Supplemental Data
  | The Sequence of the Human Genome J. Craig Venter, Mark D. Adams, Eugene W. Myers, Peter W. Li, Richard J. Mural, Granger G. Sutton, Hamilton O. Smith, Mark Yandell, Cheryl A. Evans, Robert A. Holt, Jeannine D. Gocayne, Peter Amanatides, Richard M. Ballew, Daniel H. Huson, Jennifer Russo Wortman, Qing Zhang, Chinnappa D. Kodira, Xiangqun H. Zheng, Lin Chen, Marian Skupski, Gangadharan Subramanian, Paul D. Thomas, Jinghui Zhang, George L. Gabor, Miklos, Catherine Nelson, Samuel Broder, Andrew G. Clark, Joe Nadeau, Victor A. McKusick, Norton Zinder, Arnold J. Levine, Richard J. Roberts, Mel Simon, Carolyn Slayman, Michael Hunkapiller, Randall Bolanos, Arthur Delcher, Ian Dew, Daniel Fasulo, Michael Flanigan, Liliana Florea, Aaron Halpern, Sridhar Hannenhalli, Saul Kravitz, Samuel Levy, Clark Mobarry, Knut Reinert, Karin Remington, Jane Abu-Threideh, Ellen Beasley, Kendra Biddick, Vivien Bonazzi, Rhonda Brandon, Michele Cargill, Ishwar Chandramouliswaran, Rosane Charlab, Kabir Chaturvedi, Zuoming Deng, Valentina Di Francesco, Patrick Dunn, Karen Eilbeck, Carlos Evangelista, Andrei E. Gabrielian, Weiniu Gan, Wangmao Ge, Fangcheng Gong, Zhiping Gu, Ping Guan, Thomas J. Heiman, Maureen E. Higgins, Rui-Ru Ji, Zhaoxi Ke, Karen A. Ketchum, Zhongwu Lai, Yiding Lei, Zhenya Li, Jiayin Li, Yong Liang, Xiaoying Lin, Fu Lu, Gennady V. Merkulov, Natalia Milshina, Helen M. Moore, Ashwinikumar K Naik, Vaibhav A. Narayan, Beena Neelam, Deborah Nusskern, Douglas B. Rusch, Steven Salzberg, Wei Shao, Bixiong Shue, Jingtao Sun, Zhen Yuan Wang, Aihui Wang, Xin Wang, Jian Wang, Ming-Hui Wei, Ron Wides, Chunlin Xiao, Chunhua Yan, Alison Yao, Jane Ye, Ming Zhan, Weiqing Zhang, Hongyu Zhang, Qi Zhao, Liansheng Zheng, Fei Zhong, Wenyan Zhong, Shiaoping C. Zhu, Shaying Zhao, Dennis Gilbert, Suzanna Baumhueter, Gene Spier, Christine Carter, Anibal Cravchik, Trevor Woodage, Feroze Ali, Huijin An, Aderonke Awe, Danita Baldwin, Holly Baden, Mary Barnstead, Ian Barrow, Karen Beeson, Dana Busam, Amy Carver, Angela Center, Ming Lai Cheng, Liz Curry, Steve Danaher, Lionel Davenport, Raymond Desilets, Susanne Dietz, Kristina Dodson, Lisa Doup, Steven Ferriera, Neha Garg, Andres Gluecksmann, Brit Hart, Jason Haynes, Charles Haynes, Cheryl Heiner, Suzanne Hladun, Damon Hostin, Jarrett Houck, Timothy Howland, Chinyere Ibegwam, Jeffery Johnson, Francis Kalush, Lesley Kline, Shashi Koduru, Amy Love, Felecia Mann, David May, Steven McCawley, Tina McIntosh, Ivy McMullen, Mee Moy, Linda Moy, Brian Murphy, Keith Nelson, Cynthia Pfannkoch, Eric Pratts, Vinita Puri, Hina Qureshi, Matthew Reardon, Robert Rodriguez, Yu-Hui Rogers, Deanna Romblad, Bob Ruhfel, Richard Scott, Cynthia Sitter, Michelle Smallwood, Erin Stewart, Renee Strong, Ellen Suh, Reginald Thomas, Ni Ni Tint, Sukyee Tse, Claire Vech, Gary Wang, Jeremy Wetter, Sherita Williams, Monica Williams, Sandra Windsor, Emily Winn-Deen, Keriellen Wolfe, Jayshree Zaveri, Karena Zaveri, Josep F. Abril, Roderic Guigó, Michael J. Campbell, Kimmen V. Sjolander, Brian Karlak, Anish Kejariwal, Huaiyu Mi, Betty Lazareva, Thomas Hatton, Apurva Narechania, Karen Diemer, Anushya Muruganujan, Nan Guo, Shinji Sato, Vineet Bafna, Sorin Istrail, Ross Lippert, Russell Schwartz, Brian Walenz, Shibu Yooseph, David Allen, Anand Basu, James Baxendale, Louis Blick, Marcelo Caminha, John Carnes-Stine, Parris Caulk, Yen-Hui Chiang, My Coyne, Carl Dahlke, Anne Deslattes Mays, Maria Dombroski, Michael Donnelly, Dale Ely, Shiva Esparham, Carl Fosler, Harold Gire, Stephen Glanowski, Kenneth Glasser, Anna Glodek, Mark Gorokhov, Ken Graham, Barry Gropman, Michael Harris, Jeremy Heil, Scott Henderson, Jeffrey Hoover, Donald Jennings, Catherine Jordan, James Jordan, John Kasha, Leonid Kagan, Cheryl Kraft, Alexander Levitsky, Mark Lewis, Xiangjun Liu, John Lopez, Daniel Ma, William Majoros, Joe McDaniel, Sean Murphy, Matthew Newman, Trung Nguyen, Ngoc Nguyen, Marc Nodell, Sue Pan, Jim Peck, William Rowe, Robert Sanders, John Scott, Michael Simpson, Thomas Smith, Arlan Sprague, Timothy Stockwell, Russell Turner, Eli Venter, Mei Wang, Meiyuan Wen, David Wu, Mitchell Wu, Ashley Xia, Ali Zandieh, Xiaohong Zhu |
Web Fig. 1: Annotation of the Celera Human Genome Assembly
Supplementary Material
| Supplemental Table 1.Chromosomal distribution of intronless paralogs. | |||||
| IP | SOURCE | IP | SOURCE | DEFINTION/PROTEIN NAME | SOURCE GENBANK INDEX NUMBER |
|---|---|---|---|---|---|
| hCP48693 | hCP37465 | chr20 | chr6 | BCL2-antagonist/killer 1; cell death inhibitor 1 | 4502363 |
| hCP45781 | hCP44963 | chr1 | chr13 | RNA polymerase I 16 kDa subunit | 7705740 |
| hCP45175 | hCP40330 | chr9 | chr6 | eukaryotic translation elongation factor 1 alpha 1 | 4503471 |
| hCP47770 | hCP40330 | chr5 | chr6 | eukaryotic translation elongation factor 1 alpha 1 | 4503471 |
| hCP48153 | hCP40330 | chr7 | chr6 | eukaryotic translation elongation factor 1 alpha 1 | 4503471 |
| hCP45176 | hCP40330 | chr9 | chr6 | eukaryotic translation elongation factor 1 alpha 1-like 14 | 4503473 |
| hCP47771 | hCP40330 | chr5 | chr6 | eukaryotic translation elongation factor 1 alpha 1-like 14 | 4503473 |
| hCP48154 | hCP40330 | chr7 | chr6 | eukaryotic translation elongation factor 1 alpha 1-like 14 | 4503473 |
| hCP43102 | hCP45627 | chr19 | chr8 | eukaryotic translation elongation factor 1 delta | 4503479 |
| hCP35783 | hCP52348 | chr2 | chr11 | eukaryotic translation initiation factor 3, subunit 5 | 4503519 |
| hCP34934 | hCP39451 | chr2 | chr12 | heterogeneous nuclear ribonucleoprotein A1 | 4504445 |
| hCP44529 | hCP39451 | chr13 | chr12 | heterogeneous nuclear ribonucleoprotein A1 | 4504445 |
| hCP43335 | hCP44582 | chr12 | chr17 | non-metastatic cells 2, protein (NM23B) | 4505409 |
| hCP50486 | hCP40136 | chr8 | chr14 | proteasome (prosome, macropain) 26S subunit, ATPase, 6 | 4506215 |
| hCP42158 | hCP46912 | chr12 | chr2 | prothymosin, alpha (gene sequence 28) | 4506277 |
| hCP45662 | hCP37866 | chr2 | chr18 | ras homolog gene family, member B; RhoB; | 4757764 |
| hCP36390 | hCP37104 | chr8 | chr7 | H2A histone family, member Z | 4504255 |
| hCP43150 | hCP37104 | chr15 | chr7 | H2A histone family, member Z | 4504255 |
| hCP46278 | hCP39295 | chr4 | chr3 | NADH dehydrogenase (ubiquinone) 1 beta | 6041669 |
| hCP36897 | hCP34863 | chr5 | chr12 | RAP1A, member of RAS oncogene | 4506413 |
| hCP46034 | hCP35342 | chr17 | chrX | adaptor-related protein complex 1, sigma | 4506957 |
| hCP35830 | hCP51363 | chr6 | chr4 | alcohol dehydrogenase 5 (class III), | 4501937 |
| hCP44848 | hCP40594 | chr9 | chr1 | cell division cycle 20 | 4557437 |
| hCP50246 | hCP49760 | chr4 | chr1 | cell division cycle 42 | 4757952 |
| hCP48857 | hCP48263 | chr15 | chr7 | chromobox homolog 3 | 6005780 |
| hCP46158 | hCP42461 | chr13 | chr11 | diacylglycerol kinase, zeta (104kD) | 4503317 |
| hCP37376 | hCP49621 | chr7 | chr11 | eukaryotic translation elongation factor 1 | 4503481 |
| hCP36628 | hCP39069 | chr15 | chr8 | fatty acid binding protein 5 | 4557581 |
| hCP43166 | hCP39069 | chr15 | chr8 | fatty acid binding protein 5 | 4557581 |
| hCP49159 | hCP35287 | chr20 | chr19 | ferritin, light polypeptide; hypothetical protein | 4503797 |
| hCP38447 | hCP34306 | chr19 | chr16 | glycine cleavage system protein H | 4758424 |
| hCP51879 | hCP34306 | chr1 | chr16 | glycine cleavage system protein H | 4758424 |
| hCP42685 | hCP43793 | chr20 | chr13 | high-mobility group (nonhistone chromosomal) protein | 4504425 |
| hCP42865 | hCP43793 | chr3 | chr13 | high-mobility group (nonhistone chromosomal) protein | 4504425 |
| hCP49883 | hCP43793 | chr20 | chr13 | high-mobility group (nonhistone chromosomal) protein | 4504425 |
| hCP50559 | hCP43793 | chr15 | chr13 | high-mobility group (nonhistone chromosomal) protein | 4504425 |
| hCP50984 | hCP43793 | chr22 | chr13 | high-mobility group (nonhistone chromosomal) protein | 4504425 |
| hCP37795 | hCP42486 | chrX | chr10 | phosphoglycerate mutase 1 (brain) | 4505753 |
| hCP49866 | hCP42486 | chr12 | chr10 | phosphoglycerate mutase 1 (brain) | 4505753 |
| hCP48871 | hCP33485 | chr4 | chr5 | pituitary tumor-transforming protein 1 | 4758980 |
| hCP43053 | hCP201144 | chr3 | chr6 | pre-B-cell leukemia transcription factor 2 | 4505625 |
| hCP47725 | hCP49987 | chr5 | chr14 | proteasome (prosome, macropain) activator subunit | 4506237 |
| hCP38333 | hCP35418 | chrX | chr7 | ras-related C3 botulinum toxin substrate | 5902042 |
| hCP40764 | hCP36922 | chr3 | chr6 | ribosomal protein L10a; neural precursor | 6325472 |
| hCP45150 | hCP34348 | chr17 | chr16 | ribosomal protein L13 | 4506599 |
| hCP42475 | hCP35262 | chr10 | chr19 | ribosomal protein L13a | 6912634 |
| hCP43258 | hCP35262 | chr12 | chr19 | ribosomal protein L13a | 6912634 |
| hCP43889 | hCP35262 | chr13 | chr19 | ribosomal protein L13a | 6912634 |
| hCP48078 | hCP35262 | chr12 | chr19 | ribosomal protein L13a | 6912634 |
| hCP51648 | hCP35262 | chr10 | chr19 | ribosomal protein L13a | 6912634 |
| hCP40196 | hCP41680 | chr3 | chr18 | ribosomal protein L17 | 4506617 |
| hCP35655 | hCP44971 | chr1 | chr13 | ribosomal protein L21 | 4506611 |
| hCP39305 | hCP44971 | chr14 | chr13 | ribosomal protein L21 | 4506611 |
| hCP41351 | hCP44971 | chr11 | chr13 | ribosomal protein L21 | 4506611 |
| hCP47660 | hCP44971 | chr4 | chr13 | ribosomal protein L21 | 4506611 |
| hCP47833 | hCP44971 | chr7 | chr13 | ribosomal protein L21 | 4506611 |
| hCP48726 | hCP44971 | chr4 | chr13 | ribosomal protein L21 | 4506611 |
| hCP49814 | hCP44971 | chr10 | chr13 | ribosomal protein L21 | 4506611 |
| hCP50215 | hCP44971 | chr10 | chr13 | ribosomal protein L21 | 4506611 |
| hCP34220 | hCP45368 | chr3 | chr17 | ribosomal protein L23a | 4506615 |
| hCP43068 | hCP45090 | chr12 | chr17 | ribosomal protein L26 | 4506621 |
| hCP38068 | hCP41270 | chr11 | chr11 | ribosomal protein L27a | 4506625 |
| hCP38885 | hCP41270 | chr6 | chr11 | ribosomal protein L27a | 4506625 |
| hCP34480 | hCP51948 | chr3 | chr3 | ribosomal protein L29 | 4506629 |
| hCP36437 | hCP43819 | chr7 | chr3 | ribosomal protein L32 | 4506635 |
| hCP39494 | hCP43819 | chr6 | chr3 | ribosomal protein L32 | 4506635 |
| hCP201498 | hCP44392 | chr1 | chr9 | ribosomal protein L35 | 6005860 |
| hCP51162 | hCP44392 | chr7 | chr9 | ribosomal protein L35 | 6005860 |
| hCP39467 | hCP43627 | chr14 | chr9 | ribosomal protein L7a | 4506661 |
| hCP41685 | hCP48439 | chr15 | chr4 | ribosomal protein L9 | 4506665 |
| hCP201561 | hCP35286 | chr12 | chr19 | ribosomal protein S11 | 4506681 |
| hCP42984 | hCP39006 | chr11 | chr6 | ribosomal protein S12 | 4506683 |
| hCP42446 | hCP47279 | chr1 | chr16 | ribosomal protein S15a | 4506689 |
| hCP201365 | hCP52071 | chr19 | chr19 | ribosomal protein S16 | 4506691 |
| hCP42269 | hCP52071 | chr1 | chr19 | ribosomal protein S16 | 4506691 |
| hCP40118 | hCP42669 | chr5 | chr15 | ribosomal protein S17 | 4506693 |
| hCP51382 | hCP42669 | chr22 | chr15 | ribosomal protein S17 | 4506693 |
| hCP35240 | hCP42007 | chr8 | chr12 | ribosomal protein S26 | 4506709 |
| hCP35551 | hCP42007 | chr2 | chr12 | ribosomal protein S26 | 4506709 |
| hCP36459 | hCP42007 | chrX | chr12 | ribosomal protein S26 | 4506709 |
| hCP38950 | hCP42007 | chr4 | chr12 | ribosomal protein S26 | 4506709 |
| hCP39533 | hCP42007 | chr8 | chr12 | ribosomal protein S26 | 4506709 |
| hCP41719 | hCP42007 | chr13 | chr12 | ribosomal protein S26 | 4506709 |
| hCP43701 | hCP42007 | chr9 | chr12 | ribosomal protein S26 | 4506709 |
| hCP44708 | hCP42007 | chr9 | chr12 | ribosomal protein S26 | 4506709 |
| hCP45758 | hCP42007 | chr15 | chr12 | ribosomal protein S26 | 4506709 |
| hCP46725 | hCP42007 | chr7 | chr12 | ribosomal protein S26 | 4506709 |
| hCP50862 | hCP42007 | chr8 | chr12 | ribosomal protein S26 | 4506709 |
| hCP51315 | hCP42007 | chr10 | chr12 | ribosomal protein S26 | 4506709 |
| hCP38914 | hCP34424 | chr16 | chr2 | ribosomal protein S27a | 4506713 |
| hCP50884 | hCP34424 | chr1 | chr2 | ribosomal protein S27a | 4506713 |
| hCP50962 | hCP38574 | chr22 | chr19 | ribosomal protein S9 | 4506745 |
| hCP37989 | hCP35777 | chrX | chr3 | teratocarcinoma-derived growth factor 1 | 4507425 |
| hCP40506 | hCP35239 | chr10 | chr8 | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation | 4507953 |
| hCP50191 | hCP35239 | chr2 | chr8 | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation | 4507953 |
| Supplemental Table 2. Examples of paralogs with disease associations on duplicated genome segments. (Both panels should be viewed in a linear format to appreciate the similarities in the diseases caused by the paralogous duplications) | ||||
| Gene name | Protein | Chr | Disease | OMIM |
|---|---|---|---|---|
| complement component 8 | hCP40779 | 1 | C8 deficiency, type II | 120960 |
| nuclear receptor subfamily 3, group C | hCP48259 | 4 | Pseudohypoaldosteronism type I, | 600983 |
| complement component 9 | hCP47512 | 5 | C9 deficiency Immune | 120940 |
| glucocorticoid receptor | hCP47558 | 5 | Cortisol resistance Metabolic | 138040 |
| hexosaminidase B (beta polypeptide) | hCP48123 | 5 | Sandhoff disease, Neurological | 268800 |
| homeo box A13hCP48915 | 7 | Hand-foot-uterus syndrome | 142959 | |
| tyrosine hydroxylase | hCP35709 | 11 | Segawa syndrome, | 191290 |
| phenylalanine hydroxylase | hCP39374 | 12 | Hyperphenylalaninemia, | 261600 |
| connexin 26hCP38170 | 13 | Deafness, autosomal dominant | 121011 | |
| coagulation factor VII | hCP43441 | 13 | Factor VII deficiency | 227500 |
| coagulation factor X | hCP43442 | 13 | Factor X deficiency | 227600 |
| insulin promoter transcription factor 1 | hCP44966 | 13 | Pancreatic agenesis | 600733 |
| hexosaminidase A | hCP50228 | 15 | Hex A pseudodeficiency | 272800 |
| coagulation factor IX | hCP35448 | X | Hemophilia B Hematological | 306900 |
| coagulation factor IX | hCP35448 | X | Hemophilia B Hematological | 306900 |
| connexin 32hCP37674 | X | Charcot-Marie-Tooth neuropathy | 304040 | |
| Duplicated gene name | Homolog | Chr | Disease | OMIM |
| complement component 9 | hCP47512 | 5 | C9 deficiency120940 | |
| glucocorticoid receptor | CP47558 | 5 | Cortisol resistance Metabolic | 138040 |
| complement component 8 | hCP40779 | 1 | C8 deficiency, type II Immune | 120960 |
| nuclear receptor subfamily 3 | hCP48259 | 4 | Pseudohypoaldosteronism type I | 600983 |
| hexosaminidase A | hCP50228 | 15 | Hex A pseudodeficiency Neurological | 272800 |
| insulin promoter TF-1 | hCP44966 | 13 | Pancreatic agenesis Gastrointestinal | 600733 |
| phenylalanine hydroxylase | hCP39374 | 12 | Hyperphenylalaninemia, mild Neurological | 261600 |
| tyrosine hydroxylase | hCP35709 | 11 | Segawa syndrome, recessive Neurological | 191290 |
| connexin 32 | hCP37674 | 23 | Charcot-Marie-Tooth neuropathy | 304040 |
| coagulation factor IX | hCP35448 | 23 | Hemophilia B Hematological | 306900 |
| coagulation factor IX | hCP35448 | 23 | Hemophilia B Hematological | 306900 |
| homeo box A13 | hCP48915 | 7 | Hand-foot-uterus syndrome Renal | 142959 |
| hexosaminidase B | hCP48123 | 5 | Sandhoff disease, infantile | 268800 |
| coagulation factor VII | hCP43441 | 13 | Factor VII deficiency | 227500 |
| coagulation factor X | hCP43442 | 13 | Factor X deficiency | 227600 |
| connexin 26 | hCP38170 | 13 | Deafness, autosomal dominant 3 | 121011 |
Supplemental Figure 2A. Karyotype analysis of donors.
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Supplemental Figure 2B.
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Supplemental Figure 2C.
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Supplemental Figure 2D.
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Supplemental Figure 2E.
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Supplemental Figure 3 -Chromosome 1. Comparison of the CSA and the PFP assembly. To generate the figure, Celera fragment sequences were mapped onto each assembly. The PFP assembly is indicated in the upper third of each panel; the Celera assembly is indicated in the lower third. In the center of the panel, green lines show Celera sequences that are in the same order and orientation in both assemblies and form the longest consistently ordered run of sequences. Yellow lines indicate sequence blocks that are in the same orientation, but out of order. Red lines indicate sequence blocks that are not in the same orientation. For clarity, in the latter two cases, lines are only drawn between segments of matching sequence that are at least 50 kbp long. The top and bottom thirds of each panel show the extent of Celera mate-pair violations (red, misoriented; yellow, incorrect distance between the mates) for each assembly grouped by library size. (Mate pairs that are within the correct distance, as expected from the mean library insert size, are omitted from the figure for clarity.) Predicted breakpoints, corresponding to stacks of violated mate pairs of the same type, are shown as blue ticks on each assembly axis. Runs of more than 10,000 Ns are shown as cyan bars. Plots for each of the 24 chromosomes can be seen as separate files.
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Supplemental Figure 3 -Chromosome 2.
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Supplemental Figure 3 -Chromosome 3.
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Supplemental Figure 3 -Chromosome 4.
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Supplemental Figure 3 -Chromosome 5.
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Supplemental Figure 3 -Chromosome 6.
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Supplemental Figure 3 -Chromosome 7.
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Supplemental Figure 3 -Chromosome 8.
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Supplemental Figure 3 -Chromosome 9.
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Supplemental Figure 3 -Chromosome 10.
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Supplemental Figure 3 -Chromosome 11.
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Supplemental Figure 3 -Chromosome 12.
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Supplemental Figure 3 -Chromosome 13.
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Supplemental Figure 3 -Chromosome 14.
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Supplemental Figure 3 -Chromosome 15.
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Supplemental Figure 3 -Chromosome 16.
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Supplemental Figure 3 -Chromosome 17.
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Supplemental Figure 3 -Chromosome 18.
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Supplemental Figure 3 -Chromosome 19.
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Supplemental Figure 3 -Chromosome 20.
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Supplemental Figure 3 -Chromosome 21.
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Supplemental Figure 3 -Chromosome 22.
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Supplemental Figure 3 -Chromosome 23.
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Supplemental Figure 3 -Chromosome 24.
