Generation and annotation of the DNA sequences of human chromosomes 2 and 4.

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Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, Wagner-McPherson C, Layman D, Wylie K, Sekhon M, Becker MC, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Kremitzki C, Oddy L, Du H, Sun H, Bradshaw-Cordum H, Ali J, Carter J, Cordes M, Harris A, Isak A, van Brunt A, Nguyen C, Du F, Courtney L, Kalicki J, Ozersky P, Abbott S, Armstrong J, Belter EA, Caruso L, Cedroni M, Cotton M, Davidson T, Desai A, Elliott G, Erb T, Fronick C, Gaige T, Haakenson W, Haglund K, Holmes A, Harkins R, Kim K, Kruchowski SS, Strong CM, Grewal N, Goyea E, Hou S, Levy A, Martinka S, Mead K, McLellan MD, Meyer R, Randall-Maher J, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Shah N, Swearengen-Shahid S, Snider J, Strong JT, Thompson J, Yoakum M, Leonard S, Pearman C, Trani L, Radionenko M, Waligorski JE, Wang C, Rock SM, Tin-Wollam AM, Maupin R, Latreille P, Wendl MC, Yang SP, Pohl C, Wallis JW, Spieth J, Bieri TA, Berkowicz N, Nelson JO, Osborne J, Ding L, Meyer R, Sabo A, Shotland Y, Sinha P, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Jones TA, She X, Ciccarelli FD, Izaurralde E, Taylor J, Schmutz J, Myers RM, Cox DR, Huang X, McPherson JD, Mardis ER, Clifton SW, Warren WC, Chinwalla AT, Eddy SR, Marra MA, Ovcharenko I, Furey TS, Miller W, Eichler EE, Bork P, Suyama M, Torrents D, Waterston RH, Wilson RK

Generation and annotation of the DNA sequences of human chromosomes 2 and 4.

Nature. 2005 Apr 7;434(7034):724-31.

PubMed ID
15815621 [ View in PubMed
]
Abstract

Human chromosome 2 is unique to the human lineage in being the product of a head-to-head fusion of two intermediate-sized ancestral chromosomes. Chromosome 4 has received attention primarily related to the search for the Huntington's disease gene, but also for genes associated with Wolf-Hirschhorn syndrome, polycystic kidney disease and a form of muscular dystrophy. Here we present approximately 237 million base pairs of sequence for chromosome 2, and 186 million base pairs for chromosome 4, representing more than 99.6% of their euchromatic sequences. Our initial analyses have identified 1,346 protein-coding genes and 1,239 pseudogenes on chromosome 2, and 796 protein-coding genes and 778 pseudogenes on chromosome 4. Extensive analyses confirm the underlying construction of the sequence, and expand our understanding of the structure and evolution of mammalian chromosomes, including gene deserts, segmental duplications and highly variant regions.

DrugBank Data that Cites this Article

Polypeptides
NameUniProt ID
Lipoyl amidotransferase LIPT1, mitochondrialQ9Y234Details
Glycine receptor subunit betaP48167Details
NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrialO95299Details
Sodium-dependent multivitamin transporterQ9Y289Details
Methylsterol monooxygenase 1Q15800Details
Lutropin-choriogonadotropic hormone receptorP22888Details
Sodium channel protein type 1 subunit alphaP35498Details
cGMP-specific 3',5'-cyclic phosphodiesteraseO76074Details
Microsomal triglyceride transfer protein large subunitP55157Details
Electrogenic aspartate/glutamate antiporter SLC25A12, mitochondrialO75746Details
Trifunctional enzyme subunit alpha, mitochondrialP40939Details
Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrialP13995Details
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3O43676Details
S-adenosylmethionine synthase isoform type-2P31153Details
Alanine--glyoxylate aminotransferaseP21549Details
Secretin receptorP47872Details
Calcineurin subunit B type 1P63098Details
ALK tyrosine kinase receptorQ9UM73Details
All-trans-retinol dehydrogenase [NAD(+)] ADH4P08319Details
Vascular endothelial growth factor receptor 2P35968Details
Hydroxyacyl-coenzyme A dehydrogenase, mitochondrialQ16836Details
Glutamate decarboxylase 1Q99259Details
Vitamin K-dependent protein CP04070Details
Gamma-aminobutyric acid receptor subunit alpha-2P47869Details
Substance-P receptorP25103Details
Follicle-stimulating hormone receptorP23945Details
KynureninaseQ16719Details
5-hydroxytryptamine receptor 2BP41595Details
All-trans-retinol dehydrogenase [NAD(+)] ADH1BP00325Details
Vitamin K-dependent gamma-carboxylaseP38435Details
Ornithine decarboxylaseP11926Details
Cyclin-dependent kinase 15Q96Q40Details
Mast/stem cell growth factor receptor KitP10721Details
Neurotensin receptor type 2O95665Details
Alcohol dehydrogenase 1CP00326Details
Gamma-aminobutyric acid receptor subunit alpha-4P48169Details
Neutral amino acid transporter AP43007Details
NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialP28331Details
Endothelin-1 receptorP25101Details
All-trans-retinol dehydrogenase [NAD(+)] ADH7P40394Details
AlbuminP02768Details
Dihydropteridine reductaseP09417Details
15-hydroxyprostaglandin dehydrogenase [NAD(+)]P15428Details
Phenylalanine--tRNA ligase beta subunitQ9NSD9Details
Interleukin-1 receptor type 1P14778Details
Alpha-2B adrenergic receptorP18089Details
Malate dehydrogenase, cytoplasmicP40925Details
Integrin alpha-4P13612Details
Long-chain-fatty-acid--CoA ligase 1P33121Details
UDP-glucose 6-dehydrogenaseO60701Details
Mineralocorticoid receptorP08235Details
High affinity choline transporter 1Q9GZV3Details
Voltage-gated inwardly rectifying potassium channel KCNH7Q9NS40Details
Bile salt export pumpO95342Details
Aspartate--tRNA ligase, cytoplasmicP14868Details
Glutamate receptor 2P42262Details
Platelet-derived growth factor receptor alphaP16234Details
Dipeptidyl peptidase 4P27487Details
Cytotoxic T-lymphocyte protein 4P16410Details
Alkaline phosphatase, germ cell typeP10696Details
Sepiapterin reductaseP35270Details
Lithostathine-1-alphaP05451Details
C-X-C chemokine receptor type 4P61073Details
Low-density lipoprotein receptor-related protein 2P98164Details
Platelet basic proteinP02775Details
Pro-opiomelanocortinP01189Details
Pro-epidermal growth factorP01133Details
Eukaryotic translation initiation factor 4EP06730Details
Thiamine transporter 2Q9BZV2Details
Tissue factor pathway inhibitorP10646Details
Sodium/calcium exchanger 1P32418Details
Phospholipid-transporting ATPase IAQ9Y2Q0Details
Fibroblast growth factor 2P09038Details
Coagulation factor XIP03951Details
G protein-activated inward rectifier potassium channel 1P48549Details
Interleukin-1 betaP01584Details
HeparanaseQ9Y251Details
Broad substrate specificity ATP-binding cassette transporter ABCG2Q9UNQ0Details
Inactive phospholipase C-like protein 1Q15111Details
Mitogen-activated protein kinase 10P53779Details
Microtubule-associated protein 2P11137Details
Platelet factor 4P02776Details
Amino acid transporter heavy chain SLC3A1Q07837Details
Vitamin D-binding proteinP02774Details
Sodium channel protein type 9 subunit alphaQ15858Details
FibronectinP02751Details
Transient receptor potential cation channel subfamily M member 8Q7Z2W7Details
Bifunctional purine biosynthesis protein ATICP31939Details
ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2Q10588Details
Isocitrate dehydrogenase [NADP] cytoplasmicO75874Details
Tyrosine-protein kinase ZAP-70P43403Details
Tubulin alpha-4A chainP68366Details
Dual specificity protein kinase CLK1P49759Details
Sodium channel protein type 2 subunit alphaQ99250Details
Sodium channel protein type 3 subunit alphaQ9NY46Details
Multiple coagulation factor deficiency protein 2Q8NI22Details
Insulin-like growth factor-binding protein 7Q16270Details
Collagen alpha-1(III) chainP02461Details
Fibroblast growth factor receptor 3P22607Details
O-phosphoseryl-tRNA(Sec) selenium transferaseQ9HD40Details
Bifunctional phosphoribosylaminoimidazole carboxylase/phosphoribosylaminoimidazole succinocarboxamide synthetaseP22234Details
Glutamyl-tRNA(Gln) amidotransferase subunit B, mitochondrialO75879Details
Methionine--tRNA ligase, mitochondrialQ96GW9Details
Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrialP53597Details
N-acetyl-D-glucosamine kinaseQ9UJ70Details
Glutamate receptor ionotropic, delta-2O43424Details
Glutamyl aminopeptidaseQ07075Details
Aspartyl aminopeptidaseQ9ULA0Details
Microsomal glutathione S-transferase 2Q99735Details
Sphingomyelin phosphodiesterase 4Q9NXE4Details
All-trans-retinol 13,14-reductaseQ6NUM9Details
Lipoyl synthase, mitochondrialO43766Details
Peptidyl-prolyl cis-trans isomerase GQ13427Details
Neuronal acetylcholine receptor subunit alpha-9Q9UGM1Details
Gamma-aminobutyric acid receptor subunit beta-1P18505Details
Voltage-dependent L-type calcium channel subunit beta-4O00305Details
Neuropeptide Y receptor type 2P49146Details
Histamine N-methyltransferaseP50135Details
Plasma kallikreinP03952Details
Epithelial cell adhesion moleculeP16422Details
Ribonucleoside-diphosphate reductase subunit M2P31350Details
Neuropeptide Y receptor type 5Q15761Details
Uridine phosphorylase 2O95045Details
Histone-lysine N-methyltransferase SETD7Q8WTS6Details
C-terminal-binding protein 1Q13363Details
Peroxisomal trans-2-enoyl-CoA reductaseQ9BY49Details
Estradiol 17-beta-dehydrogenase 11Q8NBQ5Details
Kinesin-like protein KIF1AQ12756Details
Sialidase-2Q9Y3R4Details
Anthrax toxin receptor 2P58335Details
ADP-ribosylation factor-like protein 5AQ9Y689Details
Glutaminyl-peptide cyclotransferaseQ16769Details
Tubulin alpha-3E chainQ6PEY2Details
Putative tubulin-like protein alpha-4BQ9H853Details
Protein kinase C epsilon typeQ02156Details
Centromere-associated protein EQ02224Details
Anthrax toxin receptor 1Q9H6X2Details
Caspase-8Q14790Details
Activin receptor type-2AP27037Details
Collagen alpha-4(IV) chainP53420Details
Prolyl endopeptidase FAPQ12884Details
Histone deacetylase 4P56524Details
UDP-glucuronosyltransferase 1A9O60656Details
Aldehyde oxidaseQ06278Details
UDP-glucuronosyltransferase 1A1P22309Details
UDP-glucuronosyltransferase 1A4P22310Details
Alcohol dehydrogenase 6P28332Details
C-X-C chemokine receptor type 1P25024Details
Dual 3',5'-cyclic-AMP and -GMP phosphodiesterase 11AQ9HCR9Details
Rho-related GTP-binding protein RhoBP62745Details
Integrin alpha-VP06756Details
Potassium channel subfamily K member 3O14649Details
Deoxyguanosine kinase, mitochondrialQ16854Details
Fatty acid-binding protein, intestinalP12104Details
DNA polymerase epsilon subunit 4Q9NR33Details
UDP-glucuronosyltransferase 1A3P35503Details
UDP-glucuronosyltransferase 1A10Q9HAW8Details
UDP-glucuronosyltransferase 2B7P16662Details
UDP-glucuronosyltransferase 2B4P06133Details
UDP-glucuronosyltransferase 1A8Q9HAW9Details
Nuclear receptor coactivator 1Q15788Details
Cyclin-A2P20248Details
Low molecular weight phosphotyrosine protein phosphataseP24666Details
[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 1, mitochondrialQ15118Details
Electron transfer flavoprotein-ubiquinone oxidoreductase, mitochondrialQ16134Details
Cytochrome c oxidase subunit 5B, mitochondrialP10606Details
Calcium/calmodulin-dependent protein kinase type II subunit deltaQ13557Details
Annexin A5P08758Details
Rho-associated protein kinase 2O75116Details
Protein phosphatase 3 catalytic subunit alphaQ08209Details
Actin-related protein 2P61160Details
Actin-related protein 3P61158Details
Tyrosine-protein kinase MerQ12866Details
Alkaline phosphatase, placental typeP05187Details
3-hydroxyisobutyryl-CoA hydrolase, mitochondrialQ6NVY1Details
Lactase/phlorizin hydrolaseP09848Details
Immunoglobulin kappa variable 2D-28P01615Details
U6 snRNA-associated Sm-like protein LSm6P62312Details
Acyl-CoA-binding proteinP07108Details
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1Q9GZU7Details
Spectrin beta chain, non-erythrocytic 1Q01082Details
Lactosylceramide alpha-2,3-sialyltransferaseQ9UNP4Details
Selenocysteine lyaseQ96I15Details
Acireductone dioxygenaseQ9BV57Details
Acetylcholine receptor subunit deltaQ07001Details
Acetylcholine receptor subunit gammaP07510Details
Carbamoyl-phosphate synthase [ammonia], mitochondrialP31327Details
Electrogenic sodium bicarbonate cotransporter 1Q9Y6R1Details
Sodium-driven chloride bicarbonate exchangerQ6U841Details
UDP-glucuronosyltransferase 1-6P19224Details
UDP-glucuronosyltransferase 1A7Q9HAW7Details
UDP-glucuronosyltransferase 2B15P54855Details
Deoxycytidylate deaminaseP32321Details
Interleukin-1 alphaP01583Details
Interleukin-1 receptor antagonist proteinP18510Details
Mitogen-activated protein kinase kinase kinase 2Q9Y2U5Details
ATP-binding cassette sub-family G member 5Q9H222Details
ATP-binding cassette sub-family G member 8Q9H221Details
Solute carrier family 2, facilitated glucose transporter member 9Q9NRM0Details
Polyprenal reductaseQ9H8P0Details
Sodium channel protein type 7 subunit alphaQ01118Details
Rod cGMP-specific 3',5'-cyclic phosphodiesterase subunit betaP35913Details
Cyclic AMP-dependent transcription factor ATF-2P15336Details
Tumor necrosis factor-inducible gene 6 proteinP98066Details
Sodium-dependent phosphate transporter 1Q8WUM9Details
Neurexin-1Q9ULB1Details
Cyclic nucleotide-gated channel alpha-1P29973Details
G-protein coupled receptor 35Q9HC97Details
Ephrin type-A receptor 5P54756Details
Mitogen-activated protein kinase kinase kinase 20Q9NYL2Details
Ubiquitin carboxyl-terminal hydrolase isozyme L1P09936Details
Sodium-dependent phosphate transport protein 2BO95436Details
GrancalcinP28676Details
Calmodulin-2P0DP24Details
60 kDa heat shock protein, mitochondrialP10809Details
Annexin A4P09525Details
AfaminP43652Details
HuntingtinP42858Details
Macrophage receptor MARCOQ9UEW3Details
Calcitonin gene-related peptide type 1 receptorQ16602Details
Lymphoid enhancer-binding factor 1Q9UJU2Details
F-box only protein 41Q8TF61Details
10 kDa heat shock protein, mitochondrialP61604Details
Cytochrome P450 26B1Q9NR63Details
Complement factor IP05156Details
Immunoglobulin kappa variable 1-17P01599Details
KAT8 regulatory NSL complex subunit 3Q9P2N6Details
Heterogeneous nuclear ribonucleoprotein D0Q14103Details
Survival motor neuron proteinB4DP61Details
Sn1-specific diacylglycerol lipase alphaF5GY58Details
Bone morphogenetic protein receptor type-2Q13873Details
Alpha-L-iduronidaseP35475Details
UDP-glucuronosyltransferase 2B10P36537Details
Splicing factor 3B subunit 1O75533Details
Serine/threonine-protein kinase 36Q9NRP7Details
STE20/SPS1-related proline-alanine-rich protein kinaseQ9UEW8Details
Serine/threonine-protein kinase tousled-like 1Q9UKI8Details
Serine/threonine-protein kinase TNNI3KQ59H18Details
Mitogen-activated protein kinase kinase kinase 19Q56UN5Details
AP2-associated protein kinase 1Q2M2I8Details
BMP-2-inducible protein kinaseQ9NSY1Details
Bone morphogenetic protein receptor type-1BO00238Details
Serine/threonine-protein kinase DCLK2Q8N568Details
Interferon-induced, double-stranded RNA-activated protein kinaseP19525Details
Ephrin type-A receptor 4P54764Details
Mitogen-activated protein kinase kinase kinase kinase 4O95819Details
CLIP-associating protein 1Q7Z460Details
Serine/threonine-protein kinase Nek1Q96PY6Details
cGMP-dependent protein kinase 2Q13237Details
Intestinal-type alkaline phosphataseP09923Details
Interleukin-1 receptor type 2P27930Details
Insulin-like growth factor-binding protein 2P18065Details
Ribulose-phosphate 3-epimeraseQ96AT9Details
Exportin-1O14980Details
Sulfotransferase 1C2O00338Details
Sulfotransferase 1C4O75897Details
Sulfotransferase 1C3Q6IMI6Details
Sulfotransferase 6B1Q6IMI4Details
Voltage-gated potassium channel regulatory subunit KCNG3Q8TAE7Details
Potassium voltage-gated channel subfamily S member 3Q9BQ31Details
Potassium voltage-gated channel subfamily E member 4Q8WWG9Details
Voltage-gated potassium channel regulatory subunit KCNF1Q9H3M0Details
FerroportinQ9NP59Details
Plasma membrane ascorbate-dependent reductase CYBRD1Q53TN4Details
DNA (cytosine-5)-methyltransferase 3AQ9Y6K1Details
Zinc transporter ZIP10Q9ULF5Details
Proton-coupled zinc antiporter SLC30A9, mitochondrialQ6PML9Details
Probable proton-coupled zinc antiporter SLC30A3Q99726Details
Metal cation symporter ZIP8Q9C0K1Details
Zinc transporter 6Q6NXT4Details
Apolipoprotein B-100P04114Details
Diacylglycerol kinase thetaP52824Details
V-type proton ATPase subunit E 2Q96A05Details
V-type proton ATPase subunit C 2Q8NEY4Details
Guanylate cyclase soluble subunit beta-1Q02153Details
Neuropilin-2O60462Details
Integrin beta-6P18564Details
Guanylate cyclase soluble subunit alpha-1Q02108Details
Toll-like receptor 6Q9Y2C9Details
Signal transducer and activator of transcription 1-alpha/betaP42224Details
Vascular endothelial growth factor CP49767Details
Nuclear factor erythroid 2-related factor 2Q16236Details
3-oxoacyl-[acyl-carrier-protein] reductaseQ8N4T8Details
Bcl-2-like protein 11O43521Details
Adenylate cyclase type 3O60266Details