The DNA sequence and comparative analysis of human chromosome 10

Deloukas, Panos; Earthrowl, M. E.; Grafham, Darren; Rubenfield, Marc; French, Lisa; Steward, Charles A.; Sims, Sarah; Jones, Matt; Searle, S.; Scott, Carol; Howe, Kevin; Hunt, Sarah; Andrews, T. Daniel; Gilbert, James; Swarbreck, David; Ashurst, Jennifer; Taylor, Amy; Battles, J K; Bird, Christine P.; Ainscough, R.; Almeida, J. P.; Ashwell, R. I. S.; Ambrose, K. D.; Babbage, Anne; Bagguley, C. L.; Bailey, J.; Banerjee, Ruby; Bates, K.; Beasley, Helen; Bray-Allen, S.; Brown, Andrew; Brown, J. Y.; Burford, D. C.; Burrill, W.; Burton, John H.; Cahill, Patrick; Camire, D.; Carter, N. P.; Chapman, J C; Clark, S. Y.; Clarke, Geraldine M.; Clee, Chris; Clegg, S.; Corby, N.; Coulson, Alan; Dhami, Pawandeep; Dutta, I.; Dunn, Matt; Faulkner, L.; Frankish, Adam; Frankland, J.; Garner, P.; Garnett, J.; Gribble, Susan; Griffiths, Chris; Grocock, Russell; Gustafson, Erik; Hammond, S.; Harley, Joanna; Hart, Elizabeth A.; Heath, P. D.; Hồ, Thiện; Hopkins, Barbara; Horne, Jane Anne; Howden, Philip; Huckle, Elizabeth J.; Hynds, Catherine; Johnson, Christopher M.; Johnson, David J.; Kana, A.; Kay, Mike; Kimberley, A. M.; Kershaw, J. K.; Kokkinaki, Maria; Lawlor, Stephanie; Lee, H. M.; Leongamornlert, Daniel; Laird, Gavin K.; Lloyd, Christine; Lloyd, D. M.; Loveland, Jane; Lovell, J.; McLaren, Stuart; McLay, Kirsten; McMurray, Amanda; Mashreghi-Mohammadi, M.; Matthews, Lucy; Milne, Sarah; Nickerson, T.; Nguyen, Minh Quang; Overton-Larty, E. K.; Palmer, Sophie; Pearce, A. V.; Peck, A. I.; Pelan, Sarah; Phillimore, Benjamin; Porter, Keith; Rice, Catherine M.; Rogosin, Andrea; Ross, Mark T.; Sarafidou, Theologia; Sehra, Harminder; Shownkeen, Ratna; Skuce, C. D.; Smith, Michelle; Standring, Lorraine S.; Sycamore, Neil; Tester, J.; Thorpe, A.; Torcasso, W; Tracey, Alan S.; Tromans, A.; Tsolas, Jason M.; Wall, M.; Walsh, Justine; Wang, H.; Weinstock, Keith G.; West, Anthony P.; Willey, David L.; Whitehead, Siobhan; Wilming, Laurens G.; Wray, Paul; Young, Lynn; Chen, Y.; Lovering, Ruth C.; Moschonas, Nicholas Κ.; Siebert, Reiner; Fechtel, Kim; Bentley, David; Durbin, Richard; Hubbard, Tim; Doucette‐Stamm, Lynn; Beck, Stephan; Smith, Doug; Rogers, Jane

doi:10.1038/nature02462

Cited by 73 publications

(72 citation statements)

References 38 publications

(38 reference statements)

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“…There is evidence of extensive alternative splicing, with gene loci having an average of 3.1 distinct transcripts and 71% having at least two transcripts. This rate of alternative splicing is comparable to recent reports 5,6 . The longest gene on chromosome 18 is DCC (deleted in colorectal carcinoma), spanning 1,190,632 bp.…”

supporting

confidence: 76%

DNA sequence and analysis of human chromosome 18

Nusbaum

Zody

Borowsky

et al. 2005

Nature

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supporting

confidence: 76%

DNA sequence and analysis of human chromosome 18

Nusbaum

Zody

Borowsky

et al. 2005

Nature

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“…In contrast, PTL-like genes were located on chicken chromosome 6 on the positive strand in the reverse order (PLR2-PLR1-PTL), which suggests that a chromosomal rearrangement has occurred in the region of the PTL-like genes, although in each case, the three genes are proximally localized on mammalian and bird genomes. Figures 1 and 2 summarize the coding exon start sites for vertebrate PTL genes, human PLR1, PLR2 and PLR3 genes and mouse PLR1 and PLR2 genes showing 12 coding exons in identical or similar positions which are consistent with previous reports [9,[63][64]. This is consistent with a common evolutionary origin for these genes.…”

Section: Secondary and Tertiary Structures For Vertebrate Ptl-like LIsupporting

confidence: 80%

“…Amino acid sequence alignments for previously reported human (Homo sapiens) PTL [56], PLR1 [61], PLR2 [6] and PLR3 [9] and mouse PTL [42,62], PLR1 [61] and PLR2 [26,42] sequences are shown in Figure 2 (also see 1). The amino acid sequence for the human PLR1 subunit contained 467 residues while the mouse PLR1 sequence contained 473 amino acids, due to an extended C-terminus sequence.…”

Section: Alignments Of Vertebrate Ptl-like Amino Acid Sequencesmentioning

confidence: 99%

“…These overall features are readily observed for the predicted frog PTL and PLR1 three-dimensional structures. Table 1 and Supplementary Table 1 summarize the predicted locations for vertebrate PTL-like genes based upon BLAT interrogations of genomes using the reported sequences for human PTL, PLR1, PLR2 and PLR3 [6,9,56,61] and the predicted sequences for other vertebrate PTL-like proteins and the UC Santa Cruz Genome Browser [49]. The mammalian PTL-like genes were predominantly transcribed on the positive strand and located in the following gene order: PLR3-PTL-PLR1-PLR2 for human (see Supplementary Figure 2), orangutan and rhesus genomes; and PTL-PLR1-PLR2 for other mammalian genomes, including mouse, rat, dog, pig, rabbit, opossum and platypus genomes (Table 1 and Supplementary Table 1).…”

Section: Secondary and Tertiary Structures For Vertebrate Ptl-like LImentioning

confidence: 99%

“…Two other PTL-related proteins, pancreatic lipase related-protein 1 (PLR1; gene PLR1 or PNLPR1) and pancreatic lipase related protein 2 (PLR2; E.C.3.1.1.3; gene PLR2 or PNLPR2) are also major pancreatic secretory proteins which are structurally similar to PTL [5][6][7][8]. A third PTL-related protein and gene, pancreatic lipase related protein 3 (PLR3; E.C.3.1.1.3; gene PLR3 or PNLPR3), has also been reported in humans [9].…”

Section: Introductionmentioning

confidence: 99%

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Bioinformatics and Evolution of Vertebrate Pancreatic Lipase and Related Proteins and Genes

Holmes¹,

Cox²

2012

JDMGP

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Background: Pancreatic lipase (PTL) functions in the presence of colipase in the hydrolysis of emulsified fats in the small intestine following secretion from the pancreas. Pancreatic lipase related protein 1 (PLR1) is also found in pancreatic secretions and may perform a regulatory role in lipolysis; PLR2 catalyses pancreatic triglyceride and galactolipase reactions while PLR3 may serve a related but unknown lipase function. Comparative PTL, PLR1, PLR2 and PLR3 amino acid sequences and structures and gene locations and sequences were examined using data from several vertebrate genome projects. Methods:Sequence alignments and conserved predicted secondary and tertiary structures were studied and key amino acid residues and domains identified based on previous reports on human and pig PTL. Comparative analyses of vertebrate PTL-like genes were conducted using the UC Santa Cruz Genome Browser. Phylogeny studies investigated the evolution of these vertebrate PTL-like genes.Data: Human and mouse PTL sequences shared 78% identities but only 64-68% identities with human and mouse PLR1 and PLR2 sequences. Several vertebrate PTL and PTL-like protein domains were predicted using bioinformatics including an N-signal peptide; N-glycosylation site(s); an α/β hydrolase fold region containing a catalytic triad; a 'lid' region for the active site; a 'hinge' separating the lipase and PLAT regions; and a C-terminal PLAT region. Eutherian mammalian PLR1 sequences retained residues (196Val/198Ala) responsible for the loss of triacylglycerol lipase activity whereas lower vertebrate PLR1 sequences retained the 'active' lipase residues. In contrast, mammalian PTL, PLR2 and PLR3 sequences exhibited lipase 'active' residues (196Ala/198Pro); chicken and frog PLR1 sequences retained the lipase 'active' residues; and opossum and platypus PLR1 sequences exhibited 196Ala/Ser198 and 196Ser/198Pro residues. A phylogenetic tree analysis provided evidence for four distinct vertebrate PTL-like gene families. Conclusions:Pancreatic lipase (PTL) and related genes and proteins (PLR1 and PLR2) are present in all vertebrate genomes examined whereas PLR3 is found only in primate genomes. The 'inactive' form of vertebrate PLR1 is restricted to eutherian mammals. Vertebrate PTL-like genes apparently originated in a vertebrate ancestor following gene duplication events of an ancestral PTL-like ancestral gene. Two separate lines of PTL-like gene evolution are proposed in lower vertebrates (PTL/PLR1 and PLR2), with a further gene duplication event (PLR2/PLR3) for primate genomes.

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Sequencing the Human Genome: Novel Insights into its Structure and Function

Kehrer‐Sawatzki¹,

Cooper²

2008

Encyclopedia of Life Sciences

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The availability of the human genome sequence has had an enormous impact on biomedical research. New discoveries emanating directly from the elucidation of the human genome sequence have included the unexpectedly low total number of genes, the existence of numerous transcribed but noncoding sequences and the multiplicity of low‐copy repeats and segmental duplications. The Human Genome Project has also spawned new research projects such as Encyclopedia of DNA Elements (ENCODE) and Haplotype Map (HapMap) which together are helping to reveal the remarkable complexity of the human genome. Finally, comparison of the human genome sequence with the genome sequences of other higher organisms has opened up numerous research avenues in evolutionary biology.

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The DNA sequence and comparative analysis of human chromosome 10

Cited by 73 publications

References 38 publications

DNA sequence and analysis of human chromosome 18

DNA sequence and analysis of human chromosome 18

Bioinformatics and Evolution of Vertebrate Pancreatic Lipase and Related Proteins and Genes

Sequencing the Human Genome: Novel Insights into its Structure and Function

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