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P31431 (SDC4_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 149. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (6) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Syndecan-4

Short name=SYND4
Alternative name(s):
Amphiglycan
Ryudocan core protein
Gene names
Name:SDC4
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length198 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Cell surface proteoglycan that bears heparan sulfate.

Subunit structure

Homodimer. Interacts (via its cytoplasmic domain) with GIPC (via its PDZ domain). Interacts (via its cytoplasmic domain) with NUDT16L1 By similarity. Interacts with CDCP1 and SDCBP. Ref.14

Subcellular location

Isoform 1: Membrane; Single-pass type I membrane protein. Secreted. Note: Shedding of the ectodomain produces a soluble form By similarity. Ref.13

Isoform 2: Secreted Ref.13.

Tissue specificity

Expressed in epithelial and fibroblastic cells. Ref.1

Post-translational modification

Shedding is enhanced by a number of factors such as heparanase, thrombin or EGF. Also by stress and wound healing. PMA-mediated shedding is inhibited by TIMP3.

Sequence similarities

Belongs to the syndecan proteoglycan family.

Ontologies

Keywords
   Cellular componentMembrane
Secreted
   Coding sequence diversityAlternative splicing
Polymorphism
   DomainSignal
Transmembrane
Transmembrane helix
   PTMGlycoprotein
Heparan sulfate
Proteoglycan
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processcarbohydrate metabolic process

Traceable author statement. Source: Reactome

chondroitin sulfate metabolic process

Traceable author statement. Source: Reactome

extracellular matrix organization

Traceable author statement. Source: Reactome

glycosaminoglycan biosynthetic process

Traceable author statement. Source: Reactome

glycosaminoglycan catabolic process

Traceable author statement. Source: Reactome

glycosaminoglycan metabolic process

Traceable author statement. Source: Reactome

phototransduction, visible light

Traceable author statement. Source: Reactome

positive regulation of focal adhesion assembly

Inferred from electronic annotation. Source: Ensembl

positive regulation of protein kinase activity

Inferred from electronic annotation. Source: Ensembl

positive regulation of stress fiber assembly

Inferred from electronic annotation. Source: Ensembl

retinoid metabolic process

Traceable author statement. Source: Reactome

small molecule metabolic process

Traceable author statement. Source: Reactome

ureteric bud development

Inferred from electronic annotation. Source: Ensembl

   Cellular_componentGolgi lumen

Traceable author statement. Source: Reactome

cell surface

Inferred from electronic annotation. Source: Ensembl

costamere

Inferred from electronic annotation. Source: Ensembl

extracellular vesicular exosome

Inferred from direct assay PubMed 19199708PubMed 23376485. Source: UniProt

focal adhesion

Inferred from electronic annotation. Source: Ensembl

integral component of plasma membrane

Non-traceable author statement Ref.1. Source: UniProtKB

lysosomal lumen

Traceable author statement. Source: Reactome

membrane raft

Inferred from electronic annotation. Source: Ensembl

plasma membrane

Traceable author statement. Source: Reactome

   Molecular_functionprotein binding

Inferred from physical interaction PubMed 12571249. Source: IntAct

thrombospondin receptor activity

Inferred from mutant phenotype PubMed 17879962. Source: BHF-UCL

Complete GO annotation...

Binary interactions

With

Entry

#Exp.

IntAct

Notes

PRKCAP172522EBI-3913237,EBI-1383528

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: P31431-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: P31431-2)

The sequence of this isoform differs from the canonical sequence as follows:
     149-198: ALIVGGIVGILFAVFLILLLMYRMKKKDEGSYDLGKKPIYKKAPTNEFYA → GCPEH
Note: Soluble form, lacks the transmembrane domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 1818 Potential
Chain19 – 198180Syndecan-4
PRO_0000033511

Regions

Topological domain19 – 145127Extracellular Potential
Transmembrane146 – 17025Helical; Potential
Topological domain171 – 19828Cytoplasmic Potential

Amino acid modifications

Glycosylation391O-linked (Xyl...) (heparan sulfate) By similarity
Glycosylation611O-linked (Xyl...) (heparan sulfate) Potential
Glycosylation631O-linked (Xyl...) (heparan sulfate) Potential

Natural variations

Alternative sequence149 – 19850ALIVG…NEFYA → GCPEH in isoform 2.
VSP_044449
Natural variant121F → L. Ref.1 Ref.6
Corresponds to variant rs4458268 [ dbSNP | Ensembl ].
VAR_021851

Secondary structure

.... 198
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified July 15, 1998. Version 2.
Checksum: 8229AA2733F77A10

FASTA19821,642
        10         20         30         40         50         60 
MAPARLFALL LFFVGGVAES IRETEVIDPQ DLLEGRYFSG ALPDDEDVVG PGQESDDFEL 

        70         80         90        100        110        120 
SGSGDLDDLE DSMIGPEVVH PLVPLDNHIP ERAGSGSQVP TEPKKLEENE VIPKRISPVE 

       130        140        150        160        170        180 
ESEDVSNKVS MSSTVQGSNI FERTEVLAAL IVGGIVGILF AVFLILLLMY RMKKKDEGSY 

       190 
DLGKKPIYKK APTNEFYA 

« Hide

Isoform 2 [UniParc].

Checksum: 25AD50751A7D2642
Show »

FASTA15316,545

References

« Hide 'large scale' references
[1]"Molecular cloning of amphiglycan, a novel integral membrane heparan sulfate proteoglycan expressed by epithelial and fibroblastic cells."
David G., van der Schueren B., Marynen P., Cassiman J.-J., van den Berghe H.
J. Cell Biol. 118:961-969(1992) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, VARIANT LEU-12.
Tissue: Lung fibroblast.
[2]"Human ryudocan core protein: molecular cloning and characterization of the cDNA, and chromosomal localization of the gene."
Kojima T., Inazawa J., Takamatsu J., Rosenberg R.D., Saito H.
Biochem. Biophys. Res. Commun. 190:814-822(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
[3]"Structural organization and promoter activity of the human ryudocan gene."
Takagi A., Kojima T., Tsuzuki S., Katsumi A., Yamazaki T., Sugiura I., Hamaguchi M., Saito H.
J. Biochem. 119:979-984(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Tissue: Placenta.
[4]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
Tissue: Thalamus.
[5]"Cloning of human full open reading frames in Gateway(TM) system entry vector (pDONR201)."
Ebert L., Schick M., Neubert P., Schatten R., Henze S., Korn B.
Submitted (JUN-2004) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
[6]Suzuki Y., Sugano S., Totoki Y., Toyoda A., Takeda T., Sakaki Y., Tanaka A., Yokoyama S.
Submitted (APR-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), VARIANT LEU-12.
Tissue: Stomach.
[7]"The DNA sequence and comparative analysis of human chromosome 20."
Deloukas P., Matthews L.H., Ashurst J.L., Burton J., Gilbert J.G.R., Jones M., Stavrides G., Almeida J.P., Babbage A.K., Bagguley C.L., Bailey J., Barlow K.F., Bates K.N., Beard L.M., Beare D.M., Beasley O.P., Bird C.P., Blakey S.E. expand/collapse author list , Bridgeman A.M., Brown A.J., Buck D., Burrill W.D., Butler A.P., Carder C., Carter N.P., Chapman J.C., Clamp M., Clark G., Clark L.N., Clark S.Y., Clee C.M., Clegg S., Cobley V.E., Collier R.E., Connor R.E., Corby N.R., Coulson A., Coville G.J., Deadman R., Dhami P.D., Dunn M., Ellington A.G., Frankland J.A., Fraser A., French L., Garner P., Grafham D.V., Griffiths C., Griffiths M.N.D., Gwilliam R., Hall R.E., Hammond S., Harley J.L., Heath P.D., Ho S., Holden J.L., Howden P.J., Huckle E., Hunt A.R., Hunt S.E., Jekosch K., Johnson C.M., Johnson D., Kay M.P., Kimberley A.M., King A., Knights A., Laird G.K., Lawlor S., Lehvaeslaiho M.H., Leversha M.A., Lloyd C., Lloyd D.M., Lovell J.D., Marsh V.L., Martin S.L., McConnachie L.J., McLay K., McMurray A.A., Milne S.A., Mistry D., Moore M.J.F., Mullikin J.C., Nickerson T., Oliver K., Parker A., Patel R., Pearce T.A.V., Peck A.I., Phillimore B.J.C.T., Prathalingam S.R., Plumb R.W., Ramsay H., Rice C.M., Ross M.T., Scott C.E., Sehra H.K., Shownkeen R., Sims S., Skuce C.D., Smith M.L., Soderlund C., Steward C.A., Sulston J.E., Swann R.M., Sycamore N., Taylor R., Tee L., Thomas D.W., Thorpe A., Tracey A., Tromans A.C., Vaudin M., Wall M., Wallis J.M., Whitehead S.L., Whittaker P., Willey D.L., Williams L., Williams S.A., Wilming L., Wray P.W., Hubbard T., Durbin R.M., Bentley D.R., Beck S., Rogers J.
Nature 414:865-871(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[8]Mural R.J., Istrail S., Sutton G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[9]"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] (ISOFORM 1).
Tissue: Lung.
[10]"The WashU-Merck EST project."
Hillier L., Clark N., Dubuque T., Elliston K., Hawkins M., Holman M., Hultman M., Kucaba T., Le M., Lennon G., Marra M., Parsons J., Rifkin L., Rohlfing T., Soares M., Tan F., Trevaskis E., Waterston R. expand/collapse author list , Williamson A., Wohldmann P., Wilson R.
Submitted (MAR-2000) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 75-153 (ISOFORM 2).
[11]"Generation and analysis of 280,000 human expressed sequence tags."
Hillier L.D., Lennon G., Becker M., Bonaldo M.F., Chiapelli B., Chissoe S., Dietrich N., DuBuque T., Favello A., Gish W., Hawkins M., Hultman M., Kucaba T., Lacy M., Le M., Le N., Mardis E., Moore B. expand/collapse author list , Morris M., Parsons J., Prange C., Rifkin L., Rohlfing T., Schellenberg K., Bento Soares M., Tan F., Thierry-Meg J., Trevaskis E., Underwood K., Wohldman P., Waterston R., Wilson R., Marra M.
Genome Res. 6:807-828(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 125-153 (ISOFORM 2).
Tissue: Uterus.
[12]"Regulated shedding of syndecan-1 and -4 ectodomains by thrombin and growth factor receptor activation."
Subramanian S.V., Fitzgerald M.L., Bernfield M.
J. Biol. Chem. 272:14713-14720(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: SHEDDING.
[13]"Widespread production of novel soluble protein isoforms by alternative splicing removal of transmembrane anchoring domains."
Xing Y., Xu Q., Lee C.
FEBS Lett. 555:572-578(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: ALTERNATIVE SPLICING (ISOFORM 2), SUBCELLULAR LOCATION.
[14]"Adhesion signaling by a novel mitotic substrate of src kinases."
Bhatt A.S., Erdjument-Bromage H., Tempst P., Craik C.S., Moasser M.M.
Oncogene 24:5333-5343(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH CDCP1.
[15]"Initial characterization of the human central proteome."
Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J.
BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[16]"Solution structure of the dimeric cytoplasmic domain of syndecan-4."
Shin J., Lee W., Lee D., Koo B.-K., Han I., Lim Y., Woods A., Couchman J.R., Oh E.-S.
Biochemistry 40:8471-8478(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: STRUCTURE BY NMR OF 171-198.
[17]"Molecular roots of degenerate specificity in syntenin's PDZ2 domain: reassessment of the PDZ recognition paradigm."
Kang B.S., Cooper D.R., Devedjiev Y., Derewenda U., Derewenda Z.S.
Structure 11:845-853(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 193-198 IN COMPLEX WITH SDCBP.
[18]"The binding of the PDZ tandem of syntenin to target proteins."
Grembecka J., Cierpicki T., Devedjiev Y., Derewenda U., Kang B.S., Bushweller J.H., Derewenda Z.S.
Biochemistry 45:3674-3683(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) OF 182-198 IN COMPLEX WITH SDCBP.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X67016 mRNA. Translation: CAA47406.1.
D13292 mRNA. Translation: BAA02550.1.
D79206 Genomic DNA. Translation: BAA19613.1.
AK312507 mRNA. Translation: BAG35408.1.
CR542045 mRNA. Translation: CAG46842.1.
CR542074 mRNA. Translation: CAG46871.1.
AK222695 mRNA. Translation: BAD96415.1.
AK223243 mRNA. Translation: BAD96963.1.
AL021578 Genomic DNA. Translation: CAA16520.1.
CH471077 Genomic DNA. Translation: EAW75861.1.
CH471077 Genomic DNA. Translation: EAW75862.1.
BC030805 mRNA. Translation: AAH30805.1.
AA151028 mRNA. No translation available.
AA258502 mRNA. No translation available.
CCDSCCDS13350.1. [P31431-1]
PIRJC1457.
RefSeqNP_002990.2. NM_002999.3. [P31431-1]
UniGeneHs.632267.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1EJPNMR-A/B171-198[»]
1EJQNMR-A/B171-198[»]
1OBYX-ray1.85P/Q193-198[»]
1YBOX-ray2.30C/D182-198[»]
ProteinModelPortalP31431.
SMRP31431. Positions 171-198.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid112286. 9 interactions.
DIPDIP-29945N.
IntActP31431. 3 interactions.
MINTMINT-140673.
STRING9606.ENSP00000361818.

Protein family/group databases

TCDB9.A.35.1.1. the peptide translocating syndecan (syndecan) family.

PTM databases

PhosphoSiteP31431.

Polymorphism databases

DMDM2851418.

Proteomic databases

MaxQBP31431.
PaxDbP31431.
PRIDEP31431.

Protocols and materials databases

DNASU6385.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000372733; ENSP00000361818; ENSG00000124145. [P31431-1]
GeneID6385.
KEGGhsa:6385.
UCSCuc002xnu.3. human. [P31431-1]

Organism-specific databases

CTD6385.
GeneCardsGC20M043953.
HGNCHGNC:10661. SDC4.
HPACAB013240.
HPA005716.
MIM600017. gene.
neXtProtNX_P31431.
PharmGKBPA35591.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG83582.
HOGENOMHOG000263414.
HOVERGENHBG004501.
InParanoidP31431.
KOK16338.
OMAIPKRISP.
OrthoDBEOG7RV9HS.
PhylomeDBP31431.
TreeFamTF320463.

Enzyme and pathway databases

ReactomeREACT_111102. Signal Transduction.
REACT_111217. Metabolism.
REACT_116125. Disease.
REACT_118779. Extracellular matrix organization.

Gene expression databases

ArrayExpressP31431.
BgeeP31431.
CleanExHS_SDC4.
GenevestigatorP31431.

Family and domain databases

InterProIPR003585. Neurexin-like.
IPR001050. Syndecan.
IPR027789. Syndecan/Neurexin_dom.
[Graphical view]
PANTHERPTHR10915. PTHR10915. 1 hit.
PfamPF01034. Syndecan. 1 hit.
[Graphical view]
SMARTSM00294. 4.1m. 1 hit.
[Graphical view]
PROSITEPS00964. SYNDECAN. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSSDC4. human.
EvolutionaryTraceP31431.
GeneWikiSDC4.
GenomeRNAi6385.
NextBio24792.
PMAP-CutDBP31431.
PROP31431.
SOURCESearch...

Entry information

Entry nameSDC4_HUMAN
AccessionPrimary (citable) accession number: P31431
Secondary accession number(s): O00773 expand/collapse secondary AC list , Q16833, Q53FN9, Q6FGN3
Entry history
Integrated into UniProtKB/Swiss-Prot: July 1, 1993
Last sequence update: July 15, 1998
Last modified: July 9, 2014
This is version 149 of the entry and version 2 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 polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 20

Human chromosome 20: entries, gene names and cross-references to MIM