Homo sapiens

This version represents the May 2004 human reference sequence of NCBI Build 35 for chromosome 16 and the resultant gene catalog.

The final version of the tiling path contains 618 bacterial artificial chromosomes (BACs), 79 cosmids, seven fosmids, five phage-derived artificial chromosomes (PACs), three yeast artificial chromosome (YAC) subclones, two P1 phages, two phage vectors and five genomic polymerase chain reaction (PCR) fragment that span the euchromatin regions of both the p and q arms. The chromosome is represented with only 4 gaps remaining, with two in each of the chromosome arms. The clone map is estimated to cover 99.9% of the euchromatic sequence.

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. One of the gaps is found in the highly duplicated pericentromeric region in the p arm, while two of the remaining non-pericentromeric gaps are resistant to stable cloning with conventional vectors, and efforts are ongoing to close the estimated ,25 kilobases (kb) of missing sequence using alternative vector. The final gap is found near the telomere of the q arm in a region of subtelomeric repeats distal to the last identifiable cosmid subclone (AC137934) of a 16q telomere half-YAC.

On the basis of internal and external quality checks, we estimate the accuracy of our finished sequence to exceed 99.99%. In total, we finished 78,884,754 base pairs and estimate the total size of the chromosome, including the four clone gaps and the recalcitrant centromere and its adjacent heterochromatic portion of the q. arm, sized together at 9.8 megabases (Mb) the total size of the chromosome is estimated at 88.7Mb.

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 16.

Gene Catalog.

We placed gene model transcripts on the chromosome 16 genomic sequence and manually reviewed a total of 880 protein-coding regions as gene loci. These loci contain 1,670 full-length (or nearly full-length) transcripts, including partial (EST) evidence for 208 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 sequence and analysis of duplication-rich human chromosome 16. Martin J, Han C, Gordon LA, Terry A, Prabhakar S, She X, Xie G, Hellsten U, Chan YM, Altherr M, Couronne O, Aerts A, Bajorek E, Black S, Blumer H, Branscomb E, Brown NC, Bruno WJ, Buckingham JM, Callen DF, Campbell CS, Campbell ML, Campbell EW, Caoile C, Challacombe JF, Chasteen LA, Chertkov O, Chi HC, Christensen M, Clark LM, Cohn JD, Denys M, Detter JC, Dickson M, Dimitrijevic-Bussod M, Escobar J, Fawcett JJ, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Goodwin LA, Grady DL, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Hildebrand CE, Huang W, Israni S, Jett J, Jewett PB, Kadner K, Kimball H, Kobayashi A, Krawczyk MC, Leyba T, Longmire JL, Lopez F, Lou Y, Lowry S, Ludeman T, Manohar CF, Mark GA, McMurray KL, Meincke LJ, Morgan J, Moyzis RK, Mundt MO, Munk AC, Nandkeshwar RD, Pitluck S, Pollard M, Predki P, Parson-Quintana B, Ramirez L, Rash S, Retterer J, Ricke DO, Robinson DL, Rodriguez A, Salamov A, Saunders EH, Scott D, Shough T, Stallings RL, Stalvey M, Sutherland RD, Tapia R, Tesmer JG, Thayer N, Thompson LS, Tice H, Torney DC, Tran-Gyamfi M, Tsai M, Ulanovsky LE, Ustaszewska A, Vo N, White PS, Williams AL, Wills PL, Wu JR, Wu K, Yang J, Dejong P, Bruce D, Doggett NA, Deaven L, Schmutz J, Grimwood J, Richardson P, Rokhsar DS, Eichler EE, Gilna P, Lucas SM, Myers RM, Rubin EM, Pennacchio LA. Nature 432, 988-994 (23 December 2004) [doi:10.1038/nature03187]
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.