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O14646 (CHD1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 133. 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:
Chromodomain-helicase-DNA-binding protein 1

Short name=CHD-1
EC=3.6.4.12
Alternative name(s):
ATP-dependent helicase CHD1
Gene names
Name:CHD1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length1710 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

ATP-dependent chromatin-remodeling factor which functions as substrate recognition component of the transcription regulatory histone acetylation (HAT) complex SAGA. Regulates polymerase II transcription. Also required for efficient transcription by RNA polymerase I, and more specifically the polymerase I transcription termination step. Regulates negatively DNA replication. Not only involved in transcription-related chromatin-remodeling, but also required to maintain a specific chromatin configuration across the genome. Is also associated with histone deacetylase (HDAC) activity By similarity. Required for the bridging of SNF2, the FACT complex, the PAF complex as well as the U2 snRNP complex to H3K4me3. Functions to modulate the efficiency of pre-mRNA splicing in part through physical bridging of spliceosomal components to H3K4me3. Required for maintaining open chromatin and pluripotency in embryonic stem cells. Ref.8

Catalytic activity

ATP + H2O = ADP + phosphate.

Subunit structure

Component of the SAGA complex By similarity. Interacts with BCLAF1, NCoR, SRP20 and SAFB By similarity. Specifically interacts with methylated H3K4me2 and H3K4me3. Interacts with the FACT complex, the PAF complex and the U2 snRNP. Interacts directly with PAF1, SFA3A1, SFA3A2, SFA3A3, SNF2 and SSRP1. Ref.4 Ref.7 Ref.8 Ref.15

Subcellular location

Nucleus. Cytoplasm By similarity. Note: Is released into the cytoplasm when cells enter mitosis and is reincorporated into chromatin during telophase-cytokinesis By similarity.

Domain

The 2 chromodomains are involved in the binding to the histone H3 methyllysine at position 4 (H3K4me3). Ref.7

Sequence similarities

Belongs to the SNF2/RAD54 helicase family.

Contains 2 chromo domains.

Contains 1 helicase ATP-binding domain.

Contains 1 helicase C-terminal domain.

Binary interactions

With

Entry

#Exp.

IntAct

Notes

NS1B2BUF13EBI-1560858,EBI-4291940From a different organism.

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: O14646-1)

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: O14646-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1684-1684: Missing.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 17101710Chromodomain-helicase-DNA-binding protein 1
PRO_0000080224

Regions

Domain272 – 36493Chromo 1
Domain389 – 45264Chromo 2
Domain493 – 663171Helicase ATP-binding
Domain792 – 943152Helicase C-terminal
Repeat1628 – 163251
Repeat1634 – 163852
Repeat1640 – 164453
Nucleotide binding506 – 5138ATP Potential
Region1628 – 1644173 X 5 AA repeats of H-S-D-H-R
Motif614 – 6174DEAH box
Compositional bias1 – 7070Ser-rich
Compositional bias117 – 13721Ser-rich

Amino acid modifications

Modified residue2151Phosphoserine Ref.14
Modified residue2161Phosphoserine Ref.14
Modified residue2371Phosphothreonine Ref.10
Modified residue2411Phosphoserine Ref.10
Modified residue2501Phosphothreonine Ref.12
Modified residue2521Phosphoserine Ref.12
Modified residue10251Phosphoserine Ref.12
Modified residue10401Phosphoserine Ref.9 Ref.10 Ref.12
Modified residue10811Phosphoserine Ref.9
Modified residue10961Phosphoserine Ref.10 Ref.14
Modified residue10981Phosphoserine Ref.10 Ref.14
Modified residue11001Phosphoserine Ref.10 Ref.14
Modified residue11021Phosphoserine Ref.14
Modified residue13531Phosphoserine Ref.14
Modified residue13551Phosphoserine Ref.14
Modified residue13561Phosphoserine Ref.14
Modified residue13601Phosphoserine Ref.14
Modified residue13631Phosphoserine Ref.14
Modified residue13711Phosphoserine Ref.14
Modified residue16771Phosphoserine Ref.9 Ref.10 Ref.12

Natural variations

Alternative sequence16841Missing in isoform 2.
VSP_038432
Natural variant2641P → T.
Corresponds to variant rs10062803 [ dbSNP | Ensembl ].
VAR_055652

Experimental info

Sequence conflict3921E → G in AAB87381. Ref.1

Secondary structure

............................................................ 1710
Helix Strand Turn

Details...

Sequences

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

Last modified November 24, 2009. Version 2.
Checksum: D888AAA46FDA31B1

FASTA1,710196,688
        10         20         30         40         50         60 
MNGHSDEESV RNSSGESSQS DDDSGSASGS GSGSSSGSSS DGSSSQSGSS DSDSGSESGS 

        70         80         90        100        110        120 
QSESESDTSR ENKVQAKPPK VDGAEFWKSS PSILAVQRSA ILKKQQQQQQ QQQHQASSNS 

       130        140        150        160        170        180 
GSEEDSSSSE DSDDSSSEVK RKKHKDEDWQ MSGSGSPSQS GSDSESEEER EKSSCDETES 

       190        200        210        220        230        240 
DYEPKNKVKS RKPQNRSKSK NGKKILGQKK RQIDSSEEDD DEEDYDNDKR SSRRQATVNV 

       250        260        270        280        290        300 
SYKEDEEMKT DSDDLLEVCG EDVPQPEEEE FETIERFMDC RIGRKGATGA TTTIYAVEAD 

       310        320        330        340        350        360 
GDPNAGFEKN KEPGEIQYLI KWKGWSHIHN TWETEETLKQ QNVRGMKKLD NYKKKDQETK 

       370        380        390        400        410        420 
RWLKNASPED VEYYNCQQEL TDDLHKQYQI VERIIAHSNQ KSAAGYPDYY CKWQGLPYSE 

       430        440        450        460        470        480 
CSWEDGALIS KKFQACIDEY FSRNQSKTTP FKDCKVLKQR PRFVALKKQP SYIGGHEGLE 

       490        500        510        520        530        540 
LRDYQLNGLN WLAHSWCKGN SCILADEMGL GKTIQTISFL NYLFHEHQLY GPFLLVVPLS 

       550        560        570        580        590        600 
TLTSWQREIQ TWASQMNAVV YLGDINSRNM IRTHEWTHHQ TKRLKFNILL TTYEILLKDK 

       610        620        630        640        650        660 
AFLGGLNWAF IGVDEAHRLK NDDSLLYKTL IDFKSNHRLL ITGTPLQNSL KELWSLLHFI 

       670        680        690        700        710        720 
MPEKFSSWED FEEEHGKGRE YGYASLHKEL EPFLLRRVKK DVEKSLPAKV EQILRMEMSA 

       730        740        750        760        770        780 
LQKQYYKWIL TRNYKALSKG SKGSTSGFLN IMMELKKCCN HCYLIKPPDN NEFYNKQEAL 

       790        800        810        820        830        840 
QHLIRSSGKL ILLDKLLIRL RERGNRVLIF SQMVRMLDIL AEYLKYRQFP FQRLDGSIKG 

       850        860        870        880        890        900 
ELRKQALDHF NAEGSEDFCF LLSTRAGGLG INLASADTVV IFDSDWNPQN DLQAQARAHR 

       910        920        930        940        950        960 
IGQKKQVNIY RLVTKGSVEE DILERAKKKM VLDHLVIQRM DTTGKTVLHT GSAPSSSTPF 

       970        980        990       1000       1010       1020 
NKEELSAILK FGAEELFKEP EGEEQEPQEM DIDEILKRAE THENEPGPLT VGDELLSQFK 

      1030       1040       1050       1060       1070       1080 
VANFSNMDED DIELEPERNS KNWEEIIPED QRRRLEEEER QKELEEIYML PRMRNCAKQI 

      1090       1100       1110       1120       1130       1140 
SFNGSEGRRS RSRRYSGSDS DSISEGKRPK KRGRPRTIPR ENIKGFSDAE IRRFIKSYKK 

      1150       1160       1170       1180       1190       1200 
FGGPLERLDA IARDAELVDK SETDLRRLGE LVHNGCIKAL KDSSSGTERT GGRLGKVKGP 

      1210       1220       1230       1240       1250       1260 
TFRISGVQVN AKLVISHEEE LIPLHKSIPS DPEERKQYTI PCHTKAAHFD IDWGKEDDSN 

      1270       1280       1290       1300       1310       1320 
LLIGIYEYGY GSWEMIKMDP DLSLTHKILP DDPDKKPQAK QLQTRADYLI KLLSRDLAKK 

      1330       1340       1350       1360       1370       1380 
EALSGAGSSK RRKARAKKNK AMKSIKVKEE IKSDSSPLPS EKSDEDDDKL SESKSDGRER 

      1390       1400       1410       1420       1430       1440 
SKKSSVSDAP VHITASGEPV PISEESEELD QKTFSICKER MRPVKAALKQ LDRPEKGLSE 

      1450       1460       1470       1480       1490       1500 
REQLEHTRQC LIKIGDHITE CLKEYTNPEQ IKQWRKNLWI FVSKFTEFDA RKLHKLYKHA 

      1510       1520       1530       1540       1550       1560 
IKKRQESQQN SDQNSNLNPH VIRNPDVERL KENTNHDDSS RDSYSSDRHL TQYHDHHKDR 

      1570       1580       1590       1600       1610       1620 
HQGDSYKKSD SRKRPYSSFS NGKDHRDWDH YKQDSRYYSD REKHRKLDDH RSRDHRSNLE 

      1630       1640       1650       1660       1670       1680 
GSLKDRSHSD HRSHSDHRLH SDHRSSSEYT HHKSSRDYRY HSDWQMDHRA SSSGPRSPLD 

      1690       1700       1710 
QRSPYGSRSP FEHSVEHKST PEHTWSSRKT 

« Hide

Isoform 2 [UniParc].

Checksum: 8B2C96C7597E55B4
Show »

FASTA1,709196,590

References

« Hide 'large scale' references
[1]"Characterization of the CHD family of proteins."
Woodage T., Basrai M.A., Baxevanis A.D., Hieter P., Collins F.S.
Proc. Natl. Acad. Sci. U.S.A. 94:11472-11477(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2).
[2]"The DNA sequence and comparative analysis of human chromosome 5."
Schmutz J., Martin J., Terry A., Couronne O., Grimwood J., Lowry S., Gordon L.A., Scott D., Xie G., Huang W., Hellsten U., Tran-Gyamfi M., She X., Prabhakar S., Aerts A., Altherr M., Bajorek E., Black S. expand/collapse author list , Branscomb E., Caoile C., Challacombe J.F., Chan Y.M., Denys M., Detter J.C., Escobar J., Flowers D., Fotopulos D., Glavina T., Gomez M., Gonzales E., Goodstein D., Grigoriev I., Groza M., Hammon N., Hawkins T., Haydu L., Israni S., Jett J., Kadner K., Kimball H., Kobayashi A., Lopez F., Lou Y., Martinez D., Medina C., Morgan J., Nandkeshwar R., Noonan J.P., Pitluck S., Pollard M., Predki P., Priest J., Ramirez L., Retterer J., Rodriguez A., Rogers S., Salamov A., Salazar A., Thayer N., Tice H., Tsai M., Ustaszewska A., Vo N., Wheeler J., Wu K., Yang J., Dickson M., Cheng J.-F., Eichler E.E., Olsen A., Pennacchio L.A., Rokhsar D.S., Richardson P., Lucas S.M., Myers R.M., Rubin E.M.
Nature 431:268-274(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[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] (ISOFORM 2).
Tissue: Cerebellum.
[4]"Human but not yeast CHD1 binds directly and selectively to histone H3 methylated at lysine 4 via its tandem chromodomains."
Sims R.J. III, Chen C.-F., Santos-Rosa H., Kouzarides T., Patel S.S., Reinberg D.
J. Biol. Chem. 280:41789-41792(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH H3K4ME2 AND H3K4ME3.
[5]"Global, in vivo, and site-specific phosphorylation dynamics in signaling networks."
Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P., Mann M.
Cell 127:635-648(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[6]"A probability-based approach for high-throughput protein phosphorylation analysis and site localization."
Beausoleil S.A., Villen J., Gerber S.A., Rush J., Gygi S.P.
Nat. Biotechnol. 24:1285-1292(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[7]"Molecular implications of evolutionary differences in CHD double chromodomains."
Flanagan J.F., Blus B.J., Kim D., Clines K.L., Rastinejad F., Khorasanizadeh S.
J. Mol. Biol. 369:334-342(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: DOMAIN, INTERACTION WITH HISTONE H3K4ME3.
[8]"Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing."
Sims R.J. III, Millhouse S., Chen C.-F., Lewis B.A., Erdjument-Bromage H., Tempst P., Manley J.L., Reinberg D.
Mol. Cell 28:665-676(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH H3K4ME3; PAF1; SFA3A1; SFA3A2; SFA3A3; SNF2 AND SSRP1.
[9]"Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle."
Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M.
Mol. Cell 31:438-448(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-1040; SER-1081 AND SER-1677, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[10]"A quantitative atlas of mitotic phosphorylation."
Dephoure N., Zhou C., Villen J., Beausoleil S.A., Bakalarski C.E., Elledge S.J., Gygi S.P.
Proc. Natl. Acad. Sci. U.S.A. 105:10762-10767(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-237; SER-241; SER-1040; SER-1096; SER-1098; SER-1100 AND SER-1677, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[11]"Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions."
Mayya V., Lundgren D.H., Hwang S.-I., Rezaul K., Wu L., Eng J.K., Rodionov V., Han D.K.
Sci. Signal. 2:RA46-RA46(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Leukemic T-cell.
[12]"Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis."
Olsen J.V., Vermeulen M., Santamaria A., Kumar C., Miller M.L., Jensen L.J., Gnad F., Cox J., Jensen T.S., Nigg E.A., Brunak S., Mann M.
Sci. Signal. 3:RA3-RA3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT THR-250; SER-252; SER-1025; SER-1040 AND SER-1677, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Tissue: Cervix carcinoma.
[13]"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].
[14]"System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation."
Rigbolt K.T., Prokhorova T.A., Akimov V., Henningsen J., Johansen P.T., Kratchmarova I., Kassem M., Mann M., Olsen J.V., Blagoev B.
Sci. Signal. 4:RS3-RS3(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-215; SER-216; SER-1096; SER-1098; SER-1100; SER-1102; SER-1353; SER-1355; SER-1356; SER-1360; SER-1363 AND SER-1371, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[15]"Double chromodomains cooperate to recognize the methylated histone H3 tail."
Flanagan J.F., Mi L.-Z., Chruszcz M., Cymborowski M., Clines K.L., Kim Y., Minor W., Rastinejad F., Khorasanizadeh S.
Nature 438:1181-1185(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) OF 268-443, INTERACTION WITH HISTONE H3K4ME3.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AF006513 mRNA. Translation: AAB87381.1.
AC022121 Genomic DNA. No translation available.
BC117134 mRNA. Translation: AAI17135.1.
RefSeqNP_001261.2. NM_001270.2.
XP_005271924.1. XM_005271867.2.
UniGeneHs.643465.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
2B2TX-ray2.45A/B268-443[»]
C268-373[»]
2B2UX-ray2.95A/B268-443[»]
C268-373[»]
2B2VX-ray2.65A/B268-443[»]
C268-373[»]
2B2WX-ray2.40A/B268-443[»]
C268-373[»]
2B2YX-ray2.35A/B268-443[»]
C268-373[»]
4B4CX-ray1.62A1119-1327[»]
4NW2X-ray1.90A/C268-443[»]
ProteinModelPortalO14646.
SMRO14646. Positions 269-1020, 1124-1327.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid107530. 19 interactions.
DIPDIP-38922N.
IntActO14646. 1 interaction.
STRING9606.ENSP00000284049.

Chemistry

DrugBankDB00445. Epirubicin.

PTM databases

PhosphoSiteO14646.

Proteomic databases

PaxDbO14646.
PRIDEO14646.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000284049; ENSP00000284049; ENSG00000153922. [O14646-1]
GeneID1105.
KEGGhsa:1105.
UCSCuc003knf.3. human. [O14646-1]

Organism-specific databases

CTD1105.
GeneCardsGC05M098219.
H-InvDBHIX0005061.
HGNCHGNC:1915. CHD1.
HPAHPA022236.
MIM602118. gene.
neXtProtNX_O14646.
PharmGKBPA26451.
GenAtlasSearch...

Phylogenomic databases

eggNOGCOG0553.
HOGENOMHOG000207917.
HOVERGENHBG005325.
InParanoidO14646.
KOK11367.
OMAHRKLDDH.
OrthoDBEOG7NPFSB.
PhylomeDBO14646.
TreeFamTF313461.

Gene expression databases

ArrayExpressO14646.
BgeeO14646.
CleanExHS_CHD1.
GenevestigatorO14646.

Family and domain databases

Gene3D3.40.50.300. 2 hits.
InterProIPR023780. Chromo_domain.
IPR000953. Chromo_domain/shadow.
IPR016197. Chromodomain-like.
IPR023779. Chromodomain_CS.
IPR025260. DUF4208.
IPR014001. Helicase_ATP-bd.
IPR001650. Helicase_C.
IPR027417. P-loop_NTPase.
IPR000330. SNF2_N.
[Graphical view]
PfamPF00385. Chromo. 2 hits.
PF13907. DUF4208. 1 hit.
PF00271. Helicase_C. 1 hit.
PF00176. SNF2_N. 1 hit.
[Graphical view]
SMARTSM00298. CHROMO. 2 hits.
SM00487. DEXDc. 1 hit.
SM00490. HELICc. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 2 hits.
SSF54160. SSF54160. 2 hits.
PROSITEPS00598. CHROMO_1. 2 hits.
PS50013. CHROMO_2. 2 hits.
PS51192. HELICASE_ATP_BIND_1. 1 hit.
PS51194. HELICASE_CTER. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceO14646.
GeneWikiCHD1.
GenomeRNAi1105.
NextBio4580.
PROO14646.
SOURCESearch...

Entry information

Entry nameCHD1_HUMAN
AccessionPrimary (citable) accession number: O14646
Secondary accession number(s): Q17RZ3
Entry history
Integrated into UniProtKB/Swiss-Prot: July 15, 1998
Last sequence update: November 24, 2009
Last modified: April 16, 2014
This is version 133 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 5

Human chromosome 5: entries, gene names and cross-references to MIM