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Q9H3R0 (KDM4C_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 122. 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·Alt products·Sequence annotation·Sequences·References·Web links·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Lysine-specific demethylase 4C

EC=1.14.11.-
Alternative name(s):
Gene amplified in squamous cell carcinoma 1 protein
Short name=GASC-1 protein
JmjC domain-containing histone demethylation protein 3C
Jumonji domain-containing protein 2C
Gene names
Name:KDM4C
Synonyms:GASC1, JHDM3C, JMJD2C, KIAA0780
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1056 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20'. Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues. Demethylation of Lys residue generates formaldehyde and succinate. Ref.6

Cofactor

Binds 1 Fe2+ ion per subunit. Ref.7

Subcellular location

Nucleus By similarity.

Tissue specificity

Overexpressed in several esophageal squamous cell carcinomas (ESCs). Ref.1

Domain

The 2 Tudor domains recognize and bind methylated histones. Double Tudor domain has an interdigitated structure and the unusual fold is required for its ability to bind methylated histone tails By similarity.

Sequence similarities

Belongs to the JHDM3 histone demethylase family.

Contains 1 JmjC domain.

Contains 1 JmjN domain.

Contains 2 PHD-type zinc fingers.

Contains 2 Tudor domains.

Sequence caution

The sequence BAA34500.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

The sequence CAI39608.1 differs from that shown. Reason: Erroneous gene model prediction.

Alternative products

This entry describes 4 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q9H3R0-1)

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: Q9H3R0-2)

The sequence of this isoform differs from the canonical sequence as follows:
     999-1056: STASDMRFED...SFQKKCQKRQ → VSAGRCHLGT...QCNIFLSGTY
Note: No experimental confirmation available.
Isoform 3 (identifier: Q9H3R0-3)

The sequence of this isoform differs from the canonical sequence as follows:
     809-813: KCIFC → GRLGI
     814-1056: Missing.
Note: No experimental confirmation available.
Isoform 4 (identifier: Q9H3R0-4)

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MKHYGLPWKRTEEAAADTALTIM
     809-813: KCIFC → GRLGI
     814-1056: Missing.
Note: No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 10561056Lysine-specific demethylase 4C
PRO_0000183177

Regions

Domain16 – 5843JmjN
Domain144 – 310167JmjC
Domain877 – 93458Tudor 1
Domain935 – 99157Tudor 2
Zinc finger689 – 74759PHD-type 1
Zinc finger809 – 86557PHD-type 2

Sites

Metal binding1901Iron; catalytic
Metal binding1921Iron; catalytic
Metal binding2361Zinc
Metal binding2421Zinc
Metal binding2781Iron; catalytic
Metal binding3081Zinc
Metal binding3101Zinc
Binding site1341Alpha-ketoglutarate By similarity
Binding site2001Alpha-ketoglutarate By similarity
Binding site2081Alpha-ketoglutarate By similarity

Natural variations

Alternative sequence11M → MKHYGLPWKRTEEAAADTAL TIM in isoform 4.
VSP_046113
Alternative sequence809 – 8135KCIFC → GRLGI in isoform 3 and isoform 4.
VSP_045462
Alternative sequence814 – 1056243Missing in isoform 3 and isoform 4.
VSP_045463
Alternative sequence999 – 105658STASD…CQKRQ → VSAGRCHLGTCQVNSLSSPH VSQAQQETYLGFWINSKKSQ CNIFLSGTY in isoform 2.
VSP_018311
Natural variant2061E → D.
Corresponds to variant rs7864351 [ dbSNP | Ensembl ].
VAR_049660
Natural variant3961D → N.
Corresponds to variant rs2296067 [ dbSNP | Ensembl ].
VAR_020340
Natural variant4921S → T. Ref.1 Ref.2 Ref.3
Corresponds to variant rs35826653 [ dbSNP | Ensembl ].
VAR_049661
Natural variant6971N → S.
Corresponds to variant rs35389625 [ dbSNP | Ensembl ].
VAR_049662
Natural variant7671Q → E.
Corresponds to variant rs1407856 [ dbSNP | Ensembl ].
VAR_024681
Natural variant7721K → R. Ref.1
Corresponds to variant rs1417290 [ dbSNP | Ensembl ].
VAR_049663
Natural variant10391V → I. Ref.5
Corresponds to variant rs913588 [ dbSNP | Ensembl ].
VAR_024682

Experimental info

Sequence conflict1551L → I in BAB16102. Ref.1
Sequence conflict5141C → S in BAG64946. Ref.3
Sequence conflict8071K → R in BAG64946. Ref.3

Secondary structure

.................................................................................... 1056
Helix Strand Turn

Details...

Sequences

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

Last modified May 16, 2006. Version 2.
Checksum: CBE871D4FAADD06D

FASTA1,056119,982
        10         20         30         40         50         60 
MEVAEVESPL NPSCKIMTFR PSMEEFREFN KYLAYMESKG AHRAGLAKVI PPKEWKPRQC 

        70         80         90        100        110        120 
YDDIDNLLIP APIQQMVTGQ SGLFTQYNIQ KKAMTVKEFR QLANSGKYCT PRYLDYEDLE 

       130        140        150        160        170        180 
RKYWKNLTFV APIYGADING SIYDEGVDEW NIARLNTVLD VVEEECGISI EGVNTPYLYF 

       190        200        210        220        230        240 
GMWKTTFAWH TEDMDLYSIN YLHFGEPKSW YAIPPEHGKR LERLAQGFFP SSSQGCDAFL 

       250        260        270        280        290        300 
RHKMTLISPS VLKKYGIPFD KITQEAGEFM ITFPYGYHAG FNHGFNCAES TNFATVRWID 

       310        320        330        340        350        360 
YGKVAKLCTC RKDMVKISMD IFVRKFQPDR YQLWKQGKDI YTIDHTKPTP ASTPEVKAWL 

       370        380        390        400        410        420 
QRRRKVRKAS RSFQCARSTS KRPKADEEEE VSDEVDGAEV PNPDSVTDDL KVSEKSEAAV 

       430        440        450        460        470        480 
KLRNTEASSE EESSASRMQV EQNLSDHIKL SGNSCLSTSV TEDIKTEDDK AYAYRSVPSI 

       490        500        510        520        530        540 
SSEADDSIPL SSGYEKPEKS DPSELSWPKS PESCSSVAES NGVLTEGEES DVESHGNGLE 

       550        560        570        580        590        600 
PGEIPAVPSG ERNSFKVPSI AEGENKTSKS WRHPLSRPPA RSPMTLVKQQ APSDEELPEV 

       610        620        630        640        650        660 
LSIEEEVEET ESWAKPLIHL WQTKSPNFAA EQEYNATVAR MKPHCAICTL LMPYHKPDSS 

       670        680        690        700        710        720 
NEENDARWET KLDEVVTSEG KTKPLIPEMC FIYSEENIEY SPPNAFLEED GTSLLISCAK 

       730        740        750        760        770        780 
CCVRVHASCY GIPSHEICDG WLCARCKRNA WTAECCLCNL RGGALKQTKN NKWAHVMCAV 

       790        800        810        820        830        840 
AVPEVRFTNV PERTQIDVGR IPLQRLKLKC IFCRHRVKRV SGACIQCSYG RCPASFHVTC 

       850        860        870        880        890        900 
AHAAGVLMEP DDWPYVVNIT CFRHKVNPNV KSKACEKVIS VGQTVITKHR NTRYYSCRVM 

       910        920        930        940        950        960 
AVTSQTFYEV MFDDGSFSRD TFPEDIVSRD CLKLGPPAEG EVVQVKWPDG KLYGAKYFGS 

       970        980        990       1000       1010       1020 
NIAHMYQVEF EDGSQIAMKR EDIYTLDEEL PKRVKARFST ASDMRFEDTF YGADIIQGER 

      1030       1040       1050 
KRQRVLSSRF KNEYVADPVY RTFLKSSFQK KCQKRQ 

« Hide

Isoform 2 [UniParc].

Checksum: 5A6E06262786B259
Show »

FASTA1,047118,416
Isoform 3 [UniParc].

Checksum: 672012048DEE27AC
Show »

FASTA81391,891
Isoform 4 [UniParc].

Checksum: B08576383C57FE4B
Show »

FASTA83594,376

References

« Hide 'large scale' references
[1]"Identification of a novel gene, GASC1, within an amplicon at 9p23-24 frequently detected in esophageal cancer cell lines."
Yang Z.Q., Imoto I., Fukuda Y., Pimkhaokham A., Shimada Y., Imamura M., Sugano S., Nakamura Y., Inazawa J.
Cancer Res. 60:4735-4739(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), TISSUE SPECIFICITY, VARIANTS THR-492 AND ARG-772.
[2]"Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
Nagase T., Ishikawa K., Suyama M., Kikuno R., Miyajima N., Tanaka A., Kotani H., Nomura N., Ohara O.
DNA Res. 5:277-286(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2), VARIANT THR-492.
Tissue: Brain.
[3]"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] (ISOFORMS 3 AND 4), VARIANT THR-492.
Tissue: Testis and Trachea.
[4]"DNA sequence and analysis of human chromosome 9."
Humphray S.J., Oliver K., Hunt A.R., Plumb R.W., Loveland J.E., Howe K.L., Andrews T.D., Searle S., Hunt S.E., Scott C.E., Jones M.C., Ainscough R., Almeida J.P., Ambrose K.D., Ashwell R.I.S., Babbage A.K., Babbage S., Bagguley C.L. expand/collapse author list , Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beasley H., Beasley O., Bird C.P., Bray-Allen S., Brown A.J., Brown J.Y., Burford D., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Chen Y., Clarke G., Clark S.Y., Clee C.M., Clegg S., Collier R.E., Corby N., Crosier M., Cummings A.T., Davies J., Dhami P., Dunn M., Dutta I., Dyer L.W., Earthrowl M.E., Faulkner L., Fleming C.J., Frankish A., Frankland J.A., French L., Fricker D.G., Garner P., Garnett J., Ghori J., Gilbert J.G.R., Glison C., Grafham D.V., Gribble S., Griffiths C., Griffiths-Jones S., Grocock R., Guy J., Hall R.E., Hammond S., Harley J.L., Harrison E.S.I., Hart E.A., Heath P.D., Henderson C.D., Hopkins B.L., Howard P.J., Howden P.J., Huckle E., Johnson C., Johnson D., Joy A.A., Kay M., Keenan S., Kershaw J.K., Kimberley A.M., King A., Knights A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C., Lloyd D.M., Lovell J., Martin S., Mashreghi-Mohammadi M., Matthews L., McLaren S., McLay K.E., McMurray A., Milne S., Nickerson T., Nisbett J., Nordsiek G., Pearce A.V., Peck A.I., Porter K.M., Pandian R., Pelan S., Phillimore B., Povey S., Ramsey Y., Rand V., Scharfe M., Sehra H.K., Shownkeen R., Sims S.K., Skuce C.D., Smith M., Steward C.A., Swarbreck D., Sycamore N., Tester J., Thorpe A., Tracey A., Tromans A., Thomas D.W., Wall M., Wallis J.M., West A.P., Whitehead S.L., Willey D.L., Williams S.A., Wilming L., Wray P.W., Young L., Ashurst J.L., Coulson A., Blocker H., Durbin R.M., Sulston J.E., Hubbard T., Jackson M.J., Bentley D.R., Beck S., Rogers J., Dunham I.
Nature 429:369-374(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[5]"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), VARIANT ILE-1039.
Tissue: Liver.
[6]"Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases."
Whetstine J.R., Nottke A., Lan F., Huarte M., Smolikov S., Chen Z., Spooner E., Li E., Zhang G., Colaiacovo M., Shi Y.
Cell 125:467-481(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, ENZYME ACTIVITY.
[7]"Structural and evolutionary basis for the dual substrate selectivity of human KDM4 histone demethylase family."
Hillringhaus L., Yue W.W., Rose N.R., Ng S.S., Gileadi C., Loenarz C., Bello S.H., Bray J.E., Schofield C.J., Oppermann U.
J. Biol. Chem. 286:41616-41625(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.55 ANGSTROMS) OF 1-347 IN COMPLEX WITH ZINC AND NICKEL ION, COFACTOR, SUBSTRATE SPECIFICITY.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AB037901 mRNA. Translation: BAB16102.1.
AB018323 mRNA. Translation: BAA34500.1. Different initiation.
AK304032 mRNA. Translation: BAG64946.1.
AK310439 mRNA. No translation available.
AL354707 expand/collapse EMBL AC list , AL137020, AL161443, AL445592, AL513412 Genomic DNA. Translation: CAH73283.1.
AL354707 expand/collapse EMBL AC list , AL137020, AL161443, AL513412, AL445592 Genomic DNA. Translation: CAH73284.1.
AL445592 expand/collapse EMBL AC list , AL161443, AL513412, AL354707, AL137020 Genomic DNA. Translation: CAI16322.1.
AL445592 expand/collapse EMBL AC list , AL137020, AL354707, AL513412, AL161443 Genomic DNA. Translation: CAI16323.1.
AL161443 expand/collapse EMBL AC list , AL137020, AL354707, AL513412, AL445592 Genomic DNA. Translation: CAI39606.1.
AL161443 expand/collapse EMBL AC list , AL513412, AL445592, AL354707, AL137020 Genomic DNA. Translation: CAI39607.1.
AL161443, AL137020, AL513412 Genomic DNA. Translation: CAI39608.1. Sequence problems.
BC104859 mRNA. Translation: AAI04860.1.
BC104861 mRNA. Translation: AAI04862.1.
BC143571 mRNA. Translation: AAI43572.1.
CCDSCCDS55285.1. [Q9H3R0-4]
CCDS55286.1. [Q9H3R0-3]
CCDS55287.1. [Q9H3R0-2]
CCDS6471.1. [Q9H3R0-1]
RefSeqNP_001140166.1. NM_001146694.1. [Q9H3R0-2]
NP_001140167.1. NM_001146695.1. [Q9H3R0-3]
NP_001140168.1. NM_001146696.1. [Q9H3R0-4]
NP_055876.2. NM_015061.3. [Q9H3R0-1]
UniGeneHs.709425.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2XDPX-ray1.56A875-995[»]
2XMLX-ray2.55A/B1-347[»]
ProteinModelPortalQ9H3R0.
SMRQ9H3R0. Positions 10-347, 713-749, 876-994.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid116712. 9 interactions.
DIPDIP-60098N.
IntActQ9H3R0. 1 interaction.
MINTMINT-4658283.
STRING9606.ENSP00000370710.

Chemistry

BindingDBQ9H3R0.
ChEMBLCHEMBL6175.

PTM databases

PhosphoSiteQ9H3R0.

Polymorphism databases

DMDM97536525.

Proteomic databases

MaxQBQ9H3R0.
PaxDbQ9H3R0.
PRIDEQ9H3R0.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000381306; ENSP00000370707; ENSG00000107077. [Q9H3R0-2]
ENST00000381309; ENSP00000370710; ENSG00000107077. [Q9H3R0-1]
ENST00000535193; ENSP00000442382; ENSG00000107077. [Q9H3R0-4]
ENST00000543771; ENSP00000445427; ENSG00000107077. [Q9H3R0-3]
GeneID23081.
KEGGhsa:23081.
UCSCuc003zkg.3. human. [Q9H3R0-2]
uc003zkh.3. human. [Q9H3R0-1]

Organism-specific databases

CTD23081.
GeneCardsGC09P006720.
H-InvDBHIX0017555.
HGNCHGNC:17071. KDM4C.
MIM605469. gene.
neXtProtNX_Q9H3R0.
PharmGKBPA164721503.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG5141.
HOGENOMHOG000231125.
InParanoidQ9H3R0.
KOK06709.
OMADIIQGER.
OrthoDBEOG7TQV03.
PhylomeDBQ9H3R0.
TreeFamTF106449.

Gene expression databases

ArrayExpressQ9H3R0.
BgeeQ9H3R0.
CleanExHS_JMJD2C.
GenevestigatorQ9H3R0.

Family and domain databases

InterProIPR003347. JmjC_dom.
IPR003349. TF_JmjN.
IPR002999. Tudor.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
[Graphical view]
PfamPF02373. JmjC. 1 hit.
PF02375. JmjN. 1 hit.
[Graphical view]
SMARTSM00558. JmjC. 1 hit.
SM00545. JmjN. 1 hit.
SM00249. PHD. 2 hits.
SM00333. TUDOR. 2 hits.
[Graphical view]
SUPFAMSSF57903. SSF57903. 1 hit.
PROSITEPS51184. JMJC. 1 hit.
PS51183. JMJN. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

ChiTaRSKDM4C. human.
EvolutionaryTraceQ9H3R0.
GeneWikiJMJD2C.
GenomeRNAi23081.
NextBio44205.
PROQ9H3R0.
SOURCESearch...

Entry information

Entry nameKDM4C_HUMAN
AccessionPrimary (citable) accession number: Q9H3R0
Secondary accession number(s): B4E1Y4 expand/collapse secondary AC list , B7ZL46, F5H347, F5H7P0, O94877, Q2M3M0, Q5JUC9, Q5VYJ2, Q5VYJ3
Entry history
Integrated into UniProtKB/Swiss-Prot: February 16, 2004
Last sequence update: May 16, 2006
Last modified: July 9, 2014
This is version 122 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 9

Human chromosome 9: entries, gene names and cross-references to MIM