Human Gene NR5A2 (ENST00000367362.8_9) from GENCODE V47lift37

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Description: nuclear receptor subfamily 5 group A member 2, transcript variant 1 (from RefSeq NM_205860.3)
Gencode Transcript: ENST00000367362.8_9
Gencode Gene: ENSG00000116833.14_15
Transcript (Including UTRs)
Position: hg19 chr1:199,996,838-200,146,543 Size: 149,706 Total Exon Count: 8 Strand: +
Coding Region
Position: hg19 chr1:199,996,976-200,143,338 Size: 146,363 Coding Exon Count: 8

Page Index	Sequence and Links	UniProtKB Comments	Primers	MalaCards	CTD
Gene Alleles	RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species
GO Annotations	mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr1:199,996,838-200,146,543)			mRNA (may differ from genome)		Protein (541 aa)
Gene Sorter	Genome Browser	Other Species FASTA	VisiGene	Gene interactions	Table Schema
AlphaFold	BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards
HGNC	Malacards	MGI	OMIM	PubMed	Reactome
UniProtKB	Wikipedia	BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: NR5A2_HUMAN DESCRIPTION: RecName: Full=Nuclear receptor subfamily 5 group A member 2; AltName: Full=Alpha-1-fetoprotein transcription factor; AltName: Full=B1-binding factor; Short=hB1F; AltName: Full=CYP7A promoter-binding factor; AltName: Full=Hepatocytic transcription factor; AltName: Full=Liver receptor homolog 1; Short=LRH-1; FUNCTION: Binds to the sequence element 5'-AACGACCGACCTTGAG-3' of the enhancer II of hepatitis B virus genes, a critical cis-element of their expression and regulation. May be responsible for the liver-specific activity of enhancer II, probably in combination with other hepatocyte transcription factors. Key regulator of cholesterol 7-alpha-hydroxylase gene (CYP7A) expression in liver. May also contribute to the regulation of pancreas-specific genes and play important roles in embryonic development. SUBUNIT: Binds DNA as a monomer (By similarity). Interacts with GRIP1, NCOA2 and NR0B2. INTERACTION: O60869:EDF1; NbExp=2; IntAct=EBI-781320, EBI-781301; SUBCELLULAR LOCATION: Nucleus (Probable). TISSUE SPECIFICITY: Abundantly expressed in pancreas, less in liver, very low levels in heart and lung. Expressed in the Hep-G2 cell line. Isoform 1 and isoform 2 seem to be present in fetal and adult liver and Hep-G2 cells. SIMILARITY: Belongs to the nuclear hormone receptor family. NR5 subfamily. SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.

Primer design for this transcript

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Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
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To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3

MalaCards Disease Associations


	MalaCards Gene Search: NR5A2 Diseases sorted by gene-association score: hepatitis b (12), hepatitis (8), testicular leydig cell tumor (2), reproductive organ benign neoplasm (1), maturity-onset diabetes of the young (1)

Comparative Toxicogenomics Database (CTD)


	The following chemicals interact with this gene D013749 Tetrachlorodibenzodioxin D000082 Acetaminophen D004958 Estradiol D004997 Ethinyl Estradiol C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl C404910 2,2-bis(4-hydroxyphenyl)-1,1,1-trichloroethane C009505 4,4'-diaminodiphenylmethane C508470 7-(2-(2,2-difluoroethoxy)-3,5-di-tert-butylbenzene)-3-methylocta-2,4,6-trienoic acid D019342 Acetic Acid D016604 Aflatoxin B1 more ... click here to view the complete list

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 13.92 RPKM in Pancreas Total median expression: 49.07 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-19.20	138	-0.139	Picture	PostScript	Text
3' UTR	-769.30	3205	-0.240	Picture	PostScript	Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

Protein Domain and Structure Information

InterPro Domains: Graphical view of domain structure
IPR008946 - Nucl_hormone_rcpt_ligand-bd
IPR000536 - Nucl_hrmn_rcpt_lig-bd_core
IPR016355 - Steroidogenic_factor_1
IPR001723 - Str_hrmn_rcpt
IPR001628 - Znf_hrmn_rcpt
IPR013088 - Znf_NHR/GATA

Pfam Domains:
PF00104 - Ligand-binding domain of nuclear hormone receptor
PF00105 - Zinc finger, C4 type (two domains)

SCOP Domains:
48508 - Nuclear receptor ligand-binding domain
57716 - Glucocorticoid receptor-like (DNA-binding domain)

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1YOK - X-ray MuPIT

1YUC - X-ray MuPIT

1ZDU - X-ray MuPIT

2A66 - X-ray MuPIT

3PLZ - X-ray MuPIT

3TX7 - X-ray MuPIT

4DOR - X-ray MuPIT

4DOS - X-ray MuPIT

ModBase Predicted Comparative 3D Structure on O00482


Front	Top	Side

The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

Orthologous Genes in Other Species

Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details	Gene Details
Gene Sorter	Gene Sorter
	RGD	Ensembl

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0000976 transcription regulatory region sequence-specific DNA binding GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding GO:0000980 RNA polymerase II distal enhancer sequence-specific DNA binding GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding GO:0003677 DNA binding GO:0003682 chromatin binding GO:0003690 double-stranded DNA binding GO:0003700 transcription factor activity, sequence-specific DNA binding GO:0003705 transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding GO:0003707 steroid hormone receptor activity GO:0004879 RNA polymerase II transcription factor activity, ligand-activated sequence-specific DNA binding GO:0005515 protein binding GO:0005543 phospholipid binding GO:0008270 zinc ion binding GO:0008289 lipid binding GO:0043565 sequence-specific DNA binding GO:0044212 transcription regulatory region DNA binding GO:0046872 metal ion binding Biological Process: GO:0006351 transcription, DNA-templated GO:0006355 regulation of transcription, DNA-templated GO:0006367 transcription initiation from RNA polymerase II promoter GO:0008206 bile acid metabolic process GO:0009755 hormone-mediated signaling pathway GO:0009792 embryo development ending in birth or egg hatching GO:0009888 tissue development GO:0030522 intracellular receptor signaling pathway GO:0030855 epithelial cell differentiation GO:0042127 regulation of cell proliferation GO:0042592 homeostatic process GO:0042632 cholesterol homeostasis GO:0043401 steroid hormone mediated signaling pathway GO:0045070 positive regulation of viral genome replication GO:0045893 positive regulation of transcription, DNA-templated GO:0045944 positive regulation of transcription from RNA polymerase II promoter GO:0061113 pancreas morphogenesis GO:0097720 calcineurin-mediated signaling GO:1990830 cellular response to leukemia inhibitory factor Cellular Component: GO:0005634 nucleus GO:0005654 nucleoplasm GO:0005737 cytoplasm GO:0090575 RNA polymerase II transcription factor complex

Descriptions from all associated GenBank mRNAs


	U93553 - Human alpha1-fetoprotein transcription factor (hFTF) mRNA, complete cds. AF146343 - Homo sapiens CYP7A promoter binding factor (CPF) mRNA, complete cds. LF205371 - JP 2014500723-A/12874: Polycomb-Associated Non-Coding RNAs. AB019246 - Homo sapiens mRNA for FTZ-F1 related protein, complete cds. BC118571 - Homo sapiens nuclear receptor subfamily 5, group A, member 2, mRNA (cDNA clone MGC:141812 IMAGE:40036188), complete cds. BC118652 - Homo sapiens nuclear receptor subfamily 5, group A, member 2, mRNA (cDNA clone MGC:141811 IMAGE:40036183), complete cds. U80251 - Homo sapiens hepatocytic transcription factor (hB1F) mRNA, complete cds. KJ891199 - Synthetic construct Homo sapiens clone ccsbBroadEn_00593 NR5A2 gene, encodes complete protein. AB590580 - Synthetic construct DNA, clone: pFN21AB5946, Homo sapiens NR5A2 gene for nuclear receptor subfamily 5, group A, member 2, without stop codon, in Flexi system. AF124247 - Homo sapiens hepatocytic transcription factor hB1F-2 (B1F2) mRNA, complete cds. HQ692857 - Homo sapiens liver nuclear receptor homolog-1 variant 2 (NR5A2) mRNA, complete cds. AK308446 - Homo sapiens cDNA, FLJ98394. AK304344 - Homo sapiens cDNA FLJ54621 complete cds, highly similar to Orphan nuclear receptor NR5A2. AB307719 - Homo sapiens NR5A2 mRNA for nuclear receptor subfamily 5, group A, complete cds. AK316513 - Homo sapiens cDNA, FLJ79412 complete cds, highly similar to Orphan nuclear receptor NR5A2. AK304365 - Homo sapiens cDNA FLJ52395 complete cds, highly similar to Orphan nuclear receptor NR5A2. AF049102 - Homo sapiens alpha1-fetoprotein transcription factor short variant (FTF) mRNA, partial cds. MA440948 - JP 2018138019-A/12874: Polycomb-Associated Non-Coding RNAs. BC027893 - Homo sapiens nuclear receptor subfamily 5, group A, member 2, mRNA (cDNA clone IMAGE:5224714), partial cds. JD078147 - Sequence 59171 from Patent EP1572962. AF124248 - Homo sapiens hepatocytic transcription factor hB1F-3 (B1F3) mRNA, partial cds. BC080182 - Homo sapiens cDNA clone IMAGE:6202544. LF319786 - JP 2014500723-A/127289: Polycomb-Associated Non-Coding RNAs. MA555363 - JP 2018138019-A/127289: Polycomb-Associated Non-Coding RNAs. LF319785 - JP 2014500723-A/127288: Polycomb-Associated Non-Coding RNAs. JD269242 - Sequence 250266 from Patent EP1572962. LF319751 - JP 2014500723-A/127254: Polycomb-Associated Non-Coding RNAs. JD066750 - Sequence 47774 from Patent EP1572962. JD045233 - Sequence 26257 from Patent EP1572962. JD242010 - Sequence 223034 from Patent EP1572962. JD106491 - Sequence 87515 from Patent EP1572962. JD289825 - Sequence 270849 from Patent EP1572962. JD099053 - Sequence 80077 from Patent EP1572962. JD291893 - Sequence 272917 from Patent EP1572962. JD293057 - Sequence 274081 from Patent EP1572962. JD249467 - Sequence 230491 from Patent EP1572962. AF112344 - Homo sapiens hepatocytic transcription factor (hB1F) mRNA, 3' UTR. AF228413 - Homo sapiens hepatocyte transcription factor mRNA, 3'UTR. JD482324 - Sequence 463348 from Patent EP1572962. JD086867 - Sequence 67891 from Patent EP1572962. JD241348 - Sequence 222372 from Patent EP1572962. LF319750 - JP 2014500723-A/127253: Polycomb-Associated Non-Coding RNAs. JD463549 - Sequence 444573 from Patent EP1572962. JD147660 - Sequence 128684 from Patent EP1572962. MA555362 - JP 2018138019-A/127288: Polycomb-Associated Non-Coding RNAs. MA555328 - JP 2018138019-A/127254: Polycomb-Associated Non-Coding RNAs. MA555327 - JP 2018138019-A/127253: Polycomb-Associated Non-Coding RNAs.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein O00482 (Reactome details) participates in the following event(s): R-HSA-376419 Formation of NR-MED1 Coactivator Complex R-HSA-210747 Regulation of gene expression in early pancreatic precursor cells R-HSA-383280 Nuclear Receptor transcription pathway R-HSA-186712 Regulation of beta-cell development R-HSA-212436 Generic Transcription Pathway R-HSA-1266738 Developmental Biology R-HSA-73857 RNA Polymerase II Transcription R-HSA-74160 Gene expression (Transcription) R-HSA-376419 Formation of NR-MED1 Coactivator Complex R-HSA-383280 Nuclear Receptor transcription pathway R-HSA-212436 Generic Transcription Pathway R-HSA-73857 RNA Polymerase II Transcription R-HSA-74160 Gene expression (Transcription) R-HSA-376419 Formation of NR-MED1 Coactivator Complex R-HSA-383280 Nuclear Receptor transcription pathway R-HSA-212436 Generic Transcription Pathway R-HSA-73857 RNA Polymerase II Transcription R-HSA-74160 Gene expression (Transcription) R-HSA-9018519 Estrogen-dependent gene expression R-HSA-8939211 ESR-mediated signaling R-HSA-9006931 Signaling by Nuclear Receptors R-HSA-162582 Signal Transduction

Other Names for This Gene


	Alternate Gene Symbols: B1F, B4E2P3, CPF, ENST00000367362.1, ENST00000367362.2, ENST00000367362.3, ENST00000367362.4, ENST00000367362.5, ENST00000367362.6, ENST00000367362.7, FTF, NM_205860, NR5A2_HUMAN, O00482, O95642, Q147U3, uc318fvx.1, uc318fvx.2 UCSC ID: ENST00000367362.8_9 RefSeq Accession: NM_205860.3 Protein: O00482 (aka NR5A2_HUMAN or NR52_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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