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. Gordon^4,2, Duncan Scott², Gary Xie^5,2, Wayne Huang², Uffe Hellsten², Mary Tran-Gyamf^4,2, Xinwei She⁶, Shyam Prabhakar³, Andrea Aerts², Michael Altherr^5,2, Eva Bajorek¹, Stacey Black¹, Elbert Branscomb^4,2, 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 Kobayashi^2,4, 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 Thayer^5,2, Hope Tice², Ming Tsai¹, Anna Ustaszewska², Nu Vo¹, Jeremy Wheeler¹, Kevin Wu¹, Joan Yang¹, Mark Dickson¹, Jan-Fang Cheng³, Evan E. Eichler⁶, Anne Olsen^4,2, Len A. Pennacchio^3,2, Daniel S. Rokhsar², Paul Richardson², Susan M. Lucas², Richard M. Myers¹, Edward M. Rubin^3,2

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