The sequence and analysis of duplication-rich human chromosome 16.

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Martin J, Han C, Gordon LA, Terry A, Prabhakar S, She X, Xie G, Hellsten U, Chan YM, Altherr M, Couronne O, Aerts A, Bajorek E, Black S, Blumer H, Branscomb E, Brown NC, Bruno WJ, Buckingham JM, Callen DF, Campbell CS, Campbell ML, Campbell EW, Caoile C, Challacombe JF, Chasteen LA, Chertkov O, Chi HC, Christensen M, Clark LM, Cohn JD, Denys M, Detter JC, Dickson M, Dimitrijevic-Bussod M, Escobar J, Fawcett JJ, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Goodwin LA, Grady DL, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Hildebrand CE, Huang W, Israni S, Jett J, Jewett PB, Kadner K, Kimball H, Kobayashi A, Krawczyk MC, Leyba T, Longmire JL, Lopez F, Lou Y, Lowry S, Ludeman T, Manohar CF, Mark GA, McMurray KL, Meincke LJ, Morgan J, Moyzis RK, Mundt MO, Munk AC, Nandkeshwar RD, Pitluck S, Pollard M, Predki P, Parson-Quintana B, Ramirez L, Rash S, Retterer J, Ricke DO, Robinson DL, Rodriguez A, Salamov A, Saunders EH, Scott D, Shough T, Stallings RL, Stalvey M, Sutherland RD, Tapia R, Tesmer JG, Thayer N, Thompson LS, Tice H, Torney DC, Tran-Gyamfi M, Tsai M, Ulanovsky LE, Ustaszewska A, Vo N, White PS, Williams AL, Wills PL, Wu JR, Wu K, Yang J, Dejong P, Bruce D, Doggett NA, Deaven L, Schmutz J, Grimwood J, Richardson P, Rokhsar DS, Eichler EE, Gilna P, Lucas SM, Myers RM, Rubin EM, Pennacchio LA

The sequence and analysis of duplication-rich human chromosome 16.

Nature. 2004 Dec 23;432(7020):988-94.

PubMed ID
15616553 [ View in PubMed
]
Abstract

Human chromosome 16 features one of the highest levels of segmentally duplicated sequence among the human autosomes. We report here the 78,884,754 base pairs of finished chromosome 16 sequence, representing over 99.9% of its euchromatin. Manual annotation revealed 880 protein-coding genes confirmed by 1,670 aligned transcripts, 19 transfer RNA genes, 341 pseudogenes and three RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukaemia. Several large-scale structural polymorphisms spanning hundreds of kilobase pairs were identified and result in gene content differences among humans. Whereas the segmental duplications of chromosome 16 are enriched in the relatively gene-poor pericentromere of the p arm, some are involved in recent gene duplication and conversion events that are likely to have had an impact on the evolution of primates and human disease susceptibility.

DrugBank Data that Cites this Article

Polypeptides
NameUniProt ID
Group 10 secretory phospholipase A2O15496Details
Ketimine reductase mu-crystallinQ14894Details
Adenine phosphoribosyltransferaseP07741Details
Hemoglobin subunit alphaP69905Details
Lysine--tRNA ligaseQ15046Details
NEDD8-activating enzyme E1 regulatory subunitQ13564Details
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10O96000Details
Methionine-R-sulfoxide reductase B1Q9NZV6Details
Alanine--tRNA ligase, cytoplasmicP49588Details
Aspartate aminotransferase, mitochondrialP00505Details
Solute carrier family 12 member 3P55017Details
Leucine carboxyl methyltransferase 1Q9UIC8Details
Sodium-dependent noradrenaline transporterP23975Details
Integrin alpha-LP20701Details
Heme oxygenase 2P30519Details
Solute carrier family 12 member 4Q9UP95Details
72 kDa type IV collagenaseP08253Details
Vitamin K epoxide reductase complex subunit 1Q9BQB6Details
Glutamate receptor ionotropic, NMDA 2AQ12879Details
Multidrug resistance-associated protein 1P33527Details
Voltage-dependent T-type calcium channel subunit alpha-1HO95180Details
Sulfotransferase 1A1P50225Details
Matrix metalloproteinase-25 (TrEMBL)O43923Details
Mitogen-activated protein kinase 3P27361Details
NAD(P)H dehydrogenase [quinone] 1P15559Details
3-phosphoinositide-dependent protein kinase 1O15530Details
Tubulin beta-3 chainQ13509Details
Tryptase beta-2P20231Details
Fructose-bisphosphate aldolase AP04075Details
Hydroxyacylglutathione hydrolase, mitochondrialQ16775Details
Somatostatin receptor type 5P35346Details
Pyridoxal-dependent decarboxylase domain-containing protein 1Q6P996Details
Alanine aminotransferase 2Q8TD30Details
CDP-diacylglycerol--inositol 3-phosphatidyltransferaseO14735Details
Prolyl 3-hydroxylase OGFOD1Q8N543Details
N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidaseQ9UK23Details
Sphingomyelin phosphodiesterase 3Q9NY59Details
Glycine cleavage system H protein, mitochondrialP23434Details
Interleukin-4 receptor subunit alphaP24394Details
Liver carboxylesterase 1P23141Details
Axin-1O15169Details
MesothelinQ13421Details
B-lymphocyte antigen CD19P15391Details
Multidrug resistance-associated protein 6O95255Details
ATP-binding cassette sub-family A member 3Q99758Details
Tryptase alpha/beta-1Q15661Details
ProstasinQ16651Details
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1O14983Details
Putative inactive carboxylesterase 4Q9UKY3Details
NmrA-like family domain-containing protein 1Q9HBL8Details
Eukaryotic peptide chain release factor GTP-binding subunit ERF3AP15170Details
Cytochrome b5 type BO43169Details
Myosin-11P35749Details
Elongation factor Tu, mitochondrialP49411Details
[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrialO14874Details
FAD-linked sulfhydryl oxidase ALRP55789Details
Serine/threonine-protein kinase TAO2Q9UL54Details
Thymidine kinase 2, mitochondrialO00142Details
Cocaine esteraseO00748Details
Sodium/glucose cotransporter 2P31639Details
Metallothionein-1AP04731Details
Cytochrome b-245 light chainP13498Details
Alpha-ketoglutarate-dependent dioxygenase FTOQ9C0B1Details
Apolipoprotein B receptorQ0VD83Details
Metallothionein-4P47944Details
Metallothionein-1XP80297Details
Metallothionein-1EP04732Details
DNA-3-methyladenine glycosylaseP29372Details
Nodal modulator 1Q15155Details
Haptoglobin-related proteinP00739Details
Insulin-like growth factor-binding protein complex acid labile subunitP35858Details
Sulfotransferase 1A3P0DMM9Details
Myosin light chain kinase 3Q32MK0Details
Membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinaseQ99640Details
Sulfotransferase 1A2P50226Details
Cadherin-11H3BUU9Details
Sulfotransferase 1A4P0DMN0Details
HaptoglobinP00738Details
Calcium-transporting ATPase type 2C member 2O75185Details
Tumor necrosis factor receptor superfamily member 17Q02223Details
Dipeptidase 3Q9H4B8Details
1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2P16885Details
Adenylate cyclase type 7P51828Details