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Q6ZMT4 (KDM7A_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 91. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Lysine-specific demethylase 7A

EC=1.14.11.-
Alternative name(s):
JmjC domain-containing histone demethylation protein 1D
Lysine-specific demethylase 7
Gene names
Name:KDM7A
Synonyms:JHDM1D, KDM7, KIAA1718
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length941 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Histone demethylase required for brain development. Specifically demethylates dimethylated 'Lys-9' and 'Lys-27' (H3K9me2 and H3K27me2, respectively) of histone H3 and monomethylated histone H4 'Lys-20' residue (H4K20Me1), thereby playing a central role in histone code. Specifically binds trimethylated 'Lys-4' of histone H3 (H3K4me3), affecting histone demethylase specificity: in presence of H3K4me3, it has no demethylase activity toward H3K9me2, while it has high activity toward H3K27me2. Demethylates H3K9me2 in absence of H3K4me3. Has activity toward H4K20Me1 only when nucleosome is used as a substrate and when not histone octamer is used as substrate. Ref.6 Ref.7 Ref.8

Cofactor

Binds 1 Fe2+ ion per subunit. Ref.6 Ref.8

Subcellular location

Nucleus.

Domain

The PHD-type zinc finger mediates the binding to H3K4me3. Binding to H3K4me3 prevents its access to H3K9me2. Ref.8

The linker region is a critical determinant of demethylase specificity. It prevents the active site of JmjC to reach the target H3K9me2 when the PHD-type zinc finger binds to H3K4me3, while it favors selectivity toward H3K27me2. Ref.8

Sequence similarities

Belongs to the JHDM1 histone demethylase family. JHDM1D subfamily.

Contains 1 JmjC domain.

Contains 1 PHD-type zinc finger.

Biophysicochemical properties

Kinetic parameters:

KM=1.2 µM for histone H3 H3K9Me2 Ref.8

Sequence caution

The sequence BAD18641.1 differs from that shown. Reason: Frameshift at position 902.

The sequence EAL24032.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
   Biological processNeurogenesis
Transcription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
Polymorphism
   DomainZinc-finger
   LigandIron
Metal-binding
Zinc
   Molecular functionChromatin regulator
Dioxygenase
Oxidoreductase
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processhistone H3-K27 demethylation

Inferred from direct assay Ref.8Ref.6Ref.7. Source: UniProtKB

histone H3-K36 demethylation

Inferred from direct assay Ref.7. Source: UniProtKB

histone H3-K9 demethylation

Inferred from direct assay Ref.8Ref.6Ref.7. Source: UniProtKB

histone H4-K20 demethylation

Inferred from direct assay Ref.7. Source: UniProtKB

midbrain development

Inferred from sequence or structural similarity. Source: UniProtKB

positive regulation of transcription, DNA-templated

Inferred from electronic annotation. Source: Ensembl

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleolus

Inferred from direct assay. Source: HPA

nucleus

Inferred by curator Ref.8. Source: UniProtKB

   Molecular_functionhistone demethylase activity (H3-K27 specific)

Inferred from direct assay Ref.8Ref.6Ref.7. Source: UniProtKB

histone demethylase activity (H3-K36 specific)

Inferred from direct assay Ref.7. Source: UniProtKB

histone demethylase activity (H3-K9 specific)

Inferred from direct assay Ref.8Ref.6Ref.7. Source: UniProtKB

histone demethylase activity (H4-K20 specific)

Inferred from direct assay Ref.7. Source: UniProtKB

iron ion binding

Inferred from direct assay Ref.8. Source: UniProtKB

methylated histone binding

Inferred from direct assay Ref.8. Source: UniProtKB

oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors

Inferred from direct assay Ref.8Ref.6. Source: UniProtKB

zinc ion binding

Inferred from direct assay Ref.8. Source: UniProtKB

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q6ZMT4-1)

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: Q6ZMT4-2)

The sequence of this isoform differs from the canonical sequence as follows:
     792-809: GYHVKTEDPDLRTSSWIK → ETRSHLCCPDWSPTPELK
     810-941: Missing.
Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. No experimental confirmation available.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 941941Lysine-specific demethylase 7A
PRO_0000226771

Regions

Domain230 – 386157JmjC
Zinc finger37 – 8852PHD-type
Region97 – 11418Linker
Compositional bias2 – 3130Ala-rich

Sites

Metal binding2821Iron; catalytic
Metal binding2841Iron; catalytic
Metal binding3541Iron; catalytic
Binding site2791Substrate By similarity
Binding site2991Substrate By similarity

Natural variations

Alternative sequence792 – 80918GYHVK…SSWIK → ETRSHLCCPDWSPTPELK in isoform 2.
VSP_017458
Alternative sequence810 – 941132Missing in isoform 2.
VSP_017459
Natural variant3921D → Y.
Corresponds to variant rs5020212 [ dbSNP | Ensembl ].
VAR_049652
Natural variant6441R → S. Ref.4
Corresponds to variant rs6950119 [ dbSNP | Ensembl ].
VAR_049653

Experimental info

Mutagenesis2821H → A: Abolishes enzymatic activity. Ref.6
Sequence conflict6771T → I in CAE46011. Ref.5

Secondary structure

................................................................................... 941
Helix Strand Turn

Details...

Sequences

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

Last modified March 7, 2006. Version 2.
Checksum: AB8161020D157F11

FASTA941106,557
        10         20         30         40         50         60 
MAGAAAAVAA GAAAGAAAAA VSVAAPGRAS APPPPPPVYC VCRQPYDVNR FMIECDICKD 

        70         80         90        100        110        120 
WFHGSCVGVE EHHAVDIDLY HCPNCAVLHG SSLMKKRRNW HRHDYTEIDD GSKPVQAGTR 

       130        140        150        160        170        180 
TFIKELRSRV FPSADEIIIK MHGSQLTQRY LEKHGFDVPI MVPKLDDLGL RLPSPTFSVM 

       190        200        210        220        230        240 
DVERYVGGDK VIDVIDVARQ ADSKMTLHNY VKYFMNPNRP KVLNVISLEF SDTKMSELVE 

       250        260        270        280        290        300 
VPDIAKKLSW VENYWPDDSV FPKPFVQKYC LMGVQDSYTD FHIDFGGTSV WYHVLWGEKI 

       310        320        330        340        350        360 
FYLIKPTDEN LARYESWSSS VTQSEVFFGD KVDKCYKCVV KQGHTLFVPT GWIHAVLTSQ 

       370        380        390        400        410        420 
DCMAFGGNFL HNLNIGMQLR CYEMEKRLKT PDLFKFPFFE AICWFVAKNL LETLKELRED 

       430        440        450        460        470        480 
GFQPQTYLVQ GVKALHTALK LWMKKELVSE HAFEIPDNVR PGHLIKELSK VIRAIEEENG 

       490        500        510        520        530        540 
KPVKSQGIPI VCPVSRSSNE ATSPYHSRRK MRKLRDHNVR TPSNLDILEL HTREVLKRLE 

       550        560        570        580        590        600 
MCPWEEDILS SKLNGKFNKH LQPSSTVPEW RAKDNDLRLL LTNGRIIKDE RQPFADQSLY 

       610        620        630        640        650        660 
TADSENEEDK RRTKKAKMKI EESSGVEGVE HEESQKPLNG FFTRVKSELR SRSSGYSDIS 

       670        680        690        700        710        720 
ESEDSGPECT ALKSIFTTEE SESSGDEKKQ EITSNFKEES NVMRNFLQKS QKPSRSEIPI 

       730        740        750        760        770        780 
KRECPTSTST EEEAIQGMLS MAGLHYSTCL QRQIQSTDCS GERNSLQDPS SCHGSNHEVR 

       790        800        810        820        830        840 
QLYRYDKPVE CGYHVKTEDP DLRTSSWIKQ FDTSRFHPQD LSRSQKCIRK EGSSEISQRV 

       850        860        870        880        890        900 
QSRNYVDSSG SSLQNGKYMQ NSNLTSGACQ ISNGSLSPER PVGETSFSVP LHPTKRPASN 

       910        920        930        940 
PPPISNQATK GKRPKKGMAT AKQRLGKILK LNRNGHARFF V 

« Hide

Isoform 2 [UniParc].

Checksum: 1561533C92AB3466
Show »

FASTA80992,001

References

« Hide 'large scale' references
[1]"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: Trachea.
[2]"The DNA sequence of human chromosome 7."
Hillier L.W., Fulton R.S., Fulton L.A., Graves T.A., Pepin K.H., Wagner-McPherson C., Layman D., Maas J., Jaeger S., Walker R., Wylie K., Sekhon M., Becker M.C., O'Laughlin M.D., Schaller M.E., Fewell G.A., Delehaunty K.D., Miner T.L. expand/collapse author list , Nash W.E., Cordes M., Du H., Sun H., Edwards J., Bradshaw-Cordum H., Ali J., Andrews S., Isak A., Vanbrunt A., Nguyen C., Du F., Lamar B., Courtney L., Kalicki J., Ozersky P., Bielicki L., Scott K., Holmes A., Harkins R., Harris A., Strong C.M., Hou S., Tomlinson C., Dauphin-Kohlberg S., Kozlowicz-Reilly A., Leonard S., Rohlfing T., Rock S.M., Tin-Wollam A.-M., Abbott A., Minx P., Maupin R., Strowmatt C., Latreille P., Miller N., Johnson D., Murray J., Woessner J.P., Wendl M.C., Yang S.-P., Schultz B.R., Wallis J.W., Spieth J., Bieri T.A., Nelson J.O., Berkowicz N., Wohldmann P.E., Cook L.L., Hickenbotham M.T., Eldred J., Williams D., Bedell J.A., Mardis E.R., Clifton S.W., Chissoe S.L., Marra M.A., Raymond C., Haugen E., Gillett W., Zhou Y., James R., Phelps K., Iadanoto S., Bubb K., Simms E., Levy R., Clendenning J., Kaul R., Kent W.J., Furey T.S., Baertsch R.A., Brent M.R., Keibler E., Flicek P., Bork P., Suyama M., Bailey J.A., Portnoy M.E., Torrents D., Chinwalla A.T., Gish W.R., Eddy S.R., McPherson J.D., Olson M.V., Eichler E.E., Green E.D., Waterston R.H., Wilson R.K.
Nature 424:157-164(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]"Human chromosome 7: DNA sequence and biology."
Scherer S.W., Cheung J., MacDonald J.R., Osborne L.R., Nakabayashi K., Herbrick J.-A., Carson A.R., Parker-Katiraee L., Skaug J., Khaja R., Zhang J., Hudek A.K., Li M., Haddad M., Duggan G.E., Fernandez B.A., Kanematsu E., Gentles S. expand/collapse author list , Christopoulos C.C., Choufani S., Kwasnicka D., Zheng X.H., Lai Z., Nusskern D.R., Zhang Q., Gu Z., Lu F., Zeesman S., Nowaczyk M.J., Teshima I., Chitayat D., Shuman C., Weksberg R., Zackai E.H., Grebe T.A., Cox S.R., Kirkpatrick S.J., Rahman N., Friedman J.M., Heng H.H.Q., Pelicci P.G., Lo-Coco F., Belloni E., Shaffer L.G., Pober B., Morton C.C., Gusella J.F., Bruns G.A.P., Korf B.R., Quade B.J., Ligon A.H., Ferguson H., Higgins A.W., Leach N.T., Herrick S.R., Lemyre E., Farra C.G., Kim H.-G., Summers A.M., Gripp K.W., Roberts W., Szatmari P., Winsor E.J.T., Grzeschik K.-H., Teebi A., Minassian B.A., Kere J., Armengol L., Pujana M.A., Estivill X., Wilson M.D., Koop B.F., Tosi S., Moore G.E., Boright A.P., Zlotorynski E., Kerem B., Kroisel P.M., Petek E., Oscier D.G., Mould S.J., Doehner H., Doehner K., Rommens J.M., Vincent J.B., Venter J.C., Li P.W., Mural R.J., Adams M.D., Tsui L.-C.
Science 300:767-772(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro."
Nagase T., Kikuno R., Hattori A., Kondo Y., Okumura K., Ohara O.
DNA Res. 7:347-355(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 565-941 (ISOFORM 1), VARIANT SER-644.
[5]"The full-ORF clone resource of the German cDNA consortium."
Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U., Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D., Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A., Wiemann S., Schupp I.
BMC Genomics 8:399-399(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 407-941 (ISOFORM 2).
Tissue: Fetal kidney.
[6]"KDM7 is a dual demethylase for histone H3 Lys 9 and Lys 27 and functions in brain development."
Tsukada Y., Ishitani T., Nakayama K.I.
Genes Dev. 24:432-437(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF HIS-282.
[7]"Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development."
Qi H.H., Sarkissian M., Hu G.Q., Wang Z., Bhattacharjee A., Gordon D.B., Gonzales M., Lan F., Ongusaha P.P., Huarte M., Yaghi N.K., Lim H., Garcia B.A., Brizuela L., Zhao K., Roberts T.M., Shi Y.
Nature 466:503-507(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[8]"Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases."
Horton J.R., Upadhyay A.K., Qi H.H., Zhang X., Shi Y., Cheng X.
Nat. Struct. Mol. Biol. 17:38-43(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.29 ANGSTROMS) OF 1-488 IN COMPLEX WITH IRON AND N-OXALYLGLYCINE, ZINC-BINDING, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, DOMAIN LINKER AND PHD-FINGER.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AK131497 mRNA. Translation: BAD18641.1. Frameshift.
AC004849 Genomic DNA. No translation available.
CH236950 Genomic DNA. Translation: EAL24032.1. Sequence problems.
AB051505 mRNA. Translation: BAB21809.1.
BX641017 mRNA. Translation: CAE46011.1.
CCDSCCDS43658.1. [Q6ZMT4-1]
RefSeqNP_085150.1. NM_030647.1. [Q6ZMT4-1]
UniGeneHs.308710.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3KV5X-ray2.39A/D1-488[»]
3KV6X-ray2.89A/D1-488[»]
3KV9X-ray2.29A92-488[»]
3KVAX-ray2.79A92-488[»]
3KVBX-ray2.69A92-488[»]
3U78X-ray2.69A92-488[»]
ProteinModelPortalQ6ZMT4.
SMRQ6ZMT4. Positions 38-479.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid123331. 1 interaction.
IntActQ6ZMT4. 1 interaction.
STRING9606.ENSP00000380692.

Chemistry

ChEMBLCHEMBL3038496.
GuidetoPHARMACOLOGY2686.

PTM databases

PhosphoSiteQ6ZMT4.

Polymorphism databases

DMDM90111764.

Proteomic databases

PaxDbQ6ZMT4.
PRIDEQ6ZMT4.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000006967; ENSP00000006967; ENSG00000006459. [Q6ZMT4-2]
ENST00000397560; ENSP00000380692; ENSG00000006459. [Q6ZMT4-1]
GeneID80853.
KEGGhsa:80853.
UCSCuc003vvm.3. human. [Q6ZMT4-1]

Organism-specific databases

CTD80853.
GeneCardsGC07M139784.
H-InvDBHIX0007139.
HGNCHGNC:22224. KDM7A.
HPAHPA012114.
neXtProtNX_Q6ZMT4.
PharmGKBPA162392512.
HUGESearch...
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG290496.
HOGENOMHOG000231232.
HOVERGENHBG045631.
InParanoidQ6ZMT4.
KOK11445.
OMALWMKKEL.
OrthoDBEOG73JKV9.
PhylomeDBQ6ZMT4.
TreeFamTF106480.

Gene expression databases

BgeeQ6ZMT4.
CleanExHS_JHDM1D.
GenevestigatorQ6ZMT4.

Family and domain databases

Gene3D3.30.40.10. 1 hit.
InterProIPR003347. JmjC_dom.
IPR019786. Zinc_finger_PHD-type_CS.
IPR011011. Znf_FYVE_PHD.
IPR001965. Znf_PHD.
IPR019787. Znf_PHD-finger.
IPR013083. Znf_RING/FYVE/PHD.
[Graphical view]
PfamPF02373. JmjC. 1 hit.
PF00628. PHD. 1 hit.
[Graphical view]
SMARTSM00558. JmjC. 1 hit.
SM00249. PHD. 1 hit.
[Graphical view]
SUPFAMSSF57903. SSF57903. 1 hit.
PROSITEPS51184. JMJC. 1 hit.
PS01359. ZF_PHD_1. 1 hit.
PS50016. ZF_PHD_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ6ZMT4.
GenomeRNAi80853.
NextBio71296.
PROQ6ZMT4.

Entry information

Entry nameKDM7A_HUMAN
AccessionPrimary (citable) accession number: Q6ZMT4
Secondary accession number(s): A4D1S9 expand/collapse secondary AC list , C9JJH9, C9JQU2, Q6MZL8, Q9C0E5
Entry history
Integrated into UniProtKB/Swiss-Prot: March 7, 2006
Last sequence update: March 7, 2006
Last modified: July 9, 2014
This is version 91 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

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 7

Human chromosome 7: entries, gene names and cross-references to MIM