Human Gene VDR (ENST00000549336.6_11) from GENCODE V47lift37
  Description: vitamin D receptor, transcript variant 5 (from RefSeq NM_001374662.1)
Gencode Transcript: ENST00000549336.6_11
Gencode Gene: ENSG00000111424.12_17
Transcript (Including UTRs)
   Position: hg19 chr12:48,235,320-48,298,777 Size: 63,458 Total Exon Count: 10 Strand: -
Coding Region
   Position: hg19 chr12:48,238,529-48,272,896 Size: 34,368 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:48,235,320-48,298,777)mRNA (may differ from genome)Protein (427 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VDR_HUMAN
DESCRIPTION: RecName: Full=Vitamin D3 receptor; Short=VDR; AltName: Full=1,25-dihydroxyvitamin D3 receptor; AltName: Full=Nuclear receptor subfamily 1 group I member 1;
FUNCTION: Nuclear hormone receptor. Transcription factor that mediates the action of vitamin D3 by controlling the expression of hormone sensitive genes. Regulates transcription of hormone sensitive genes via its association with the WINAC complex, a chromatin-remodeling complex. Recruited to promoters via its interaction with the WINAC complex subunit BAZ1B/WSTF, which mediates the interaction with acetylated histones, an essential step for VDR-promoter association. Plays a central role in calcium homeostasis.
SUBUNIT: Homodimer in the absence of bound vitamin D3. Heterodimer with RXRA after vitamin D3 binding. Interacts with SMAD3. Interacts with MED1, NCOA1, NCOA2, NCOA3 and NCOA6 coactivators, leading to a strong increase of transcription of target genes. Interacts (in a ligand-dependent manner) with BAZ1B/WSTF.
INTERACTION: Q9JLI4:Ncoa6 (xeno); NbExp=2; IntAct=EBI-286357, EBI-286271; P26045:PTPN3; NbExp=4; IntAct=EBI-286357, EBI-1047946; P04637:TP53; NbExp=6; IntAct=EBI-286357, EBI-366083;
SUBCELLULAR LOCATION: Nucleus.
DOMAIN: Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.
POLYMORPHISM: Genetic variations in VDR may determine Mycobacterium tuberculosis susceptibility [MIM:607948].
DISEASE: Defects in VDR are the cause of rickets vitamin D- dependent type 2A (VDDR2A) [MIM:277440]. A disorder of vitamin D metabolism resulting in severe rickets, hypocalcemia and secondary hyperparathyroidism. Most patients have total alopecia in addition to rickets.
SIMILARITY: Belongs to the nuclear hormone receptor family. NR1 subfamily.
SIMILARITY: Contains 1 nuclear receptor DNA-binding domain.
CAUTION: It is uncertain whether Met-1 or Met-4 is the initiator.
SEQUENCE CAUTION: Sequence=AAP88938.1; Type=Erroneous gene model prediction;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/VDR";
WEB RESOURCE: Name=NIEHS-SNPs; URL="http://egp.gs.washington.edu/data/vdr/";
WEB RESOURCE: Name=SHMPD; Note=The Singapore human mutation and polymorphism database; URL="http://shmpd.bii.a-star.edu.sg/gene.php?genestart=A&genename=VDR";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

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: VDR
Diseases sorted by gene-association score: rickets, vitamin d-resistant, type iia* (1571), vitamin d-dependent rickets type ii* (528), osteoporosis* (77), rickets (56), tuberculosis (22), hyperparathyroidism (18), secondary hyperparathyroidism of renal origin (16), atrichia with papular lesions (16), alopecia (16), prostatitis (15), hypercalciuria, absorptive (13), idiopathic hypercalciuria (13), renal osteodystrophy (12), osteomalacia (12), hyperphosphatemia (12), uremia (11), rosacea (11), mn1 (10), chronic kidney failure (10), hypophosphatemic rickets, x-linked dominant (10), pulmonary tuberculosis (10), degenerative disc disease (10), multidrug-resistant tuberculosis (9), colon adenoma (9), calciphylaxis (9), intervertebral disc disease (9), adult dermatomyositis (9), spondylosis (8), adolescent idiopathic scoliosis (8), thalassemia major (8), van buchem disease (8), colorectal adenoma (8), syringomyelia (7), hypercalcemia, infantile, 1 (7), campylobacteriosis (7), hyperparathyroidism, familial primary (7), glucocorticoid-induced osteoporosis (6), hypocalcemia, autosomal dominant (6), primary biliary cholangitis (6), bone remodeling disease (6), bone resorption disease (6), parathyroid gland disease (6), plasmablastic lymphoma (6), sclerosteosis (6), phosphorus metabolism disease (5), salmonellosis (5), nephrolithiasis, calcium oxalate (5), mineral metabolism disease (5), xanthinuria, type i (4), hair disease (4), primary biliary cirrhosis (4), colorectal cancer (4), prostate cancer (2), diabetes mellitus, insulin-dependent (2), multiple sclerosis, disease progression, modifier of (2), eye disease (1), prostate cancer susceptibility (1), leber congenital amaurosis (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 18.56 RPKM in Small Intestine - Terminal Ileum
Total median expression: 149.13 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -43.40123-0.353 Picture PostScript Text
3' UTR -1160.803209-0.362 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
IPR001723 - Str_hrmn_rcpt
IPR000324 - VitD_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)
57889 - Cysteine-rich domain

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1DB1 - X-ray MuPIT 1IE8 - X-ray MuPIT 1IE9 - X-ray MuPIT 1KB2 - X-ray MuPIT 1KB4 - X-ray MuPIT 1KB6 - X-ray MuPIT 1S0Z - X-ray MuPIT 1S19 - X-ray MuPIT 1TXI - X-ray MuPIT 1YNW - X-ray MuPIT 2HAM - X-ray MuPIT 2HAR - X-ray MuPIT 2HAS - X-ray MuPIT 2HB7 - X-ray MuPIT 2HB8 - X-ray MuPIT 3A2I - X-ray MuPIT 3A2J - X-ray MuPIT 3A3Z - X-ray MuPIT 3A40 - X-ray MuPIT 3A78 - X-ray MuPIT 3AUQ - X-ray MuPIT 3AUR - X-ray MuPIT 3AX8 - X-ray MuPIT 3AZ1 - X-ray MuPIT 3AZ2 - X-ray MuPIT 3AZ3 - X-ray MuPIT 3B0T - X-ray MuPIT 3CS4 - X-ray MuPIT 3CS6 - X-ray MuPIT 3M7R - X-ray MuPIT 3OGT - X-ray MuPIT 3P8X - X-ray MuPIT 3TKC - X-ray MuPIT 4G2I - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P11473
FrontTopSide
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.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003700 transcription factor activity, sequence-specific DNA 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:0008270 zinc ion binding
GO:0008434 calcitriol receptor activity
GO:0038186 lithocholic acid receptor activity
GO:0043565 sequence-specific DNA binding
GO:0046872 metal ion binding
GO:0046965 retinoid X receptor binding
GO:1902098 calcitriol binding
GO:1902121 lithocholic acid binding
GO:0070644 vitamin D response element binding

Biological Process:
GO:0000122 negative regulation of transcription from RNA polymerase II promoter
GO:0000902 cell morphogenesis
GO:0001501 skeletal system development
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006367 transcription initiation from RNA polymerase II promoter
GO:0006816 calcium ion transport
GO:0006874 cellular calcium ion homeostasis
GO:0007165 signal transduction
GO:0007275 multicellular organism development
GO:0007595 lactation
GO:0008285 negative regulation of cell proliferation
GO:0009887 animal organ morphogenesis
GO:0010628 positive regulation of gene expression
GO:0010839 negative regulation of keratinocyte proliferation
GO:0010980 positive regulation of vitamin D 24-hydroxylase activity
GO:0038183 bile acid signaling pathway
GO:0042359 vitamin D metabolic process
GO:0043401 steroid hormone mediated signaling pathway
GO:0045618 positive regulation of keratinocyte differentiation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0046697 decidualization
GO:0050892 intestinal absorption
GO:0060058 positive regulation of apoptotic process involved in mammary gland involution
GO:0060558 regulation of calcidiol 1-monooxygenase activity
GO:0060745 mammary gland branching involved in pregnancy
GO:0070561 vitamin D receptor signaling pathway

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0043235 receptor complex
GO:0090575 RNA polymerase II transcription factor complex


-  Descriptions from all associated GenBank mRNAs
  FW340016 - Screening.
J03258 - Human vitamin D receptor mRNA, complete cds.
JD382414 - Sequence 363438 from Patent EP1572962.
JD183561 - Sequence 164585 from Patent EP1572962.
JD297388 - Sequence 278412 from Patent EP1572962.
JD038151 - Sequence 19175 from Patent EP1572962.
JD146086 - Sequence 127110 from Patent EP1572962.
JD044167 - Sequence 25191 from Patent EP1572962.
JD250821 - Sequence 231845 from Patent EP1572962.
JD338269 - Sequence 319293 from Patent EP1572962.
JD323448 - Sequence 304472 from Patent EP1572962.
JD513281 - Sequence 494305 from Patent EP1572962.
JD465583 - Sequence 446607 from Patent EP1572962.
JD230480 - Sequence 211504 from Patent EP1572962.
JD385789 - Sequence 366813 from Patent EP1572962.
JD310164 - Sequence 291188 from Patent EP1572962.
JD424909 - Sequence 405933 from Patent EP1572962.
JD448778 - Sequence 429802 from Patent EP1572962.
JD222949 - Sequence 203973 from Patent EP1572962.
JD123998 - Sequence 105022 from Patent EP1572962.
JD123447 - Sequence 104471 from Patent EP1572962.
JD551043 - Sequence 532067 from Patent EP1572962.
JD250178 - Sequence 231202 from Patent EP1572962.
JD541151 - Sequence 522175 from Patent EP1572962.
JD250924 - Sequence 231948 from Patent EP1572962.
JD148725 - Sequence 129749 from Patent EP1572962.
JD257739 - Sequence 238763 from Patent EP1572962.
JD444401 - Sequence 425425 from Patent EP1572962.
JD112296 - Sequence 93320 from Patent EP1572962.
JD283316 - Sequence 264340 from Patent EP1572962.
JD395609 - Sequence 376633 from Patent EP1572962.
JD089485 - Sequence 70509 from Patent EP1572962.
AK024830 - Homo sapiens cDNA: FLJ21177 fis, clone CAS11130, highly similar to HUMVDR Human vitamin D receptor mRNA.
AK225844 - Homo sapiens mRNA for vitamin D receptor variant, clone: FCC126E05.
BC060832 - Homo sapiens vitamin D (1,25- dihydroxyvitamin D3) receptor, mRNA (cDNA clone MGC:71709 IMAGE:30343975), complete cds.
JD482050 - Sequence 463074 from Patent EP1572962.
JD533785 - Sequence 514809 from Patent EP1572962.
JD446530 - Sequence 427554 from Patent EP1572962.
JD446529 - Sequence 427553 from Patent EP1572962.
JD294279 - Sequence 275303 from Patent EP1572962.
JD481855 - Sequence 462879 from Patent EP1572962.
JD246949 - Sequence 227973 from Patent EP1572962.
JD413408 - Sequence 394432 from Patent EP1572962.
JD198107 - Sequence 179131 from Patent EP1572962.
JD212719 - Sequence 193743 from Patent EP1572962.
JD327918 - Sequence 308942 from Patent EP1572962.
JD112736 - Sequence 93760 from Patent EP1572962.
JD159251 - Sequence 140275 from Patent EP1572962.
JD113444 - Sequence 94468 from Patent EP1572962.
BC033465 - Homo sapiens vitamin D (1,25- dihydroxyvitamin D3) receptor, mRNA (cDNA clone IMAGE:5181453).
JD182554 - Sequence 163578 from Patent EP1572962.
JD167843 - Sequence 148867 from Patent EP1572962.
JD495805 - Sequence 476829 from Patent EP1572962.
JD555308 - Sequence 536332 from Patent EP1572962.
JD347576 - Sequence 328600 from Patent EP1572962.
JD044951 - Sequence 25975 from Patent EP1572962.
AK309587 - Homo sapiens cDNA, FLJ99628.
JD475252 - Sequence 456276 from Patent EP1572962.
JD353641 - Sequence 334665 from Patent EP1572962.
JD443468 - Sequence 424492 from Patent EP1572962.
JD532403 - Sequence 513427 from Patent EP1572962.
JD495931 - Sequence 476955 from Patent EP1572962.
JD204488 - Sequence 185512 from Patent EP1572962.
JD215718 - Sequence 196742 from Patent EP1572962.
JD384298 - Sequence 365322 from Patent EP1572962.
JD253118 - Sequence 234142 from Patent EP1572962.
JD104714 - Sequence 85738 from Patent EP1572962.
JD457101 - Sequence 438125 from Patent EP1572962.
JD172945 - Sequence 153969 from Patent EP1572962.
JD160696 - Sequence 141720 from Patent EP1572962.
JD039879 - Sequence 20903 from Patent EP1572962.
JD067653 - Sequence 48677 from Patent EP1572962.
JD100191 - Sequence 81215 from Patent EP1572962.
JD490449 - Sequence 471473 from Patent EP1572962.
JD123288 - Sequence 104312 from Patent EP1572962.
JD082953 - Sequence 63977 from Patent EP1572962.
JD146528 - Sequence 127552 from Patent EP1572962.
JD183201 - Sequence 164225 from Patent EP1572962.
JD200726 - Sequence 181750 from Patent EP1572962.
JD445211 - Sequence 426235 from Patent EP1572962.
JD483147 - Sequence 464171 from Patent EP1572962.
JD362761 - Sequence 343785 from Patent EP1572962.
AK299446 - Homo sapiens cDNA FLJ51539 complete cds, highly similar to Vitamin D3 receptor.
JD329532 - Sequence 310556 from Patent EP1572962.
JD266088 - Sequence 247112 from Patent EP1572962.
JD554814 - Sequence 535838 from Patent EP1572962.
JD321856 - Sequence 302880 from Patent EP1572962.
JD335903 - Sequence 316927 from Patent EP1572962.
JD200665 - Sequence 181689 from Patent EP1572962.
JD538309 - Sequence 519333 from Patent EP1572962.
X67482 - H.sapiens mRNA for 1,25-dihydroxyvitamin D-3 receptor.
AB307700 - Homo sapiens NR1I1 mRNA for vitamin D (1,25- dihydroxyvitamin D3) receptor, complete cds.
AF026260 - Homo sapiens vitamin D receptor (VDR) mRNA, complete cds.
EU831779 - Synthetic construct Homo sapiens clone HAIB:100066808; DKFZo008C1121 vitamin D (1,25- dihydroxyvitamin D3) receptor protein (VDR) gene, encodes complete protein.
EU831857 - Synthetic construct Homo sapiens clone HAIB:100066886; DKFZo004C1122 vitamin D (1,25- dihydroxyvitamin D3) receptor protein (VDR) gene, encodes complete protein.
HQ692836 - Homo sapiens vitamin D nuclear receptor variant 1 (NR1i1) mRNA, complete cds.
AK312267 - Homo sapiens cDNA, FLJ92563, Homo sapiens vitamin D (1,25-dihydroxyvitamin D3) receptor (VDR),mRNA.
KJ892373 - Synthetic construct Homo sapiens clone ccsbBroadEn_01767 VDR gene, encodes complete protein.
KR710970 - Synthetic construct Homo sapiens clone CCSBHm_00018433 VDR (VDR) mRNA, encodes complete protein.
KR710971 - Synthetic construct Homo sapiens clone CCSBHm_00018444 VDR (VDR) mRNA, encodes complete protein.
KR710972 - Synthetic construct Homo sapiens clone CCSBHm_00018448 VDR (VDR) mRNA, encodes complete protein.
KR710973 - Synthetic construct Homo sapiens clone CCSBHm_00018454 VDR (VDR) mRNA, encodes complete protein.
EU446665 - Synthetic construct Homo sapiens clone IMAGE:100069929; IMAGE:100011874; FLH257096.01L vitamin D (1,25- dihydroxyvitamin D3) receptor (VDR) gene, encodes complete protein.
AB464346 - Synthetic construct DNA, clone: pF1KB7719, Homo sapiens VDR gene for vitamin D (1,25- dihydroxyvitamin D3) receptor, without stop codon, in Flexi system.
CU687452 - Synthetic construct Homo sapiens gateway clone IMAGE:100021187 5' read VDR mRNA.
M65208 - Human vitamin D receptor (intestinal) binding domain.
JD530657 - Sequence 511681 from Patent EP1572962.
LF212633 - JP 2014500723-A/20136: Polycomb-Associated Non-Coding RNAs.
LF210423 - JP 2014500723-A/17926: Polycomb-Associated Non-Coding RNAs.
MA448210 - JP 2018138019-A/20136: Polycomb-Associated Non-Coding RNAs.
MA446000 - JP 2018138019-A/17926: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_vdrPathway - Control of Gene Expression by Vitamin D Receptor
h_nuclearRsPathway - Nuclear Receptors in Lipid Metabolism and Toxicity

Reactome (by CSHL, EBI, and GO)

Protein P11473 (Reactome details) participates in the following event(s):

R-HSA-4546387 PIAS4 SUMOylates VDR with SUMO2
R-HSA-8963915 1,25(OH)2D binds VDR
R-HSA-376419 Formation of NR-MED1 Coactivator Complex
R-HSA-196791 Vitamin D (calciferol) metabolism
R-HSA-383280 Nuclear Receptor transcription pathway
R-HSA-209943 Steroid hormones
R-HSA-8957322 Metabolism of steroids
R-HSA-212436 Generic Transcription Pathway
R-HSA-556833 Metabolism of lipids
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-1430728 Metabolism
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: B2R5Q1, ENST00000549336.1, ENST00000549336.2, ENST00000549336.3, ENST00000549336.4, ENST00000549336.5, G3V1V9, NM_001374662, NR1I1, P11473, Q5PSV3, uc325agy.1, uc325agy.2, VDR , VDR_HUMAN
UCSC ID: ENST00000549336.6_11
RefSeq Accession: NM_001364085.2
Protein: P11473 (aka VDR_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.