chr3:1-19941174 chr3:19941175-39882348 chr3:39882349-59823522 chr3:59823523-79764696 chr3:79764697-99705870 chr3:99705871-119647044 chr3:119647045-139588218 chr3:139588219-159529392 chr3:159529393-179470566 chr3:179470567-199411732
The DNA Sequence, Annotation and Analysis of Human Chromosome 3

Accepted for publication in Nature, 03/2006

( Finished Chr 3 sequence GenBank accession #: NC_000003 )

Corresponding authors:

Steven Scherer (
Human Genome Sequencing Center, Baylor College of Medicine

Huanming Yang (
Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China

Complete author and affiliation list

HGSC Genboree
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After the completion of a draft human genome sequence1, the International Human Genome Sequencing Consortium has proceeded to finish, annotate and describe each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chromosomes. Chromosome 3 comprises just four contigs, one of which currently represents the longest contiguous stretch of finished DNA sequence known so far. The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. It also contains a chemokine receptor gene cluster as well as numerous loci involved in multiple human cancers such as the gene encoding FHIT, which contains the most common constitutive fragile site in the genome, FRA3B. Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion.

Figure List:

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Complete Author & Affiliation List:

Donna M. Muzny1, Steven E. Scherer1, Rajinder Kaul2, Jing Wang3, Jun Yu3, Ralf Sudbrak4,5, Christian J. Buhay1, Rui Chen1, Andrew Cree1, Yan Ding1, Shannon Dugan-Rocha1, Rachel Gill1, Preethi Gunaratne1, R. Alan Harris1, Alicia C. Hawes1, Judith Hernandez1, Anne V. Hodgson1, Jennifer Hume1, Andrew Jackson1, Ziad Mohid Khan1, Christie Kovar-Smith1, Lora R. Lewis1, Ryan J. Lozado1, Michael L. Metzker1, Aleksandar Milosavljevic1, George R. Miner1, Margaret B. Morgan1, Lynne V. Nazareth1, Graham Scott1, Erica Sodergren1, Xing-Zhi Song1, David Steffen1, Sharon Wei1, David A. Wheeler1, Mathew W. Wright6, Kim C. Worley1, Ye Yuan1, Zhengdong Zhang1, Charles Q. Adams1, M. Ali Ansari-Lari1, Mulu Ayele1, Mary J. Brown1, Guan Chen1, Zhijian Chen1, James Clendenning2, Kerstin P. Clerc-Blankenburg1, Runsheng Chen3, Zhu Chen3, Clay Davis1, Oliver Delgado1, Huyen H. Dinh1, Wei Dong3, Heather Draper1, Stephen Ernst2, Gang Fu3, Manuel L. Gonzalez-Garay1, Dawn K. Garcia7, Will Gillett2, Jun Gu3, Bailin Hao3, Eric Haugen2, Paul Havlak1, Xin He7, Steffen Hennig8, Songnian Hu3, Wei Huang3, Laronda R. Jackson1, Leni S. Jacob1, Susan H. Kelly1, Michael Kube4, Ruth Levy2, Zhangwan Li1, Bin Liu3, Jing Liu1, Wen Liu1, Jing Lu1, Manjula Maheshwari1, Bao-Viet Nguyen1, Geoffrey O. Okwuonu1, Anthony Palmeiri2, Shiran Pasternak1, Lesette M. Perez1, Karen A. Phelps2, Farah J. H. Plopper1, Boqin Qiang3, Christopher Raymond2, Ruben Rodriguez7, Channakhone Saenphimmachak2, Jireh Santibanez1, Hua Shen1, Yan Shen3, Sandhya Subramanian2, Paul E. Tabor1, Daniel Verduzco1, Lenee Waldron1, Jian Wang3, Jun Wang3, Qiaoyan Wang1, Gabrielle A. Williams1, Gane K.-S. Wong3, Zhijian Yao3, JingKun Zhang1, Xiuqing Zhang3, Guoping Zhao3, Jianling Zhou1, Yang Zhou2, David Nelson1, Hans Lehrach4, Richard Reinhardt4, Susan L. Naylor7, Huanming Yang3, Maynard Olson2, George Weinstock1 & Richard A. Gibbs1


  1. Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas 77030, USA
  2. Department of Medicine, Division of Medical Genetics, University of Washington Genome Center, Fluke Hall on Mason Rd, Box 352145 Seattle, Washington 98195, USA
  3. Beijing Genomics Institute, Chinese Academy of Sciences, Beijing 101300, China; James D. Watson Institute of Genome Sciences, Zhejiang University, Hangzhou 310008, China; Chinese National Human Genome Center at Shanghai (CHGC), Shanghai 201203, China; and Chinese National Human Genome Center, Beijing (CHGB), Beijing 100176, China
  4. Max Planck Institute for Molecular Genetics, 14195 Berlin-Dahlem, Germany
  5. Institute for Clinical Molecular Biology, Christian-Albrechts University, 24105 Kiel, Germany
  6. HUGO Gene Nomenclature Committee, The Galton Laboratory, Department of Biology, University College London, Wolfson House, 4 Stephenson Way, London NW1 2HE, UK
  7. University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, USA
  8. RZPD German Resource Center for Genome Research, 14059 Berlin, Germany.



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