin D1 expression via inhibition of Mir302a.
Title: GCNF-dependent activation of cyclin D1 expression via repression of Mir302a during ESC differentiation.
Gcnf is expressed in fetal ovarian germ cells.
Title: The ligand binding domain of GCNF is not required for repression of pluripotency genes in mouse fetal ovarian germ cells.
characterize the let-7 target Nr6a1, an embryonic transcriptional repressor that regulates gene expression in adult fibroblasts following miRNA loss
Title: Let-7 represses Nr6a1 and a mid-gestation developmental program in adult fibroblasts.
GCNF initiates the repression and epigenetic modification of Oct4 gene during ESC differentiation.
Title: Differential recruitment of methyl CpG-binding domain factors and DNA methyltransferases by the orphan receptor germ cell nuclear factor initiates the repression and silencing of Oct4.
These experiments confirmed that NR6A1 works as a regulator for hypocretin transcription.
Title: Transcriptional regulation of the hypocretin/orexin gene by NR6A1.
Nr6a1 is expressed not only in the germ cells of mouse but also in a variety of somatic tissues, including epididymis, oviduct, brain, and pituitary.
Title: Extra-germ cell expression of mouse nuclear receptor subfamily 6, group A, member 1 (NR6A1).
The suppression of Oct4 by GCNF is important for the transition from primitive to definitive neural stem cells and restriction of the non-neural competency in the early neural stem cell lineage.
Title: Suppression of Oct4 by germ cell nuclear factor restricts pluripotency and promotes neural stem cell development in the early neural lineage.

Submit: New GeneRIF Correction See all GeneRIFs (25)

Variation

Go to the top of the page Help

Alleles

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

Gene trapped (1) 1 citation
Targeted (10) 1 citation
Endonuclease-mediated (1)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

NoName (e-PCR)
- UniSTS:234382

NoName (e-PCR)
- UniSTS:234383

RH138284 (e-PCR)
- UniSTS:220371

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor activity	IEA Inferred from Electronic Annotation 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 cis-regulatory region sequence-specific DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables estrogen response element binding	IBA Inferred from Biological aspect of Ancestor more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nuclear receptor activity	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay 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 zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in gamete generation	IEP Inferred from Expression Pattern 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 transcription by RNA polymerase II	IDA Inferred from Direct Assay 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 positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within spermatogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of chromatin	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
part_of transcription regulator complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

Go to the top of the page Help

Preferred Names: nuclear receptor subfamily 6 group A member 1

Names: germ cell nuclear factor; mGCNF; retinoid receptor-related testis-specific receptor

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

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)

NM_001159548.1 → NP_001153020.1 nuclear receptor subfamily 6 group A member 1 isoform 2

See identical proteins and their annotated locations for NP_001153020.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (2) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AL844842, CK638822, CN532747, CN537407

Consensus CDS

CCDS50581.1

UniProtKB/Swiss-Prot

Q64249

Related

ENSMUSP00000126009.2, ENSMUST00000168098.8

Conserved Domains (2) summary

cd06953
Location:214 → 425

NR_LBD_DHR4_like; The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4

cd07169
Location:10 → 99

NR_DBD_GCNF_like; DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers
NM_001159549.1 → NP_001153021.1 nuclear receptor subfamily 6 group A member 1 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) has a shorter and distinct N-terminus compared to isoform 1.

Source sequence(s)

AL844842, CK638822, CN532747, CN537360, CN537407

Conserved Domains (2) summary

cd06953
Location:213 → 424

NR_LBD_DHR4_like; The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4

cd07169
Location:10 → 99

NR_DBD_GCNF_like; DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers
NM_001428791.1 → NP_001415720.1 nuclear receptor subfamily 6 group A member 1 isoform 4

Status: VALIDATED

Source sequence(s)

AL844842, AL935155
NM_010264.5 → NP_034394.1 nuclear receptor subfamily 6 group A member 1 isoform 1

See identical proteins and their annotated locations for NP_034394.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AL844842, AL935155

Consensus CDS

CCDS16012.1

UniProtKB/Swiss-Prot

A2AQL8, A2AQM1, Q64249, Q687Z3

Related

ENSMUSP00000075624.5, ENSMUST00000076275.11

Conserved Domains (2) summary

cd06953
Location:271 → 482

NR_LBD_DHR4_like; The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4

cd07169
Location:67 → 156

NR_DBD_GCNF_like; DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000068.8 Reference GRCm39 C57BL/6J

Range

38613381..38816464 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011239025.3 → XP_011237327.1 nuclear receptor subfamily 6 group A member 1 isoform X1

Conserved Domains (2) summary

cd06953
Location:270 → 481

NR_LBD_DHR4_like; The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4

cd07169
Location:67 → 156

NR_DBD_GCNF_like; DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers
XM_036158420.1 → XP_036014313.1 nuclear receptor subfamily 6 group A member 1 isoform X3

Conserved Domains (2) summary

cd06953
Location:153 → 364

NR_LBD_DHR4_like; The ligand binding domain of orphan nuclear receptor Ecdysone-induced receptor DHR4

cl02596
Location:1 → 38

NR_DBD_like; DNA-binding domain of nuclear receptors is composed of two C4-type zinc fingers
XM_036158418.1 → XP_036014311.1 nuclear receptor subfamily 6 group A member 1 isoform X2

Conserved Domains (2) summary

cd07169
Location:67 → 156

NR_DBD_GCNF_like; DNA-binding domain of Germ cell nuclear factor (GCNF) F1 is composed of two C4-type zinc fingers

cl11397
Location:271 → 377

NR_LBD; The ligand binding domain of nuclear receptors, a family of ligand-activated transcription regulators