Chromosome 6 Explained

Length Bp:172,126,628 bp
(CHM13)
Genes:996 (CCDS)
Type:Autosome
Centromere Position:Submetacentric[1]
(59.8 Mbp[2])
Chr:6
Ensembl Id:6
Entrez Id:6
Ncbi Id:6
Ucsc Id:6
Refseq Id:NC_000006
Genbank Id:CM000668

Chromosome 6 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 6 spans more than 172 million base pairs (the building material of DNA) and represents between 5.5 and 6% of the total DNA in cells. It contains the major histocompatibility complex, which contains over 100 genes related to the immune response, and plays a vital role in organ transplantation.

The evolution of human centromere 6

The centromere of chromosome 6 illustrates an interesting example of centromere evolution. It was known that in a Catarrhini ancestor the chromosome 6 centromere was situated near position 26 Mb of the modern human chromosome. In Macaca mulatta, this old centromere went defunct and repositioned to a different chromosomal location. In case of humans, the old centromere went defunct and a more recent form emerged near the modern position of human cen6 (size of 60 Mb). Such cases are known as Evolutionary New Centromeres (ENC). This assembly phenomenon of the human chromosome 6 gives researchers an opportunity to investigate the origin of the ENC on chromosome 6. [3]

Genes

The human leukocyte antigen lies on chromosome 6, with the exception of the gene for β2-microglobulin (which is located on chromosome 15), and encodes cell-surface antigen-presenting proteins among other functions.

Number of genes

In 2003, the entirety of chromosome 6 was manually annotated for proteins, resulting in the identification of 1,557 genes, and 633 pseudogenes.[4]

The following are some of the newer gene count estimates. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies (for technical details, see gene prediction). Among various projects, the collaborative consensus coding sequence project (CCDS) takes an extremely conservative strategy. So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes.[5]

Estimated byProtein-coding genesNon-coding RNA genesPseudogenesSourceRelease date
996 — —[6] 2016-09-08
HGNC1,007 422 736[7] 2017-05-12
1,038 985 800[8] 2017-03-29
1,111 — —[9] 2018-02-28
1,053 1,188 911[10] [11] [12] 2017-05-19

Gene list

The following is a partial list of genes on human chromosome 6. For complete list, see the link in the infobox on the right.

p-arm

The following are some of the genes located on p-arm (short arm) of human chromosome 6:

q-arm

The following are some of the genes located on q-arm (long arm) of human chromosome 6:

Diseases and disorders

The following diseases are some of those related to genes on chromosome 6:

Cytogenetic band

G-bands of human chromosome 6 in resolution 850 bphs[13] ! Chr. ! Arm[14] ! Band[15] ! ISCN
start[16] ! ISCN
stop! Basepair
start ! Basepair
stop ! Stain[17] ! Density
6 p 25.3 0 118 gneg
6 p 25.2 118 207 gpos 25
6 p 25.1 207 355 gneg
6 p 24.3 355 548 gpos 50
6 p 24.2 548 592 gneg
6 p 24.1 592 740 gpos 25
6 p 23 740 844 gneg
6 p 22.3 844 1185 gpos 75
6 p 22.2 1185 1348 gneg
6 p 22.1 1348 1585 gpos 50
6 p 21.33 1585 1718 gneg
6 p 21.32 1718 1836 gpos 25
6 p 21.31 1836 2162 gneg
6 p 21.2 2162 2310 gpos 25
6 p 21.1 2310 2755 gneg
6 p 12.3 2755 3080 gpos 100
6 p 12.2 3080 3140 gneg
6 p 12.1 3140 3377 1 gpos 100
6 p 11.2 3377 3421 gneg
6 p 11.1 3421 3554 acen
6 q 11.1 3554 3658 acen
6 q 11.2 3658 3732 gneg
6 q 12 3732 4147 gpos 100
6 q 13 4147 4324 gneg
6 q 14.1 4324 4621 gpos 50
6 q 14.2 4621 4709 gneg
6 q 14.3 4709 4917 gpos 50
6 q 15 4917 5228 gneg
6 q 16.1 5228 5613 gpos 100
6 q 16.2 5613 5687 gneg
6 q 16.3 5687 5983 1 gpos 100
6 q 21 5983 6531 1 gneg
6 q 22.1 6531 6753 gpos 75
6 q 22.2 6753 6872 gneg
6 q 22.31 6872 7168 gpos 100
6 q 22.32 7168 7345 gneg
6 q 22.33 7345 7642 gpos 75
6 q 23.1 7642 7923 1 gneg
6 q 23.2 7923 8145 gpos 50
6 q 23.3 8145 8352 gneg
6 q 24.1 8352 8560 gpos 75
6 q 24.2 8560 8708 gneg
6 q 24.3 8708 8886 gpos 75
6 q 25.1 8886 9078 gneg
6 q 25.2 9078 9241 gpos 50
6 q 25.3 9241 9596 gneg
6 q 26 9596 9774 gpos 50
6 q 27 9774 10100 gneg

References

Notes

Further reading

External links

Notes and References

  1. Book: Tom Strachan. Andrew Read. Human Molecular Genetics. 2 April 2010. Garland Science. 978-1-136-84407-2. 45.
  2. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  3. Altemose . Nicolas . Logsdon . Glennis A. . Bzikadze . Andrey V. . Sidhwani . Pragya . Langley . Sasha A. . Caldas . Gina V. . Hoyt . Savannah J. . Uralsky . Lev . Ryabov . Fedor D. . Shew . Colin J. . Sauria . Michael E. G. . Borchers . Matthew . Gershman . Ariel . Mikheenko . Alla . Shepelev . Valery A. . April 2022 . Complete genomic and epigenetic maps of human centromeres . Science . en . 376 . 6588 . eabl4178 . 10.1126/science.abl4178 . 0036-8075 . 9233505 . 35357911.
  4. Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, Jones MC, Horton R, Hunt SE, Scott CE, Gilbert JG, Clamp ME, Bethel G, Milne S, Ainscough R, Almeida JP, Ambrose KD, Andrews TD, Ashwell RI, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beare DM, Beasley H, Beasley O, Bird CP, Blakey S, Bray-Allen S, Brook J, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Clark SY, Clark G, Clee CM, Clegg S, Cobley V, Collier RE, Collins JE, Colman LK, Corby NR, Coville GJ, Culley KM, Dhami P, Davies J, Dunn M, Earthrowl ME, Ellington AE, Evans KA, Faulkner L, Francis MD, Frankish A, Frankland J, French L, Garner P, Garnett J, Ghori MJ, Gilby LM, Gillson CJ, Glithero RJ, Grafham DV, Grant M, Gribble S, Griffiths C, Griffiths M, Hall R, Halls KS, Hammond S, Harley JL, Hart EA, Heath PD, Heathcott R, Holmes SJ, Howden PJ, Howe KL, Howell GR, Huckle E, Humphray SJ, Humphries MD, Hunt AR, Johnson CM, Joy AA, Kay M, Keenan SJ, Kimberley AM, King A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd CR, Lloyd DM, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, Maslen GL, Matthews L, McCann OT, McLaren SJ, McLay K, McMurray A, Moore MJ, Mullikin JC, Niblett D, Nickerson T, Novik KL, Oliver K, Overton-Larty EK, Parker A, Patel R, Pearce AV, Peck AI, Phillimore B, Phillips S, Plumb RW, Porter KM, Ramsey Y, Ranby SA, Rice CM, Ross MT, Searle SM, Sehra HK, Sheridan E, Skuce CD, Smith S, Smith M, Spraggon L, Squares SL, Steward CA, Sycamore N, Tamlyn-Hall G, Tester J, Theaker AJ, Thomas DW, Thorpe A, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, White SS, Whitehead SL, Whittaker H, Wild A, Willey DJ, Wilmer TE, Wood JM, Wray PW, Wyatt JC, Young L, Younger RM, Bentley DR, Coulson A, Durbin R, Hubbard T, Sulston JE, Dunham I, Rogers J, Beck S. 6 . The DNA sequence and analysis of human chromosome 6 . Nature . 425 . 6960 . 805–11 . October 2003 . 14574404 . 10.1038/nature02055 . free . 2003Natur.425..805M .
  5. Pertea M, Salzberg SL . Between a chicken and a grape: estimating the number of human genes. . Genome Biol . 2010 . 11 . 5 . 206 . 20441615 . 10.1186/gb-2010-11-5-206 . 2898077 . free .
  6. Web site: Search results - 6[CHR] AND "Homo sapiens"[Organism] AND ("has ccds"[Properties] AND alive[prop]) - Gene . NCBI . CCDS Release 20 for Homo sapiens . 2016-09-08 . 2017-05-28.
  7. Web site: Statistics & Downloads for chromosome 6 . HUGO Gene Nomenclature Committee . 2017-05-12 . 2017-05-19 . 2017-08-18 . https://web.archive.org/web/20170818175240/http://www.genenames.org/cgi-bin/statistics?c=6 . dead .
  8. Web site: Chromosome 6: Chromosome summary - Homo sapiens . Ensembl Release 88 . 2017-03-29 . 2017-05-19.
  9. Web site: Human chromosome 6: entries, gene names and cross-references to MIM . UniProt . 2018-02-28 . 2018-03-16.
  10. Web site: Search results - 6[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene . NCBI . 2017-05-19 . 2017-05-20.
  11. Web site: Search results - 6[CHR] AND "Homo sapiens"[Organism] AND (("genetype miscrna"[Properties] OR "genetype ncrna"[Properties] OR "genetype rrna"[Properties] OR "genetype trna"[Properties] OR "genetype scrna"[Properties] OR "genetype snrna"[Properties] OR "genetype snorna"[Properties]) NOT "genetype protein coding"[Properties] AND alive[prop]) - Gene . NCBI . 2017-05-19 . 2017-05-20.
  12. Web site: Search results - 6[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene . NCBI . 2017-05-19 . 2017-05-20.
  13. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  14. "p": Short arm; "q": Long arm.
  15. For cytogenetic banding nomenclature, see article locus.
  16. These values (ISCN start/stop) are based on the length of bands/ideograms from the ISCN book, An International System for Human Cytogenetic Nomenclature (2013). Arbitrary unit.
  17. gpos: Region which is positively stained by G banding, generally AT-rich and gene poor; gneg: Region which is negatively stained by G banding, generally CG-rich and gene rich; acen Centromere. var: Variable region; stalk: Stalk.

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