Homo sapiens

This version represents the May 2004 human reference sequence of NCBI Build 35 for chromosome 5 and the resultant gene catalog.

The final version of the tiling path contains 1,763 large-insert clones, 96% of which are BACs that span the euchromatin regions of both the p and q arms. The chromosome is represented with only 4 gaps remaining, all in the long arm and the clone map is estimated to cover 99.9% of the euchromatic sequence None of these remaining physical gaps could be cloned in current vector systems or are part of large duplications.

Sequence was generated using a clone-by-clone shotgun sequencing strategy followed by finishing using a custom primer approach. Recalcitrant areas or hard gaps were closed with additional sequence data derived from transposon sequencing, small insert shatter libraries or PCR.

On the basis of internal and external quality checks, we estimate the accuracy of our finished sequence to exceed 99.99%7. In total, we finished 177,702,766 base pairs and estimate the total size of the chromosome, including the four clone gaps and the recalcitrant centromeric and subtelomeric regions, to be 180.8 Mb. The finished sequence is estimated to cover 99.9% of the euchromatic sequence and to have captured all known genes that were previously mapped to chromosome 5.

Gene Catalog. We placed gene model transcripts on the chromosome 5 genomic sequence and manually reviewed a total of 923 protein-coding regions as gene loci. These loci contain 1,598 full-length (or nearly full-length) transcripts, including partial evidence for additional splice variants.


Jeremy Schmutz1, Joel Martin2, Astrid Terry2, Olivier Couronne3, Jane Grimwood1, Steve Lowry2, Laurie A. Gordon4,2, Duncan Scott2, Gary Xie5,2, Wayne Huang2, Uffe Hellsten2, Mary Tran-Gyamf4,2, Xinwei She6, Shyam Prabhakar3, Andrea Aerts2, Michael Altherr5,2, Eva Bajorek1, Stacey Black1, Elbert Branscomb4,2, Chenier Caoile1, Jean F. Challacombe5, Yee Man Chan1, Mirian Denys1, Chris Detter2, Julio Escobar1, Dave Flowers1, Dea Fotopulos1, Tijana Glavina2, Maria Gomez1, Eidelyn Gonzales1, David Goodstein2, Igor Grigoriev2, Matthew Groza4, Nancy Hammon2, Trevor Hawkins2, Lauren Haydu1, Sanjay Israni2, Jamie Jett2, Kristen Kadner2, Heather Kimball2, Arthur Kobayashi2,4, Frederick Lopez1, Yunian Lou2, Diego Martinez2, Catherine Medina1, Jenna Morgan2, Richard Nandkeshwar4, James P. Noonan7, Sam Pitluck2, Martin Pollard2, Paul Predki2, James Priest3, Lucia Ramirez1, Sam Rash2, James Retterer1, Alex Rodriguez1, Stephanie Rogers1, Asaf Salamov2, Angelica Salazar1, Nina Thayer5,2, Hope Tice2, Ming Tsai1, Anna Ustaszewska2, Nu Vo1, Jeremy Wheeler1, Kevin Wu1, Joan Yang1, Mark Dickson1, Jan-Fang Cheng3, Evan E. Eichler6, Anne Olsen4,2, Len A. Pennacchio3,2, Daniel S. Rokhsar2, Paul Richardson2, Susan M. Lucas2, Richard M. Myers1, Edward M. Rubin3,2

  1. Stanford Human Genome Center, Department of Genetics, Stanford University School of Medicine, 975 California Ave, Palo Alto, California 94304, USA

  2. DOE’s Joint Genome Institute, 2800 Mitchell Avenue, Walnut Creek, California 94598, USA

  3. Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720, USA

  4. Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94550, USA

  5. Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA

  6. Department of Genetics, Center for Computational Genomics and Center for Human Genetics, Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, Ohio 44106, USA

  7. Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA

The DNA sequence and comparative analysis of human chromosome 5. Schmutz J, Martin J, Terry A, Couronne O, Grimwood J, Lowry S, Gordon LA, Scott D, Xie G, Huang W, Hellsten U, Tran-Gyamfi M, She X, Prabhakar S, Aerts A, Altherr M, Bajorek E, Black S, Branscomb E, Caoile C, Challacombe JF, Chan YM, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Lopez F, Lou Y, Martinez D, Medina C, Morgan J, Nandkeshwar R, Noonan JP, Pitluck S, Pollard M, Predki P, Priest J, Ramirez L, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wheeler J, Wu K, Yang J, Dickson M, Cheng JF, Eichler EE, Olsen A, Pennacchio LA, Rokhsar DS, Richardson P, Lucas SM, Myers RM, Rubin EM. Nature 431, 268-274 (16 September 2004) | [doi:10.1038/nature02919]
This work was performed under the auspices of the US Department of Energy's Office of Science, Biological and Environmental Research Program and the by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098 and Los Alamos National Laboratory under contract No. W-7405-ENG-36.