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Table S1 Special features of human autosomes 1-22 and the sex chromosomes, including respective lengths, gene number and density

From: Human genetics and genomics a decade after the release of the draft sequence of the human genome

Chromosome

Chromosome length (bp)a

Number of known protein-coding genes per chromosomea

Gene density (genes/Mb)

Special features

Reference

1

247,249,719

2,189

8.85

Largest human chromosome. Rich in disease genes. Huge (~30 Mb) pericentromeric heterochromatic region at 1q12 spans ~5% of the length of the chromosome. Contains clusters of amylase genes (1p21), U1 snRNA genes (1q12-q22) and 5S RNA genes (1q) as well as multiple (~250) tRNA genes

1

2

242,951,149

1,328

5.47

Chromosome 2 (along with chromosome 4) exhibits the lowest recombination rate of all the autosomes. Contains at 2q13 an ancient telomere-telomere fusion junction at the position where two ape chromosomes once fused to give rise to this human chromosome

2

3

199,501,827

1,112

5.57

Lowest rate of segmental duplication of all human chromosomes. Contains several olfactory receptor gene clusters

3

4

191,273,063

797

4.17

Chromosome 4 (along with chromosome 2) exhibits the lowest recombination rate of all the autosomes. Highest percentage of LINE elements among all chromosomes

2

5

180,857,866

903

4.99

Rich in intra-chromosomal duplications. Contains interleukin and protocadherin gene clusters on 5q31

4

6

170,899,992

1,133

6.62

Harbours the major histocompatibility complex and the largest tRNA gene cluster in the human genome. Contains at least three imprinted genes

5

7

158,821,424

1,023

6.44

Contains the highest number of intra-chromosomal duplications among all human chromosomes. Contains at least six imprinted genes

6, 7

8

146,274,826

747

5.11

Contains a fast-evolving 15 Mb region on distal 8p with genes related to the innate immunity and nervous systems that appear to have evolved under positive selection

8

9

140,273,252

929

6.62

Structurally highly polymorphic. Contains the large (~14 Mb) block of pericentromeric heterochromatin. Contains large numbers of intra- and inter-chromosomal segmental duplications, as well as the largest interferon gene cluster in the human genome (9p22)

9

10

135,374,737

834

6.16

Region of extensive segmental duplication located on 10q11

10

11

134,452,384

1,385

10.30

Rich in both genes and disease genes. Contains 40% of all olfactory receptor gene clusters. Contains at least nine imprinted genes

11

12

132,349,534

1,080

8.16

Chromosome 12 has a unique history of evolutionary rearrangements that occurred in the rodent and primate lineages. Contains clusters of proline-rich protein and type II keratin genes at 12q13

12

13

114,142,980

361

3.16

Low gene density in general; contains a central 38 Mb segment where the gene density drops to only 3.1 genes per Mb. This acrocentric chromosome contains ribosomal RNA genes at 13p12 and at least one imprinted gene

13

14

106,368,585

669

6.29

This acrocentric chromosome contains ribosomal RNA genes at 14p12. Contains two 1 Mb regions of crucial importance to the immune system (T cell receptor and immunoglobulin heavy chain genes). Contains serpin gene cluster at 14q32.1 and several regions with imprinted genes

14

15

100,338,915

641

6.39

This acrocentric chromosome contains ribosomal RNA genes at 15p12. Two large clusters of clinically important segmental duplications are located in the proximal and distal regions of 15q. Contains a number of imprinted genes

15

16

88,827,254

925

10.41

Relatively high gene density. Contains a large number of segmental duplications

16

17

78,774,742

1,236

15.69

High gene density. Has undergone extensive intra-chromosomal rearrangement, many of which were probably mediated by segmental duplications. High G + C content of 45% (genome average: 41%)

17

18

76,117,153

295

3.88

Low gene density overall. Contains serpin gene cluster at 18q21.3

18

19

63,811,651

1,443

22.61

Highest gene density of all human chromosomes. One quarter of the genes on chromosome 19 belong to tandemly arranged gene families, encompassing 25% of the length of the chromosome. High G + C content of 48-49% (genome average: 41%). Repetitive sequences constitute 53-57% of the chromosome, as compared with a genome average of 40-44%. Contains clusters of olfactory receptor genes and cytochrome P450 genes, and multiple clusters of zinc finger genes, and at least two imprinted genes

19

20

62,435,964

617

9.88

Smallest metacentric autosome. Rich in both genes and disease genes. Contains type 2 cystatin gene cluster and at least two imprinted genes

20

21

46,944,323

284

6.05

Smallest human chromosome with fewer genes than any other autosome. This acrocentric chromosome contains ribosomal RNA genes at 21p12

21

22

49,691,432

519

10.44

This acrocentric chromosome contains ribosomal RNA genes at 22p12. Relatively high gene density. Clusters of segmental duplications at 22q11.2 are associated with several genomic disorders

22

X

154,913,754

891

5.75

Contains the pseudoautosomal regions, PAR1 and PAR2, at the tips of the short and long arms, respectively. These regions are essential for normal male meiosis and recombination. PAR1 undergoes an obligate crossover with the Y chromosome, thereby giving this region the highest recombination rate in the human genome, at least in males. One X chromosome is subject to inactivation in females. Highly enriched in interspersed repeats and has a low G + C content of 39% (genome average: 41%)

23

Y

57,772,954

80

1.38

Lowest gene density of all human chromosomes (contains only 82 known genes). Contains the male-specific region which is a mosaic of heterochromatin and euchromatic X-transposed, X-degenerate and ampliconic sequences that make up 30% of the euchromatin. PAR1 undergoes an obligate crossover with the X chromosome. The virtual absence of homologous recombination between the X and the Y chromosomes has led to a gradual degeneration of Y chromosomal genes over evolutionary time. However, the absence of recombination, at least within the extensive non-recombining region of the Y chromosome, has also favoured the evolutionary accumulation of transposable elements on the Y chromosome

24

  1. aChromosome lengths and the numbers of genes per chromosome are according to the Ensembl database, version 47.36. The chromosome length corresponds to the length of each chromosome that has been sequenced so far. The number of known protein-coding genes represents a conservative estimate of the likely total number, comprising genes which have been fully annotated. An earlier version of this table was published by Kehrer-Sawatzki and Cooper.25
  2. 1Gregory, S.G., Barlow, K.F., McLay, K.E., Kaul, R. et al. (2006), 'The DNA sequence and biological annotation of human chromosome 1', Nature Vol. 441, pp. 315-321.
  3. 2Hillier, L.W., Graves, T.A., Fulton, R.S., Fulton, L.A. et al. (2005), 'Generation and annotation of the DNA sequences of human chromosomes 2 and 4', Nature Vol. 434, pp. 724-731.
  4. 3Muzny, D.M., Scherer, S.E., Kaul, R., Wang, J. et al. (2006), 'The DNA sequence, annotation and analysis of human chromosome 3', Nature Vol. 440, pp. 1194-1198.
  5. 4Schmutz, J., Martin, J., Terry, A., Couronne, O. et al. (2004), 'The DNA sequence and comparative analysis of human chromosome 5', Nature Vol. 431, pp. 268-274.
  6. 5Mungall, A.J., Palmer, S.A., Sims, S.K., Edwards, C.A. et al. (2003), 'The DNA sequence and analysis of human chromosome 6', Nature Vol. 425, pp. 805-811.
  7. 6Hillier, L.W., Fulton, R.S., Fulton, L.A., Graves, T.A. et al. (2003), 'The DNA sequence of human chromosome 7', Nature Vol. 424, pp. 157-164.
  8. 7Scherer, S.W., Cheung, J., MacDonald, J.R., Osborne, L.R. et al. (2003), 'Human chromosome 7: DNA sequence and biology', Science Vol. 300, pp. 767-772.
  9. 8Nusbaum, C., Mikkelsen, T.S., Zody, M.C., Asakawa, S. et al. (2006), 'DNA sequence and analysis of human chromosome 8', Nature Vol. 439, pp. 331-335.
  10. 9Humphray, S.J., Oliver, K., Hunt, A.R., Plumb, R.W. et al. (2004), 'DNA sequence and analysis of human chromosome 9', Nature Vol. 429, pp. 369-374.
  11. 10Deloukas, P., Earthrowl, M.E., Grafham, D.V., Rubenfield, M. et al. (2004), 'The DNA sequence and comparative analysis of human chromosome 10', Nature Vol. 429, pp. 375-381.
  12. 11Taylor, T.D., Noguchi, H., Totoki, Y., Toyoda, A. et al. (2006), 'Human chromosome 11 DNA sequence and analysis including novel gene identification', Nature Vol. 440, pp. 497-500.
  13. 12Scherer, S.E., Muzny, D.M., Buhay, C.J., Chen, R. et al. (2006), 'The finished DNA sequence of human chromosome 12', Nature Vol. 440, pp. 346-351.
  14. 13Dunham, A., Matthews, L.H., Burton, J., Ashurst, J.L. et al. (2004), 'The DNA sequence and analysis of human chromosome 13', Nature Vol. 428, pp. 522-528.
  15. 14Heilig, R., Eckenberg, R., Petit, J.L., Fonknechten, N. et al. (2003), 'The DNA sequence and analysis of human chromosome 14', Nature Vol. 421, pp. 601-607.
  16. 15Zody, M.C., Garber, M., Sharpe, T., Young, S.K. et al. (2006), 'Analysis of the DNA sequence and duplication history of human chromosome 15', Nature Vol. 440, pp. 671-675.
  17. 16Martin, J., Han, C., Gordon, L.A., Terry, A. et al. (2004), 'The sequence and analysis of duplication-rich human chromosome 16', Nature Vol. 432, pp. 988-994.
  18. 17Zody, M.C., Garber, M., Adams, D.J., Sharpe, T. et al. (2006), 'DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage', Nature Vol. 440, pp. 1045-1049.
  19. 18Nusbaum, C., Zody, M.C., Borowsky, M.L., Kamal, M. et al. (2005), 'DNA sequence and analysis of human chromosome 18', Nature Vol. 437, pp. 551-555.
  20. 19Grimwood, J., Gordon, L.A., Olsen, A., Terry, A. et al. (2004), 'The DNA sequence and biology of human chromosome 19', Nature Vol. 428, pp. 529-535.
  21. 20Deloukas, P., Matthews, L.H., Ashurst, J., Burton, J. et al. (2001), 'The DNA sequence and comparative analysis of human chromosome 20', Nature Vol. 414, pp. 865-871.
  22. 21Hattori, M., Fujiyama, A., Taylor, T.D., Watanabe, H. et al. (2000), 'The DNA sequence of human chromosome 21', Nature Vol. 405, pp. 311-319.
  23. 22Dunham, I., Shimizu, N., Roe, B.A., Chissoe, S. et al. (1999), 'The DNA sequence of human chromosome 22', Nature Vol. 402, pp. 489-495.
  24. 23Ross, M.T., Grafham, D.V., Coffey, A.J., Scherer, S. et al. (2005), 'The DNA sequence of the human X chromosome', Nature Vol. 434, pp. 325-337.
  25. 24Skaletsky, H., Kuroda-Kawaguchi, T., Minx, P.J., Cordum, H.S. et al. (2003), 'The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes', Nature Vol. 423, pp. 825-837.
  26. 25Kehrer-Sawatzki, H. and Cooper, D.N. (2008), 'Sequencing the human genome: novel insights into its structure and function', in: Encyclopedia of Life Sciences (ELS), John Wiley & Sons Ltd, Chichester.
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Human Genomics

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