Analysis of the DNA sequence and duplication history of human chromosome 15.

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Zody MC, Garber M, Sharpe T, Young SK, Rowen L, O'Neill K, Whittaker CA, Kamal M, Chang JL, Cuomo CA, Dewar K, FitzGerald MG, Kodira CD, Madan A, Qin S, Yang X, Abbasi N, Abouelleil A, Arachchi HM, Baradarani L, Birditt B, Bloom S, Bloom T, Borowsky ML, Burke J, Butler J, Cook A, DeArellano K, DeCaprio D, Dorris L 3rd, Dors M, Eichler EE, Engels R, Fahey J, Fleetwood P, Friedman C, Gearin G, Hall JL, Hensley G, Johnson E, Jones C, Kamat A, Kaur A, Locke DP, Madan A, Munson G, Jaffe DB, Lui A, Macdonald P, Mauceli E, Naylor JW, Nesbitt R, Nicol R, O'Leary SB, Ratcliffe A, Rounsley S, She X, Sneddon KM, Stewart S, Sougnez C, Stone SM, Topham K, Vincent D, Wang S, Zimmer AR, Birren BW, Hood L, Lander ES, Nusbaum C

Analysis of the DNA sequence and duplication history of human chromosome 15.

Nature. 2006 Mar 30;440(7084):671-5.

PubMed ID
16572171 [ View in PubMed
]
Abstract

Here we present a finished sequence of human chromosome 15, together with a high-quality gene catalogue. As chromosome 15 is one of seven human chromosomes with a high rate of segmental duplication, we have carried out a detailed analysis of the duplication structure of the chromosome. Segmental duplications in chromosome 15 are largely clustered in two regions, on proximal and distal 15q; the proximal region is notable because recombination among the segmental duplications can result in deletions causing Prader-Willi and Angelman syndromes. Sequence analysis shows that the proximal and distal regions of 15q share extensive ancient similarity. Using a simple approach, we have been able to reconstruct many of the events by which the current duplication structure arose. We find that most of the intrachromosomal duplications seem to share a common ancestry. Finally, we demonstrate that some remaining gaps in the genome sequence are probably due to structural polymorphisms between haplotypes; this may explain a significant fraction of the gaps remaining in the human genome.

DrugBank Data that Cites this Article

Polypeptides
NameUniProt ID
Histidine decarboxylaseP19113Details
Pyruvate kinase PKMP14618Details
Solute carrier family 12 member 6Q9UHW9Details
Sorbitol dehydrogenaseQ00796Details
Glycine amidinotransferase, mitochondrialP50440Details
Isovaleryl-CoA dehydrogenase, mitochondrialP26440Details
Solute carrier family 12 member 1Q13621Details
Retinal dehydrogenase 2O94788Details
Insulin-like growth factor 1 receptorP08069Details
Aminopeptidase NP15144Details
Microtubule-associated protein 1AP78559Details
Annexin A2P07355Details
AromataseP11511Details
Methionyl-tRNA formyltransferase, mitochondrialQ96DP5Details
Peptidyl-prolyl cis-trans isomerase BP23284Details
Neuronal acetylcholine receptor subunit alpha-7P36544Details
Gamma-aminobutyric acid receptor subunit beta-3P28472Details
Disintegrin and metalloproteinase domain-containing protein 10O14672Details
DNA repair protein RAD51 homolog 1Q06609Details
Phosphopantothenoylcysteine decarboxylaseQ96CD2Details
Endonuclease 8-like 1Q96FI4Details
Calpain-3P20807Details
Cholesterol side-chain cleavage enzyme, mitochondrialP05108Details
Cytochrome P450 1A1P04798Details
Neuronal acetylcholine receptor subunit beta-4P30926Details
Neuronal acetylcholine receptor subunit alpha-3P32297Details
Gamma-aminobutyric acid receptor subunit gamma-3Q99928Details
Solute carrier organic anion transporter family member 3A1Q9UIG8Details
High affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8AO60658Details
Proteasome subunit alpha type-4P25789Details
Ammonium transporter Rh type CQ9UBD6Details
CHRNA7-FAM7A fusion proteinQ494W8Details
Pro-cathepsin HP09668Details
Cytochrome c oxidase subunit 5A, mitochondrialP20674Details
Dual specificity protein kinase CLK3P49761Details
Elongation factor-like GTPase 1Q7Z2Z2Details
Lactase-like proteinQ6UWM7Details
Long-chain-fatty-acid--CoA ligase ACSBG1Q96GR2Details
Ras-related protein Rab-8BQ92930Details
Signal recognition particle 14 kDa proteinP37108Details
Isocitrate dehydrogenase [NADP], mitochondrialP48735Details
FumarylacetoacetaseP16930Details
Unconventional myosin-IeQ12965Details
Nuclear receptor ROR-alphaP35398Details
Ras-related protein Rab-11AP62491Details
Neutral alpha-glucosidase CQ8TET4Details
Sodium/nucleoside cotransporter 1O00337Details
Ryanodine receptor 3Q15413Details
Protein PMLP29590Details
Calcium and integrin-binding family member 2O75838Details
Tropomyosin alpha-1 chainP09493Details
Small ribosomal subunit protein eS17P08708Details
Serine/threonine-protein kinase ULK3Q6PHR2Details
Death-associated protein kinase 2Q9UIK4Details
eIF-2-alpha kinase GCN2Q9P2K8Details
Tyrosine-protein kinase Fes/FpsP07332Details
Leukocyte tyrosine kinase receptorP29376Details
Dual specificity mitogen-activated protein kinase kinase 5Q13163Details
NT-3 growth factor receptorQ16288Details
Serine/threonine-protein kinase PAK 6Q9NQU5Details
Long-chain fatty acid transport protein 2O14975Details
Receptor for retinol uptake STRA6Q9BX79Details
Aquaporin-9O43315Details
Perilipin-1O60240Details