Chromosome 2

Short description: Human chromosome

Chromosome 2

Human chromosome 2 pair after G banding. One is from mother, one is from father.

Chromosome 2 pair
in human male karyogram.

Features
Length (bp)| 242,696,752 bp
(CHM13)
No. of genes| 1,194 (CCDS)[1]
Type| Autosome
Centromere position| Submetacentric[2]
(93.9 Mbp[3])
Complete gene lists
CCDS| Gene list
HGNC| Gene list
UniProt| Gene list
NCBI| Gene list
External map viewers
Ensembl| Chromosome 2
Entrez| Chromosome 2
NCBI| Chromosome 2
UCSC| Chromosome 2
Full DNA sequences
RefSeq| NC_000002 (FASTA)
GenBank| CM000664 (FASTA)

Fusion of ancestral chromosomes left distinctive remnants of telomeres, and a vestigial centromere

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[4] and representing almost eight percent of the total DNA in human cells.

Chromosome 2 contains the HOXD homeobox gene cluster.[5]

## Contents

* 1 Chromosomes
* 2 Genes
* 2.1 Number of genes
* 2.2 List of genes
* 2.2.1 p-arm
* 2.2.2 q-arm
* 3 Related disorders and traits
* 4 Cytogenetic band
* 5 References
* 6 External links

## Chromosomes

Further information: Biology:Chimpanzee genome project

Humans have only twenty-three pairs of chromosomes, while all other extant members of Hominidae have twenty-four pairs.[6] It is believed that Neanderthals and Denisovans had twenty-three pairs.[6]

Human chromosome 2 is a result of an end-to-end fusion of two ancestral chromosomes.[7][8][9] 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.[10][11]
* 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.[12]
* 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.[13]

“  | We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2.  | ”

|
|

— Jacob W. Ijdo[13]

## 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.[14]

Estimated by  | Protein-coding genes  | Non-coding RNA genes | Pseudogenes | Source  | Release date

|
|
|
|
|

CCDS | 1,194 | — | —  | [1] | 2016-09-08
HGNC | 1,196 | 450 | 931  | [15] | 2017-05-12
Ensembl | 1,292 | 1,598 | 1,029  | [16] | 2017-03-29
UniProt | 1,274 | — | —  | [17] | 2018-02-28
NCBI | 1,281 | 1,446 | 1,207  | [18][19][20] | 2017-05-19

### List of genes

See also: Category:Genes on human chromosome 2

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 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-banding ideograms of human chromosome 2

G-banding ideogram of human chromosome 2 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 2 in three different resolutions (400,[25] 550[26] and 850[3]). Band length in this diagram is based on the ideograms from ISCN (2013).[27] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[28]

G-bands of human chromosome 2 in resolution 850 bphs[3] Chr.  | Arm[29] | Band[30] | ISCN
start[31] | ISCN
stop[31] | Basepair
start  | Basepair
stop  | Stain[32] | Density

|
|
|
|
|
|
|
|

2 | p  | 25.3 | 0 | 388 | 1 | 4,400,000 | gneg |
2 | p  | 25.2 | 388 | 566 | 4,400,001 | 6,900,000 | gpos | 50
2 | p  | 25.1 | 566 | 954 | 6,900,001 | 12,000,000 | gneg |
2 | p  | 24.3 | 954 | 1193 | 12,000,001 | 16,500,000 | gpos | 75
2 | p  | 24.2 | 1193 | 1312 | 16,500,001 | 19,000,000 | gneg |
2 | p  | 24.1 | 1312 | 1565 | 19,000,001 | 23,800,000 | gpos | 75
2 | p  | 23.3 | 1565 | 1789 | 23,800,001 | 27,700,000 | gneg |
2 | p  | 23.2 | 1789 | 1908 | 27,700,001 | 29,800,000 | gpos | 25
2 | p  | 23.1 | 1908 | 2027 | 29,800,001 | 31,800,000 | gneg |
2 | p  | 22.3 | 2027 | 2296 | 31,800,001 | 36,300,000 | gpos | 75
2 | p  | 22.2 | 2296 | 2415 | 36,300,001 | 38,300,000 | gneg |
2 | p  | 22.1 | 2415 | 2609 | 38,300,001 | 41,500,000 | gpos | 50
2 | p  | 21 | 2609 | 2966 | 41,500,001 | 47,500,000 | gneg |
2 | p  | 16.3 | 2966 | 3220 | 47,500,001 | 52,600,000 | gpos | 100
2 | p  | 16.2 | 3220 | 3294 | 52,600,001 | 54,700,000 | gneg |
2 | p  | 16.1 | 3294 | 3548 | 54,700,001 | 61,000,000 | gpos | 100
2 | p  | 15 | 3548 | 3757 | 61,000,001 | 63,900,000 | gneg |
2 | p  | 14 | 3757 | 3935 | 63,900,001 | 68,400,000 | gpos | 50
2 | p  | 13.3 | 3935 | 4114 | 68,400,001 | 71,300,000 | gneg |
2 | p  | 13.2 | 4114 | 4248 | 71,300,001 | 73,300,000 | gpos | 50
2 | p  | 13.1 | 4248 | 4353 | 73,300,001 | 74,800,000 | gneg |
2 | p  | 12 | 4353 | 4860 | 74,800,001 | 83,100,000 | gpos | 100
2 | p  | 11.2 | 4860 | 5307 | 83,100,001 | 91,800,000 | gneg |
2 | p  | 11.1 | 5307 | 5545 | 91,800,001 | 93,900,000 | acen |
2 | q  | 11.1 | 5545 | 5724 | 93,900,001 | 96,000,000 | acen |
2 | q  | 11.2 | 5724 | 6022 | 96,000,001 | 102,100,000 | gneg |
2 | q  | 12.1 | 6022 | 6261 | 102,100,001 | 105,300,000 | gpos | 50
2 | q  | 12.2 | 6261 | 6395 | 105,300,001 | 106,700,000 | gneg |
2 | q  | 12.3 | 6395 | 6559 | 106,700,001 | 108,700,000 | gpos | 25
2 | q  | 13 | 6559 | 6812 | 108,700,001 | 112,200,000 | gneg |
2 | q  | 14.1 | 6812 | 7036 | 112,200,001 | 118,100,000 | gpos | 50
2 | q  | 14.2 | 7036 | 7334 | 118,100,001 | 121,600,000 | gneg |
2 | q  | 14.3 | 7334 | 7602 | 121,600,001 | 129,100,000 | gpos | 50
2 | q  | 21.1 | 7602 | 7826 | 129,100,001 | 131,700,000 | gneg |
2 | q  | 21.2 | 7826 | 8050 | 131,700,001 | 134,300,000 | gpos | 25
2 | q  | 21.3 | 8050 | 8169 | 134,300,001 | 136,100,000 | gneg |
2 | q  | 22.1 | 8169 | 8437 | 136,100,001 | 141,500,000 | gpos | 100
2 | q  | 22.2 | 8437 | 8497 | 141,500,001 | 143,400,000 | gneg |
2 | q  | 22.3 | 8497 | 8646 | 143,400,001 | 147,900,000 | gpos | 100
2 | q  | 23.1 | 8646 | 8735 | 147,900,001 | 149,000,000 | gneg |
2 | q  | 23.2 | 8735 | 8795 | 149,000,001 | 149,600,000 | gpos | 25
2 | q  | 23.3 | 8795 | 9078 | 149,600,001 | 154,000,000 | gneg |
2 | q  | 24.1 | 9078 | 9361 | 154,000,001 | 158,900,000 | gpos | 75
2 | q  | 24.2 | 9361 | 9585 | 158,900,001 | 162,900,000 | gneg |
2 | q  | 24.3 | 9585 | 9928 | 162,900,001 | 168,900,000 | gpos | 75
2 | q  | 31.1 | 9928 | 10435 | 168,900,001 | 177,100,000 | gneg |
2 | q  | 31.2 | 10435 | 10599 | 177,100,001 | 179,700,000 | gpos | 50
2 | q  | 31.3 | 10599 | 10733 | 179,700,001 | 182,100,000 | gneg |
2 | q  | 32.1 | 10733 | 11091 | 182,100,001 | 188,500,000 | gpos | 75
2 | q  | 32.2 | 11091 | 11225 | 188,500,001 | 191,100,000 | gneg |
2 | q  | 32.3 | 11225 | 11538 | 191,100,001 | 196,600,000 | gpos | 75
2 | q  | 33.1 | 11538 | 11925 | 196,600,001 | 202,500,000 | gneg |
2 | q  | 33.2 | 11925 | 12060 | 202,500,001 | 204,100,000 | gpos | 50
2 | q  | 33.3 | 12060 | 12283 | 204,100,001 | 208,200,000 | gneg |
2 | q  | 34 | 12283 | 12641 | 208,200,001 | 214,500,000 | gpos | 100
2 | q  | 35 | 12641 | 13014 | 214,500,001 | 220,700,000 | gneg |
2 | q  | 36.1 | 13014 | 13237 | 220,700,001 | 224,300,000 | gpos | 75
2 | q  | 36.2 | 13237 | 13297 | 224,300,001 | 225,200,000 | gneg |
2 | q  | 36.3 | 13297 | 13595 | 225,200,001 | 230,100,000 | gpos | 100
2 | q  | 37.1 | 13595 | 13893 | 230,100,001 | 234,700,000 | gneg |
2 | q  | 37.2 | 13893 | 13998 | 234,700,001 | 236,400,000 | gpos | 50
2 | q  | 37.3 | 13998 | 14400 | 236,400,001 | 242,193,529 | gneg |

## References

1. ↑ 1.0 1.1 "Search results – 2[CHR] AND "Homo sapiens"[Organism] AND ("has ccds"[Properties] AND alive[prop]) – Gene". 2016-09-08. https://www.ncbi.nlm.nih.gov/gene?term=2[Chr] AND "Homo sapiens"[Organism] AND ("has ccds"[Properties] AND alive[prop])&cmd=DetailsSearch.
2. ↑ Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2. https://books.google.com/books?id=dSwWBAAAQBAJ&pg=PA45.
3. ↑ 3.0 3.1 3.2 Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
4. ↑ Hillier et al. (2005). "Generation and annotation of the DNAD sequences of human chromosomes 2 and 4". Nature 434 (7034): 724–31. doi:10.1038/nature03466. PMID 15815621. Bibcode: 2005Natur.434..724H.
5. ↑ Vega Homo sapiens genome browser: HoxD cluster on Chromosome 2
6. ↑ 6.0 6.1 "A high-coverage genome sequence from an archaic Denisovan individual". Science 338 (6104): 222–6. October 2012. doi:10.1126/science.1224344. PMID 22936568. Bibcode: 2012Sci...338..222M.
7. ↑ It has been hypothesized that Human Chromosome 2 is a fusion of two ancestral chromosomes by Alec MacAndrew; accessed 18 May 2006.
8. ↑ "Chromosome 2 in the Great Apes – YouTube". https://www.youtube.com/watch?v=3sKScsbhOd4&feature=youtu.be.
9. ↑ "Chromosome 2--Re-Upload – YouTube". https://www.youtube.com/watch?v=mcdQ4_RkSnk&feature=youtu.be.
10. ↑ Yunis and Prakash; Prakash, O (1982). "The origin of man: a chromosomal pictorial legacy". Science 215 (4539): 1525–30. doi:10.1126/science.7063861. PMID 7063861. Bibcode: 1982Sci...215.1525Y.
11. ↑ Human and Ape Chromosomes ; accessed 8 September 2007.
12. ↑ Avarello et al. (1992). "Evidence for an ancestral alphoid domain on the long arm of human chromosome 2". Human Genetics 89 (2): 247–9. doi:10.1007/BF00217134. PMID 1587535.
13. ↑ 13.0 13.1 Ijdo, Jacob W. et al. (1991). "Origin of human chromosome 2: an ancestral telomere-telomere fusion". Proc. Natl. Acad. Sci. U.S.A. 88 (20): 9051–5. doi:10.1073/pnas.88.20.9051. PMID 1924367. Bibcode: 1991PNAS...88.9051I.
14. ↑ Pertea M, Salzberg SL (2010). "Between a chicken and a grape: estimating the number of human genes.". Genome Biol 11 (5): 206. doi:10.1186/gb-2010-11-5-206. PMID 20441615.
15. ↑ "Statistics & Downloads for chromosome 2". 2017-05-12. https://www.genenames.org/cgi-bin/statistics?c=2.
16. ↑ "Chromosome 2: Chromosome summary – Homo sapiens". 2017-03-29. http://mar2017.archive.ensembl.org/Homo_sapiens/Location/Chromosome?r=2.
17. ↑ "Human chromosome 2: entries, gene names and cross-references to MIM". 2018-02-28. https://www.uniprot.org/docs/humchr02.txt.
18. ↑ "Search results – 2[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) – Gene". 2017-05-19. https://www.ncbi.nlm.nih.gov/gene?term=2[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop])&cmd=DetailsSearch.
19. ↑ "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". 2017-05-19. https://www.ncbi.nlm.nih.gov/gene?term=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])&cmd=DetailsSearch.
20. ↑ "Search results – 2[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) – Gene". 2017-05-19. https://www.ncbi.nlm.nih.gov/gene?term=2[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop])&cmd=DetailsSearch.
21. ↑ Swaminathan, Nikhil. "Largest Ever Autism Study Identifies Two Genetic Culprits". https://www.scientificamerican.com/article/largest-autism-study-finds-two-genes/.
22. ↑ "Cleft Chin | AncestryDNA® Traits Learning Hub" (in en). https://www.ancestry.com/lp/traits/cleft-chin.
23. ↑ Shelihan, I.; Ehresmann, S.; Magnani, C.; Forzano, F.; Baldo, C.; Brunetti-Pierri, N.; Campeau, P. M. (2018). "Lowry-Wood syndrome: Further evidence of association with RNU4ATAC, and correlation between genotype and phenotype". Human Genetics 137 (11–12): 905–909. doi:10.1007/s00439-018-1950-8. PMID 30368667. https://pubmed.ncbi.nlm.nih.gov/30368667/.
24. ↑ "Photic Sneeze Reflex | AncestryDNA® Traits Learning Hub" (in en). https://www.ancestry.com/lp/traits/photic-sneeze-reflex.
25. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
26. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
27. ↑ 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. https://books.google.com/books?id=lGCLrh0DIwEC.
28. ↑ Sethakulvichai, W.; Manitpornsut, S.; Wiboonrat, M.; Lilakiatsakun, W.; Assawamakin, A.; Tongsima, S. (2012). "Estimation of band level resolutions of human chromosome images". 2012 Ninth International Conference on Computer Science and Software Engineering (JCSSE). pp. 276–282. doi:10.1109/JCSSE.2012.6261965. ISBN 978-1-4673-1921-8. https://www.researchgate.net/publication/261304470.
29. ↑ "p": Short arm; "q": Long arm.
30. ↑ For cytogenetic banding nomenclature, see article locus.
31. ↑ 31.0 31.1 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.
32. ↑ 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.

## External links

* National Institutes of Health. "Chromosome 2". Genetics Home Reference. http://ghr.nlm.nih.gov/chromosome=2.
* "Chromosome 2". http://web.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/chromo02.shtml.

* v
* t
* e

Cytogenetics: chromosomes

Basic
concepts|

* Karyotype
* Ploidy
* Genetic material/Genome
* Chromatin
* Euchromatin
* Heterochromatin
* Chromosome
* Chromatid
* Nucleosome
* Nuclear organization

Types|

* Autosome/Sex chromosome (or allosome or heterosome)
* Macrochromosome/Microchromosome
* Circular chromosome/Linear chromosome
* Extra chromosome (or accessory chromosome)
* Supernumerary chromosome
* A chromosome/B chromosome
* Lampbrush chromosome
* Polytene chromosome
* Dinoflagellate chromosomes
* Homologous chromosome
* Isochromosome
* Satellite chromosome
* Centromere position
* Metacentric
* Submetacentric
* Telocentric
* Acrocentric
* Holocentric
* Centromere number
* Acentric
* Monocentric
* Dicentric
* Polycentric

Processes
and evolution|

* Mitosis
* Meiosis
* Structural alterations
* Chromosomal inversion
* Chromosomal translocation
* Numerical alterations
* Aneuploidy
* Euploidy
* Polyploidy
* Paleopolyploidy
* Polyploidization

Structures|

* Telomere: Telomere-binding protein (TINF2)
* Protamine

| Histone|

* H1
* H2A
* H2B
* H3
* H4

|

Centromere|

* A
* B
* C1
* C2
* E
* F
* H
* I
* J
* K
* M
* N
* O
* P
* Q
* T

See also|

* Extrachromosomal DNA
* Plasmid
* List of organisms by chromosome count
* List of sequenced genomes
* International System for Human Cytogenetic Nomenclature

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