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P20393 (NR1D1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 165. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Nuclear receptor subfamily 1 group D member 1
Alternative name(s):
Rev-erbA-alpha
V-erbA-related protein 1
Short name=EAR-1
Gene names
Name:NR1D1
Synonyms:EAR1, HREV, THRAL
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length614 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Transcriptional repressor which coordinates circadian rhythm and metabolic pathways in a heme-dependent manner. Integral component of the complex transcription machinery that governs circadian rhythmicity and forms a critical negative limb of the circadian clock by directly repressing the expression of core clock components ARTNL/BMAL1, CLOCK and CRY1. Also regulates genes involved in metabolic functions, including lipid and bile acid metabolism, adipogenesis, gluconeogenesis and the macrophage inflammatory response. Acts as a receptor for heme which stimulates its interaction with the NCOR1/HDAC3 corepressor complex, enhancing transcriptional repression. Recognizes two classes of DNA response elements within the promoter of its target genes and can bind to DNA as either monomers or homodimers, depending on the nature of the response element. Binds as a monomer to a response element composed of the consensus half-site motif 5'-[A/G]GGTCA-3' preceded by an A/T-rich 5' sequence (RevRE), or as a homodimer to a direct repeat of the core motif spaced by two nucleotides (RevDR-2). Acts as a potent competitive repressor of ROR alpha (RORA) function and regulates the levels of its ligand heme by repressing the expression of PPARGC1A, a potent inducer of heme synthesis. Regulates lipid metabolism by repressing the expression of APOC3 and by influencing the activity of sterol response element binding proteins (SREBPs); represses INSIG2 which interferes with the proteolytic activation of SREBPs which in turn govern the rhythmic expression of enzymes with key functions in sterol and fatty acid synthesis. Regulates gluconeogenesis via repression of G6PC and PEPCK and adipocyte differentiation via repression of PPARG. Regulates glucagon release in pancreatic alpha-cells via the AMPK-NAMPT-SIRT1 pathway and the proliferation, glucose-induced insulin secretion and expression of key lipogenic genes in pancreatic-beta cells. Positively regulates bile acid synthesis by increasing hepatic expression of CYP7A1 via repression of NR0B2 and NFIL3 which are negative regulators of CYP7A1. Modulates skeletal muscle oxidative capacity by regulating mitochondrial biogenesis and autophagy; controls mitochondrial biogenesis and respiration by interfering with the STK11-PRKAA1/2-SIRT1-PPARGC1A signaling pathway. Represses the expression of SERPINE1/PAI1, an important modulator of cardiovascular disease and the expression of inflammatory cytokines and chemokines in macrophages. Represses gene expression at a distance in macrophages by inhibiting the transcription of enhancer-derived RNAs (eRNAs). Plays a role in the circadian regulation of body temperature and negatively regulates thermogenic transcriptional programs in brown adipose tissue (BAT); imposes a circadian oscillation in BAT activity, increasing body temperature when awake and depressing thermogenesis during sleep. In concert with NR2E3, regulates transcriptional networks critical for photoreceptor development and function. In addition to its activity as a repressor, can also act as a transcriptional activator. In the ovarian granulosa cells acts as a transcriptional activator of STAR which plays a role in steroid biosynthesis. In collaboration with SP1, activates GJA1 transcription in a heme-independent manner. Ref.1 Ref.2 Ref.5 Ref.6 Ref.7 Ref.10 Ref.11 Ref.15 Ref.18

Subunit structure

Binds DNA as a monomer or a homodimer. Interacts with C1D, NR2E3 and SP1. Interacts with OPHN1 (via C-terminus). Interacts with ZNHIT1. Interacts with PER2; the interaction associates PER2 to ARNTL promoter region. Interacts with CRY1. Ref.9 Ref.13 Ref.14

Subcellular location

Nucleus. Cytoplasm By similarity. Cell projectiondendrite By similarity. Cell projectiondendritic spine By similarity. Note: Localizes to the cytoplasm, dendrites and dendritic spine in the presence of OPHN1 By similarity.

Tissue specificity

Widely expressed. Expressed at high levels in the liver, adipose tissue, skeletal muscle and brain. Also expressed in endothelial cells (ECs), vascular smooth muscle cells (VSMCs) and macrophages. Expression oscillates diurnally in the suprachiasmatic nucleus (SCN) of the hypothalamus as well as in peripheral tissues. Expression increases during the differentiation of pre-adipocytes into mature adipocytes. Expressed at high levels in some squamous carcinoma cell lines. Ref.1

Domain

Composed of three domains: a modulating N-terminal domain, a DNA-binding domain and a C-terminal ligand-binding domain.

Post-translational modification

Ubiquitinated, leading to its proteasomal degradation. Ref.8

Sequence similarities

Belongs to the nuclear hormone receptor family. NR1 subfamily.

Contains 1 nuclear receptor DNA-binding domain.

Ontologies

Keywords
   Biological processBiological rhythms
Differentiation
Transcription
Transcription regulation
   Cellular componentCell projection
Cytoplasm
Nucleus
   DomainZinc-finger
   LigandDNA-binding
Heme
Iron
Metal-binding
Zinc
   Molecular functionActivator
Receptor
Repressor
   PTMAcetylation
Phosphoprotein
Ubl conjugation
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcell differentiation

Inferred from electronic annotation. Source: UniProtKB-KW

cellular response to lipopolysaccharide

Inferred from mutant phenotype PubMed 18511497. Source: BHF-UCL

circadian regulation of gene expression

Inferred from sequence or structural similarity. Source: UniProtKB

circadian temperature homeostasis

Inferred from sequence or structural similarity. Source: UniProtKB

gene expression

Traceable author statement. Source: Reactome

glycogen biosynthetic process

Inferred from sequence or structural similarity. Source: UniProtKB

intracellular receptor signaling pathway

Traceable author statement PubMed 8622974. Source: GOC

negative regulation of receptor biosynthetic process

Inferred from mutant phenotype PubMed 18511497. Source: BHF-UCL

negative regulation of toll-like receptor 4 signaling pathway

Inferred from mutant phenotype PubMed 18511497. Source: BHF-UCL

negative regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 18511497. Source: BHF-UCL

negative regulation of transcription, DNA-templated

Inferred from direct assay Ref.6. Source: UniProtKB

positive regulation of bile acid biosynthetic process

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of transcription, DNA-templated

Inferred from sequence or structural similarity. Source: UniProtKB

proteasomal protein catabolic process

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of cholesterol homeostasis

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of circadian rhythm

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of fat cell differentiation

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype Ref.10. Source: UniProtKB

regulation of insulin secretion involved in cellular response to glucose stimulus

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of lipid metabolic process

Inferred from sequence or structural similarity. Source: UniProtKB

regulation of type B pancreatic cell proliferation

Inferred from sequence or structural similarity. Source: UniProtKB

response to leptin

Inferred from sequence or structural similarity. Source: UniProtKB

transcription initiation from RNA polymerase II promoter

Traceable author statement. Source: Reactome

   Cellular_componentcytoplasm

Inferred from sequence or structural similarity. Source: UniProtKB

dendrite

Inferred from sequence or structural similarity. Source: UniProtKB

dendritic spine

Inferred from sequence or structural similarity. Source: UniProtKB

nuclear chromatin

Inferred from direct assay PubMed 18511497. Source: BHF-UCL

nucleoplasm

Traceable author statement. Source: Reactome

nucleus

Inferred from sequence or structural similarity. Source: UniProtKB

   Molecular_functioncore promoter sequence-specific DNA binding

Inferred from direct assay Ref.6. Source: UniProtKB

heme binding

Inferred from direct assay Ref.10. Source: UniProtKB

ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity

Traceable author statement PubMed 8622974. Source: ProtInc

protein binding

Inferred from physical interaction Ref.9Ref.13Ref.14. Source: UniProtKB

steroid hormone receptor activity

Traceable author statement Ref.2. Source: ProtInc

transcription corepressor activity

Traceable author statement PubMed 8622974. Source: ProtInc

transcription corepressor binding

Inferred from direct assay Ref.6. Source: UniProtKB

transcription regulatory region DNA binding

Inferred from direct assay PubMed 18511497. Source: BHF-UCL

zinc ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 614614Nuclear receptor subfamily 1 group D member 1
PRO_0000053499

Regions

DNA binding129 – 20577Nuclear receptor
Zinc finger132 – 15221NR C4-type
Zinc finger169 – 19325NR C4-type
Region1 – 128128Modulating
Region49 – 284236Crucial for activation of GJA1 By similarity
Region206 – 28479Hinge
Region285 – 614330Ligand-binding
Compositional bias82 – 9312Poly-Ser

Sites

Binding site4181Heme By similarity
Binding site6021Heme

Amino acid modifications

Modified residue551Phosphoserine; by GSK3-beta Ref.8
Modified residue591Phosphoserine; by GSK3-beta Ref.8
Modified residue1911N6-acetyllysine; by KAT5 By similarity
Modified residue1921N6-acetyllysine; by KAT5 By similarity

Experimental info

Sequence conflict1471H → L in CAB53540. Ref.2
Sequence conflict5641E → Q Ref.2

Secondary structure

......................................... 614
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P20393 [UniParc].

Last modified February 1, 1991. Version 1.
Checksum: 67C71758E166508A

FASTA61466,805
        10         20         30         40         50         60 
MTTLDSNNNT GGVITYIGSS GSSPSRTSPE SLYSDNSNGS FQSLTQGCPT YFPPSPTGSL 

        70         80         90        100        110        120 
TQDPARSFGS IPPSLSDDGS PSSSSSSSSS SSSFYNGSPP GSLQVAMEDS SRVSPSKSTS 

       130        140        150        160        170        180 
NITKLNGMVL LCKVCGDVAS GFHYGVHACE GCKGFFRRSI QQNIQYKRCL KNENCSIVRI 

       190        200        210        220        230        240 
NRNRCQQCRF KKCLSVGMSR DAVRFGRIPK REKQRMLAEM QSAMNLANNQ LSSQCPLETS 

       250        260        270        280        290        300 
PTQHPTPGPM GPSPPPAPVP SPLVGFSQFP QQLTPPRSPS PEPTVEDVIS QVARAHREIF 

       310        320        330        340        350        360 
TYAHDKLGSS PGNFNANHAS GSPPATTPHR WENQGCPPAP NDNNTLAAQR HNEALNGLRQ 

       370        380        390        400        410        420 
APSSYPPTWP PGPAHHSCHQ SNSNGHRLCP THVYAAPEGK APANSPRQGN SKNVLLACPM 

       430        440        450        460        470        480 
NMYPHGRSGR TVQEIWEDFS MSFTPAVREV VEFAKHIPGF RDLSQHDQVT LLKAGTFEVL 

       490        500        510        520        530        540 
MVRFASLFNV KDQTVMFLSR TTYSLQELGA MGMGDLLSAM FDFSEKLNSL ALTEEELGLF 

       550        560        570        580        590        600 
TAVVLVSADR SGMENSASVE QLQETLLRAL RALVLKNRPL ETSRFTKLLL KLPDLRTLNN 

       610 
MHSEKLLSFR VDAQ 

« Hide

References

« Hide 'large scale' references
[1]"Two erbA homologs encoding proteins with different T3 binding capacities are transcribed from opposite DNA strands of the same genetic locus."
Miyajima N., Horiuchi R., Shibuya Y., Fukushige S., Matsubara K., Toyoshima K., Yamamoto T.
Cell 57:31-39(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, TISSUE SPECIFICITY.
Tissue: Placenta.
[2]"Isolation of a cDNA encoding human Rev-ErbA alpha: transcription from the noncoding DNA strand of a thyroid hormone receptor gene results in a related protein that does not bind thyroid hormone."
Lazar M.A., Jones K.E., Chin W.W.
DNA Cell Biol. 9:77-83(1990) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA], FUNCTION.
Tissue: Fetal skeletal muscle.
[3]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
Tissue: PNS.
[4]"Genomic organization of the human thyroid hormone receptor alpha (c-erbA-1) gene."
Laudet V., Begue A., Henry C., Joubel A., Martin P., Stehelin D., Saule S.
Nucleic Acids Res. 19:1105-1112(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 549-614.
[5]"Orphan nuclear hormone receptor Rev-erbalpha regulates the human apolipoprotein CIII promoter."
Coste H., Rodriguez J.C.
J. Biol. Chem. 277:27120-27129(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[6]"The orphan nuclear receptor Rev-erbalpha recruits the N-CoR/histone deacetylase 3 corepressor to regulate the circadian Bmal1 gene."
Yin L., Lazar M.A.
Mol. Endocrinol. 19:1452-1459(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[7]"The orphan nuclear receptor Rev-erb alpha regulates circadian expression of plasminogen activator inhibitor type 1."
Wang J., Yin L., Lazar M.A.
J. Biol. Chem. 281:33842-33848(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[8]"Nuclear receptor Rev-erbalpha is a critical lithium-sensitive component of the circadian clock."
Yin L., Wang J., Klein P.S., Lazar M.A.
Science 311:1002-1005(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION AT SER-55 AND SER-59, UBIQUITINATION.
[9]"A zinc finger HIT domain-containing protein, ZNHIT-1, interacts with orphan nuclear hormone receptor Rev-erbbeta and removes Rev-erbbeta-induced inhibition of apoCIII transcription."
Wang J., Li Y., Zhang M., Liu Z., Wu C., Yuan H., Li Y.Y., Zhao X., Lu H.
FEBS J. 274:5370-5381(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH ZNHIT1.
[10]"Rev-erbalpha, a heme sensor that coordinates metabolic and circadian pathways."
Yin L., Wu N., Curtin J.C., Qatanani M., Szwergold N.R., Reid R.A., Waitt G.M., Parks D.J., Pearce K.H., Wisely G.B., Lazar M.A.
Science 318:1786-1789(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, HEME-BINDING.
[11]"Negative feedback maintenance of heme homeostasis by its receptor, Rev-erbalpha."
Wu N., Yin L., Hanniman E.A., Joshi S., Lazar M.A.
Genes Dev. 23:2201-2209(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[12]"Nuclear receptor Rev-erbalpha: a heme receptor that coordinates circadian rhythm and metabolism."
Yin L., Wu N., Lazar M.A.
Nucl. Recept. Signal. 8:E001-E001(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
[13]"A circadian clock in hippocampus is regulated by interaction between oligophrenin-1 and Rev-erbalpha."
Valnegri P., Khelfaoui M., Dorseuil O., Bassani S., Lagneaux C., Gianfelice A., Benfante R., Chelly J., Billuart P., Sala C., Passafaro M.
Nat. Neurosci. 14:1293-1301(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH OPHN1.
[14]"Cryptochromes mediate rhythmic repression of the glucocorticoid receptor."
Lamia K.A., Papp S.J., Yu R.T., Barish G.D., Uhlenhaut N.H., Jonker J.W., Downes M., Evans R.M.
Nature 480:552-556(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH CRY1 AND PER2.
[15]"Direct regulation of CLOCK expression by REV-ERB."
Crumbley C., Burris T.P.
PLoS ONE 6:E17290-E17290(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[16]"REV-ERBs: more than the sum of the individual parts."
Stratmann M., Schibler U.
Cell Metab. 15:791-793(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
[17]"REV-ERB-erating nuclear receptor functions in circadian metabolism and physiology."
Ripperger J.A., Albrecht U.
Cell Res. 22:1319-1321(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: REVIEW.
[18]"The nuclear receptor REV-ERBalpha mediates circadian regulation of innate immunity through selective regulation of inflammatory cytokines."
Gibbs J.E., Blaikley J., Beesley S., Matthews L., Simpson K.D., Boyce S.H., Farrow S.N., Else K.J., Singh D., Ray D.W., Loudon A.S.
Proc. Natl. Acad. Sci. U.S.A. 109:582-587(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[19]"Structural elements of an orphan nuclear receptor-DNA complex."
Zhao Q., Khorasanizadeh S., Miyoshi Y., Lazar M.A., Rastinejad F.
Mol. Cell 1:849-861(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 123-215.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M24898 mRNA. Translation: AAA52335.1.
M24900 mRNA. Translation: AAA52332.1.
X55066 Genomic DNA. No translation available.
X55067 Genomic DNA. No translation available.
X72631 mRNA. Translation: CAB53540.1.
BC047875 mRNA. Translation: AAH47875.1.
BC056148 mRNA. Translation: AAH56148.1.
M34339 mRNA. Translation: AAA36561.1.
M34340 mRNA. Translation: AAA36562.2.
CCDSCCDS11361.1.
PIRA32608. A32286.
RefSeqNP_068370.1. NM_021724.4.
UniGeneHs.592130.
Hs.724.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1A6YX-ray2.30A/B123-216[»]
1EF6model-A281-301[»]
B430-614[»]
1GA5X-ray2.40A/B/E/F123-216[»]
1HLZX-ray2.80A/B123-216[»]
3N00X-ray2.60A281-614[»]
ProteinModelPortalP20393.
SMRP20393. Positions 127-613.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid114941. 9 interactions.
DIPDIP-48396N.
IntActP20393. 1 interaction.
STRING9606.ENSP00000246672.

Chemistry

BindingDBP20393.
ChEMBLCHEMBL1961783.
GuidetoPHARMACOLOGY596.

PTM databases

PhosphoSiteP20393.

Polymorphism databases

DMDM119100.

Proteomic databases

MaxQBP20393.
PaxDbP20393.
PRIDEP20393.

Protocols and materials databases

DNASU9572.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000246672; ENSP00000246672; ENSG00000126368.
GeneID9572.
KEGGhsa:9572.
UCSCuc002htz.3. human.

Organism-specific databases

CTD9572.
GeneCardsGC17M038249.
HGNCHGNC:7962. NR1D1.
HPAHPA007935.
MIM602408. gene.
neXtProtNX_P20393.
PharmGKBPA31748.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG324222.
HOGENOMHOG000261691.
HOVERGENHBG106790.
InParanoidP20393.
KOK03728.
OMAGTSPGNF.
OrthoDBEOG776SQ0.
PhylomeDBP20393.
TreeFamTF328382.

Enzyme and pathway databases

ReactomeREACT_24941. Circadian Clock.
REACT_71. Gene Expression.
SignaLinkP20393.

Gene expression databases

ArrayExpressP20393.
BgeeP20393.
CleanExHS_NR1D1.
GenevestigatorP20393.

Family and domain databases

Gene3D1.10.565.10. 2 hits.
3.30.50.10. 1 hit.
InterProIPR008946. Nucl_hormone_rcpt_ligand-bd.
IPR000536. Nucl_hrmn_rcpt_lig-bd_core.
IPR001723. Str_hrmn_rcpt.
IPR001628. Znf_hrmn_rcpt.
IPR013088. Znf_NHR/GATA.
[Graphical view]
PfamPF00104. Hormone_recep. 1 hit.
PF00105. zf-C4. 1 hit.
[Graphical view]
PRINTSPR00398. STRDHORMONER.
PR00047. STROIDFINGER.
SMARTSM00430. HOLI. 1 hit.
SM00399. ZnF_C4. 1 hit.
[Graphical view]
SUPFAMSSF48508. SSF48508. 1 hit.
PROSITEPS00031. NUCLEAR_REC_DBD_1. 1 hit.
PS51030. NUCLEAR_REC_DBD_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSNR1D1. human.
EvolutionaryTraceP20393.
GeneWikiRev-ErbA_alpha.
GenomeRNAi9572.
NextBio35899.
PROP20393.
SOURCESearch...

Entry information

Entry nameNR1D1_HUMAN
AccessionPrimary (citable) accession number: P20393
Secondary accession number(s): Q0P5Z4, Q15304
Entry history
Integrated into UniProtKB/Swiss-Prot: February 1, 1991
Last sequence update: February 1, 1991
Last modified: July 9, 2014
This is version 165 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human chromosome 17

Human chromosome 17: entries, gene names and cross-references to MIM