Chromosome 6

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This article is about a chromosome. For the novel of the same name, see Chromosome 6 (novel).
Chromosome 6
Human chromosome 6 pair after G-banding.
One is from mother, one is from father.
Chromosome 6 pair in human male karyogram.
Features
Length (bp)170,805,979 bp[1]
No. of genes3,000[2]
2,516[3]
TypeAutosome
Centromere positionSubmetacentric
Complete gene lists
CCDS?
HGNC?
UniProt?
NCBI?
External map viewers
EnsemblChromosome 6
EntrezChromosome 6
NCBIChromosome 6
UCSCChromosome 6
Full DNA sequences
RefSeqNC_000006 (FASTA)
GenBankCM000668 (FASTA)

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 170 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.

Identifying genes on each chromosome is an active area of genetic research. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies. In January 2017, two estimates differed by 16%, with one estimate giving 3,000[2] genes, and the other estimate giving 2,516[3] genes.

History

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

Genes

See also: Category:Genes on human chromosome 6

The human leukocyte antigen lies on chromosome 6 (exception: the gene for β2-microglobulin which is located on chromosome 15), and encodes cell-surface antigen-presenting proteins among other functions. The following are some of the genes and their corresponding Cytogenetic location on chromosome 6:

q-arm

  • AIM1: encoding protein Absent in melanoma 1 protein (6q21)
  • AIG1: encoding protein Androgen-induced protein 1 (6q24.2)
  • BCKDHB: branched-chain keto acid dehydrogenase E1, beta polypeptide (maple syrup urine disease) (6q14.1)
  • MYO6: myosin VI (6q14.1)
  • CNR1: cannabinoid 1 receptor (6q14-q15)[5]
  • HACE1: HECT domain and Ankyrin repeat containing, E3 ubiquitin protein ligase 1 (6q21)
  • TAAR1: trace amine associated receptor 1 (6q23.1)
  • TAAR2: trace amine associated receptor 2 (6q24)
  • EYA4: eyes absent homolog 4 (Drosophila)(6q23.2)
  • IFNGR: interferon-γ receptor gene (6q23-q24)
  • OPRM1: μ-opioid receptors (6q24-q25)
  • IGF2R: insulin-like growth factor 2 receptor (6q25.3)
  • PLG: plasminogen (6q26)
  • PARK2: Parkinson disease (autosomal recessive, juvenile) 2, parkin (6q26)
  • T: T brachyury transcription factor (more commonly known as the T gene) linked to Hepatocellular carcinoma and Chordoma (6q27)[6]
  • ESR1: Estrogen receptor 1 (6q25)

p-arm

  • APOM: encoding protein Apolipoprotein M (6p21.33)
  • MUT: methylmalonyl Coenzyme A mutase (6p12.3)
  • VEGF: vascular endothelial growth factor A (angiogenic growth factor) (6p21.1)
  • PKHD1: polycystic kidney and hepatic disease 1 (autosomal recessive) (6p21.2-p12)
  • COL11A2: collagen, type XI, alpha 2(6p21.3)
  • CYP21A2: cytochrome P450, family 21, subfamily A, polypeptide 2 (6p21.33)
  • HFE: hemochromatosis (6p21.3)
  • HLA-A, HLA-B, HLA-C: major histocompatibility complex (MHC), class I, A, B, and C loci. (6p21.3)
  • HLA-DQA1 and HLA-DQB1 form HLA-DQ heterodimer MHC class II, DQ: Celiac1, IDDM (6p21.3)
  • HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5 forms HLA-DR, heterodimer MHC class II, DR (6p21.3)
  • HLA-DPA1 and HLA-DPB1 forms HLA-DR, MHC class II, DP (6p21.3)
  • HLA-Cw*06:02: gene variation related to psoriasis (6p21.3)
  • TNXB: tenascin XB (6p21.3)
  • DSP: Desmoplakin gene linked to cardiomyopathy (6p24.3)

Diseases and disorders

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

Cytogenetic band

G-banding ideograms of human chromosome 6
G-banding ideogram of human chromosome 6 in resolution 850 bphs. Band length in this diagram is proportional to base-pair length. This type of ideogram is generally used in genome browsers (e.g. Ensembl, UCSC Genome Browser).
G-banding patterns of human chromosome 6 in three different resolutions (400,[7] 550[8] and 850[9]). Band length in this diagram is based on the ideograms from ISCN (2013).[10] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[11]
G-bands of human chromosome 6 in resolution 850 bphs[12]
Chr. Arm[13] Band[14] ISCN
start[15] 		ISCN
stop[15] 		Basepair
start 		Basepair
stop 		Stain[16] Density
6 p 25.3 0 118 1 2,300,000 gneg
6 p 25.2 118 207 2,300,001 4,200,000 gpos 25
6 p 25.1 207 355 4,200,001 7,100,000 gneg
6 p 24.3 355 548 7,100,001 10,600,000 gpos 50
6 p 24.2 548 592 10,600,001 11,600,000 gneg
6 p 24.1 592 740 11,600,001 13,400,000 gpos 25
6 p 23 740 844 13,400,001 15,200,000 gneg
6 p 22.3 844 1185 15,200,001 25,200,000 gpos 75
6 p 22.2 1185 1348 25,200,001 27,100,000 gneg
6 p 22.1 1348 1585 27,100,001 30,500,000 gpos 50
6 p 21.33 1585 1718 30,500,001 32,100,000 gneg
6 p 21.32 1718 1836 32,100,001 33,500,000 gpos 25
6 p 21.31 1836 2162 33,500,001 36,600,000 gneg
6 p 21.2 2162 2310 36,600,001 40,500,000 gpos 25
6 p 21.1 2310 2755 40,500,001 46,200,000 gneg
6 p 12.3 2755 3080 46,200,001 51,800,000 gpos 100
6 p 12.2 3080 3140 51,800,001 53,000,000 gneg
6 p 12.1 3140 3377 5,300,0001 57,200,000 gpos 100
6 p 11.2 3377 3421 57,200,001 58,500,000 gneg
6 p 11.1 3421 3554 58,500,001 59,800,000 acen
6 q 11.1 3554 3658 59,800,001 62,600,000 acen
6 q 11.2 3658 3732 62,600,001 62,700,000 gneg
6 q 12 3732 4147 62,700,001 69,200,000 gpos 100
6 q 13 4147 4324 69,200,001 75,200,000 gneg
6 q 14.1 4324 4621 75,200,001 83,200,000 gpos 50
6 q 14.2 4621 4709 83,200,001 84,200,000 gneg
6 q 14.3 4709 4917 84,200,001 87,300,000 gpos 50
6 q 15 4917 5228 87,300,001 92,500,000 gneg
6 q 16.1 5228 5613 92,500,001 98,900,000 gpos 100
6 q 16.2 5613 5687 98,900,001 100,000,000 gneg
6 q 16.3 5687 5983 10,000,0001 105,000,000 gpos 100
6 q 21 5983 6531 10,500,0001 114,200,000 gneg
6 q 22.1 6531 6753 114,200,001 117,900,000 gpos 75
6 q 22.2 6753 6872 117,900,001 118,100,000 gneg
6 q 22.31 6872 7168 118,100,001 125,800,000 gpos 100
6 q 22.32 7168 7345 125,800,001 126,800,000 gneg
6 q 22.33 7345 7642 126,800,001 130,000,000 gpos 75
6 q 23.1 7642 7923 13,000,0001 130,900,000 gneg
6 q 23.2 7923 8145 130,900,001 134,700,000 gpos 50
6 q 23.3 8145 8352 134,700,001 138,300,000 gneg
6 q 24.1 8352 8560 138,300,001 142,200,000 gpos 75
6 q 24.2 8560 8708 142,200,001 145,100,000 gneg
6 q 24.3 8708 8886 145,100,001 148,500,000 gpos 75
6 q 25.1 8886 9078 148,500,001 152,100,000 gneg
6 q 25.2 9078 9241 152,100,001 155,200,000 gpos 50
6 q 25.3 9241 9596 155,200,001 160,600,000 gneg
6 q 26 9596 9774 160,600,001 164,100,000 gpos 50
6 q 27 9774 10100 164,100,001 170,805,979 gneg

References

  1. ^ "Human Genome Assembly GRCh38.p10 - Genome Reference Consortium". National Center for Biotechnology Information. 2017-01-06. Retrieved 2017-03-04.
  2. ^ a b "Homo sapiens (human) Chromosome 6". NCBI Map Viewer. National Center for Biotechnology Information. Retrieved January 20, 2017.
  3. ^ a b "Homo sapiens: Chromosome summary: Chromosome 6:1-170805979". Wellcome Trust Sanger Institute. Vega Genome Browser 58. Retrieved January 20, 2017.
  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; Palmer; Sims; Edwards; Ashurst; Wilming; Jones; Horton; Hunt; Scott; Gilbert; Clamp; Bethel; Milne; Ainscough; Almeida; Ambrose; Andrews; Ashwell; Babbage; Bagguley; Bailey; Banerjee; Barker; Barlow; Bates; Beare; Beasley; Beasley; et al. (October 2003). "The DNA sequence and analysis of human chromosome 6". Nature. 425 (6960): 805–11. doi:10.1038/nature02055. PMID 14574404.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  5. ^ Matsuda LA, Lolait SJ, Brownstein MJ, Young AC, Bonner TI; Lolait; Brownstein; Young; Bonner (August 1990). "Structure of a cannabinoid receptor and functional expression of the cloned cDNA". Nature. 346 (6284): 561–4. Bibcode:1990Natur.346..561M. doi:10.1038/346561a0. PMID 2165569.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  6. ^ "T brachyury transcription factor". T - T brachyury transcription factor - Genetics Home Reference.
  7. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  8. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  9. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  10. ^ International Standing Committee on Human Cytogenetic Nomenclature (2013). ISCN 2013: An International System for Human Cytogenetic Nomenclature (2013). Karger Medical and Scientific Publishers. ISBN 978-3-318-02253-7.
  11. ^ Sethakulvichai, W.; Manitpornsut, S.; Wiboonrat, M.; Lilakiatsakun, W.; Assawamakin, A.; Tongsima, S. (2012). "Estimation of band level resolutions of human chromosome images" (PDF). In Computer Science and Software Engineering (JCSSE), 2012 International Joint Conference on: 276–282. doi:10.1109/JCSSE.2012.6261965.
  12. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  13. ^ "p": Short arm; "q": Long arm.
  14. ^ For cytogenetic banding nomenclature, see article locus.
  15. ^ a b 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.
  16. ^ 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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