Chromosome 2 Explained

Length Bp:	242,696,752 bp (CHM13)
Genes:	1,194 (CCDS)
Type:	Autosome
Centromere Position:	Submetacentric^[1] (93.9 Mbp^[2])
Chr:	2
Ensembl Id:	2
Entrez Id:	2
Ncbi Id:	2
Ucsc Id:	2
Refseq Id:	NC_000002
Genbank Id:	CM000664

Chromosome 2 is one of the twenty-three pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 2 is the second-largest human chromosome, spanning more than 242 million base pairs^[3] and representing almost eight percent of the total DNA in human cells.

Chromosome 2 contains the HOXD homeobox gene cluster.^[4]

Chromosomes

Humans have only twenty-three pairs of chromosomes, while all other extant members of Hominidae have twenty-four pairs.^[5] It is believed that Neanderthals and Denisovans had twenty-three pairs.^[5]

Human chromosome 2 is a result of an end-to-end fusion of two ancestral chromosomes.^{[6] [7] [8]} The evidence for this includes:

• The correspondence of chromosome 2 to two ape chromosomes. The closest human relative, the chimpanzee, has nearly identical DNA sequences to human chromosome 2, but they are found in two separate chromosomes. The same is true of the more distant gorilla and orangutan.^{[9] [10]}
• The presence of a vestigial centromere. Normally a chromosome has just one centromere, but in chromosome 2 there are remnants of a second centromere in the q21.3–q22.1 region.^[11]
• The presence of vestigial telomeres. These are normally found only at the ends of a chromosome, but in chromosome 2 there are additional telomere sequences in the q13 band, far from either end of the chromosome.^[12]

Genes

Number of genes

The following are some of the gene count estimates of human chromosome 2. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome vary. 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.^[13]

Estimated by	Protein-coding genes	Non-coding RNA genes	Pseudogenes	Source	Release date
	1,194	—	—	^[14]	2016-09-08
HGNC	1,196	450	931	^[15]	2017-05-12
	1,292	1,598	1,029	^[16]	2017-03-29
	1,274	—	—	^[17]	2018-02-28
	1,281	1,446	1,207	^[18] ^[19] ^[20]	2017-05-19

List of genes

The following is a partial list of genes on human chromosome 2. For complete list, see the link in the infobox on the right.

p-arm

Partial list of the genes located on p-arm (short arm) of human chromosome 2:

q-arm

Partial list of the genes located on q-arm (long arm) of human chromosome 2:

Related disorders and traits

The following diseases and traits are related to genes located on chromosome 2:

• 2p15-16.1 microdeletion syndrome
• Autism^[21]
• Alport syndrome
• Alström syndrome
• Amyotrophic lateral sclerosis
• Brachydactyly type D
• Cleft chin^[22]
• Congenital hypothyroidism
• Crigler–Najjar syndrome types I/II
• Dementia with Lewy bodies
• Ehlers–Danlos syndrome
• Ehlers–Danlos syndrome, classical type
• Ehlers–Danlos syndrome, vascular type
• Fibrodysplasia ossificans progressiva
• Gilbert's syndrome
• Harlequin-type ichthyosis
• Hemochromatosis
• Hemochromatosis type 4
• Hereditary nonpolyposis colorectal cancer
• Infantile-onset ascending hereditary spastic paralysis
• Juvenile primary lateral sclerosis
• Lactose intolerance
• Long-chain 3-hydroxyacyl-coenzyme A dehydrogenase deficiency
• Lowry-Wood syndrome^[23]
• Maturity-onset diabetes of the young type 6
• Mitochondrial trifunctional protein deficiency
• Nonsyndromic deafness
• Photic sneeze reflex^[24]
• Primary hyperoxaluria
• Primary pulmonary hypertension
• Sitosterolemia (knockout of either ABCG5 or ABCG8)
• Sensenbrenner syndrome
• Synesthesia
• Waardenburg syndrome

Cytogenetic band

G-bands of human chromosome 2 in resolution 850 bphs! Chr.! Arm^[25] ! Band^[26] ! ISCN
start^[27] ! ISCN
stop! Basepair
start! Basepair
stop! Stain^[28] ! Density

2	p	25.3	0	388			gneg
2	p	25.2	388	566			gpos	50
2	p	25.1	566	954			gneg
2	p	24.3	954	1193			gpos	75
2	p	24.2	1193	1312			gneg
2	p	24.1	1312	1565			gpos	75
2	p	23.3	1565	1789			gneg
2	p	23.2	1789	1908			gpos	25
2	p	23.1	1908	2027			gneg
2	p	22.3	2027	2296			gpos	75
2	p	22.2	2296	2415			gneg
2	p	22.1	2415	2609			gpos	50
2	p	21	2609	2966			gneg
2	p	16.3	2966	3220			gpos	100
2	p	16.2	3220	3294			gneg
2	p	16.1	3294	3548			gpos	100
2	p	15	3548	3757			gneg
2	p	14	3757	3935			gpos	50
2	p	13.3	3935	4114			gneg
2	p	13.2	4114	4248			gpos	50
2	p	13.1	4248	4353			gneg
2	p	12	4353	4860			gpos	100
2	p	11.2	4860	5307			gneg
2	p	11.1	5307	5545			acen
2	q	11.1	5545	5724			acen
2	q	11.2	5724	6022			gneg
2	q	12.1	6022	6261			gpos	50
2	q	12.2	6261	6395			gneg
2	q	12.3	6395	6559			gpos	25
2	q	13	6559	6812			gneg
2	q	14.1	6812	7036			gpos	50
2	q	14.2	7036	7334			gneg
2	q	14.3	7334	7602			gpos	50
2	q	21.1	7602	7826			gneg
2	q	21.2	7826	8050			gpos	25
2	q	21.3	8050	8169			gneg
2	q	22.1	8169	8437			gpos	100
2	q	22.2	8437	8497			gneg
2	q	22.3	8497	8646			gpos	100
2	q	23.1	8646	8735			gneg
2	q	23.2	8735	8795			gpos	25
2	q	23.3	8795	9078			gneg
2	q	24.1	9078	9361			gpos	75
2	q	24.2	9361	9585			gneg
2	q	24.3	9585	9928			gpos	75
2	q	31.1	9928	10435			gneg
2	q	31.2	10435	10599			gpos	50
2	q	31.3	10599	10733			gneg
2	q	32.1	10733	11091			gpos	75
2	q	32.2	11091	11225			gneg
2	q	32.3	11225	11538			gpos	75
2	q	33.1	11538	11925			gneg
2	q	33.2	11925	12060			gpos	50
2	q	33.3	12060	12283			gneg
2	q	34	12283	12641			gpos	100
2	q	35	12641	13014			gneg
2	q	36.1	13014	13237			gpos	75
2	q	36.2	13237	13297			gneg
2	q	36.3	13297	13595			gpos	100
2	q	37.1	13595	13893			gneg
2	q	37.2	13893	13998			gpos	50
2	q	37.3	13998	14400			gneg

External links

• Web site: National Institutes of Health . Chromosome 2 . Genetics Home Reference . 2017-05-06 . 9 March 2016 . https://web.archive.org/web/20160309183348/https://ghr.nlm.nih.gov/chromosome=2 . dead .
• Web site: Chromosome 2. Human Genome Project Information Archive 1990–2003. 2017-05-06.

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. Hillier . Ladeana Hillier . Generation and annotation of the DNAD sequences of human chromosomes 2 and 4 . Nature . 2005 . 724–31 . 434 . 7034 . 15815621 . 10.1038/nature03466 . Graves . TA . Fulton . RS . Fulton . LA . Pepin . KH . Minx . P . Wagner-Mcpherson . C . Layman . D . Wylie . K . Sekhon . 1. 2005Natur.434..724H . Becker . Fewell . Delehaunty . Miner . Nash . Kremitzki . Oddy . Du . Sun . Bradshaw-Cordum . Ali . Carter . Cordes . Harris . Isak . Van Brunt . Nguyen . Du . Courtney . Kalicki . free .
4. http://vega.sanger.ac.uk/Homo_sapiens/Location/View?db=core;g=OTTHUMG00000154173;r=2:176880740-177056400;region=AC009336.13.1.175667;t=OTTHUMT00000359252 Vega Homo sapiens genome browser: HoxD cluster on Chromosome 2
5. Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S . A high-coverage genome sequence from an archaic Denisovan individual . Science . 338 . 6104 . 222–6 . October 2012 . 22936568 . 3617501 . 10.1126/science.1224344 . 6. 2012Sci...338..222M .
6. http://www.evolutionpages.com/chromosome_2.htm It has been hypothesized that Human Chromosome 2 is a fusion of two ancestral chromosomes
7. Web site: Chromosome 2 in the Great Apes – YouTube. 8 November 2007 . https://ghostarchive.org/varchive/youtube/20211221/3sKScsbhOd4 . 2021-12-21 . live. 2020-07-24. YouTube.
8. Web site: Chromosome 2--Re-Upload – YouTube. 11 April 2018 . https://ghostarchive.org/varchive/youtube/20211221/mcdQ4_RkSnk . 2021-12-21 . live. 2020-07-24. YouTube.
9. Yunis and Prakash . The origin of man: a chromosomal pictorial legacy . Science . 1982 . 1525–30 . 215 . 7063861 . 10.1126/science.7063861 . Prakash . O . 4539. 1982Sci...215.1525Y .
10. http://www.gate.net/~rwms/hum_ape_chrom.html Human and Ape Chromosomes
11. Avarello . Evidence for an ancestral alphoid domain on the long arm of human chromosome 2 . Human Genetics . 1992 . 247–9 . 89 . 1587535 . 10.1007/BF00217134 . Pedicini . A . Caiulo . A . Zuffardi . O . Fraccaro . M . 2 . 1441285 . 1.
12. Ijdo, Jacob W. . Origin of human chromosome 2: an ancestral telomere-telomere fusion . Proc. Natl. Acad. Sci. U.S.A. . 1991 . 9051–5 . 88 . 1924367 . 10.1073/pnas.88.20.9051 . Baldini . A . Ward . DC . Reeders . ST . Wells . RA . 20 . 52649 . 1. 1991PNAS...88.9051I . free .
13. 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 .
14. Web site: Search results – 2[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.
15. Web site: Statistics & Downloads for chromosome 2 . HUGO Gene Nomenclature Committee . 2017-05-12 . 2017-05-19 . 29 June 2017 . https://web.archive.org/web/20170629075313/http://www.genenames.org/cgi-bin/statistics?c=2 . dead .
16. Web site: Chromosome 2: Chromosome summary – Homo sapiens . Ensembl Release 88 . 2017-03-29 . 2017-05-19.
17. Web site: Human chromosome 2: entries, gene names and cross-references to MIM . UniProt . 2018-02-28 . 2018-03-16.
18. Web site: Search results – 2[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) – Gene . NCBI . 2017-05-19 . 2017-05-20.
19. Web site: Search results – 2[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.
20. Web site: Search results – 2[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) – Gene . NCBI . 2017-05-19 . 2017-05-20.
21. Web site: Swaminathan. Nikhil. Largest Ever Autism Study Identifies Two Genetic Culprits. Scientific American. 25 January 2018.
22. Web site: Cleft Chin AncestryDNA® Traits Learning Hub. 2022-02-22. ancestry.com. en.
23. Lowry-Wood syndrome: Further evidence of association with RNU4ATAC, and correlation between genotype and phenotype . 30368667 . 2018 . Shelihan . I. . Ehresmann . S. . Magnani . C. . Forzano . F. . Baldo . C. . Brunetti-Pierri . N. . Campeau . P. M. . Human Genetics . 137 . 11–12 . 905–909 . 10.1007/s00439-018-1950-8 . 53079178 .
24. Web site: Photic Sneeze Reflex AncestryDNA® Traits Learning Hub. 2022-02-22. ancestry.com. en.
25. "p": Short arm; "q": Long arm.
26. For cytogenetic banding nomenclature, see article locus.
27. 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.
28. 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.