Chromosome 2 (human)

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Chromosome 2 (human)
File:Human male karyotpe high resolution - Chromosome 2 cropped.png
Human chromosome 2 pair after G banding. One is from mother, one is from father.
File:Human male karyotpe high resolution - Chromosome 2.png
Chromosome 2 pair
in human male karyogram.
Features
Length (bp)242,193,529 bp
(GRCh38)[1]
No. of genes1,194 (CCDS)[2]
TypeAutosome
Centromere positionSubmetacentric[3]
(93.9 Mbp[4])
Complete gene lists
CCDS?
HGNC?
UniProt?
NCBI?
External map viewers
EnsemblChromosome 2
EntrezChromosome 2
NCBIChromosome 2
UCSCChromosome 2
Full DNA sequences
RefSeqNC_000002 (FASTA)
GenBankCM000664 (FASTA)
Fusion of ancestral chromosomes left distinctive remnants of telomeres, and a vestigial centromere

Chromosome 2 is one of the 23 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[5] (the building material of DNA) and representing almost 8% of the total DNA in human cells.

Chromosome 2 contains the HOXD homeobox gene cluster.[6]

Evolution

Further information: Chimpanzee genome project

All members of Hominidae except humans, Neanderthals, and Denisovans have 24 pairs of chromosomes.[7] Humans have only 23 pairs of chromosomes. Human chromosome 2 is a result of an end-to-end fusion of two ancestral chromosomes.[8][9]

The evidence for this includes:

  • The correspondence of chromosome 2 to two ape chromosomes. The closest human relative, the chimpanzee, has near-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]

According to researcher J. W. IJdo, "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." [13]

Genes

See also: Category:Genes on human chromosome 2.

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 (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.[14]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS 1,194 - - [2] 2016-09-08
HGNC 1,196 450 931 [15] 2017-05-12
Ensembl 1,292 1,598 1,029 [16] 2017-03-29
NCBI 1,281 1,446 1,207 [17][18][19] 2017-05-19

Some genes requiring arm identification:

p-arm

The following are some of the genes located on p-arm (short arm) of human chromosome 2:

  • ACTR2: encoding protein Actin-related protein 2
  • ADI1: encoding enzyme 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
  • AFF3: encoding protein AF4/FMR2 family member 3
  • AFTPH: encoding protein Aftiphilin
  • ALMS1
  • ABCG5 and ABCG8: ATP-binding cassette, subfamily A, members 5 and 8
  • C2orf18: encoding protein Transmembrane protein C2orf18
  • C2orf28: encoding protein Apoptosis-related protein 3
  • CAPG: capping acting protein
  • CCDC142: Coiled-Coil Domain Containing 142
  • CTLA4: cytotoxic T-Lymphocyte Antigen 4
  • DHX57: DExH-box helicase 57
  • DPYSL5: Dihydropyrimidinase like 5
  • ERLEC1: Endoplasmic reticulum lectin 1
  • EVA1A: encoding protein Eva-1 homolog A (C. elegans)
  • FAM49A: Family with sequence similarity 49 member A
  • FAM98A: Family with sequence similarity 98 member A
  • FAM136A: Family with sequence similarity 136 member A
  • FBXO11: F-box protein 11
  • GFPT1: glutamine—fructose-6-phosphate transaminase 1
  • GKN1: gastrokine 1
  • GPATCH11: G-patch domain containing protein 11
  • GTF2A1L: General transcription factor IIA subunit 1 like
  • HADHA: hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit
  • HADHB: hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit
  • HSPC159: Galectin-related protein
  • LEPQTL1: Leptin, serum levels of
  • MEMO1: Mediator of cell motility 1
  • MPHOSPH10: M-phase phosphoprotein 10
  • MSH2: mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)
  • MSH6: mutS homolog 6 (E. coli)
  • MTHFD2: Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
  • MTIF2: mitochondrial translational initiation factor 2
  • NRBP1: Nuclear receptor-binding protein 1
  • ODC1: Ornithine decarboxylase
  • OTOF: otoferlin
  • PCYOX1: prenylcysteine oxidase 1
  • PELI1: Ubiquitin ligase
  • PLGLB2: Plasminogen-related protein B
  • POLR1A: DNA-directed RNA polymerase I subunit RPA1
  • PREPL: Prolyl endopeptidase-like
  • PXDN: Peroxidasin homolog
  • QPCT: Glutaminyl-peptide cyclotransferase
  • RETSAT: All-trans-retinol 13,14-reductase
  • SH3YL1: SH3 and SYLF domain-containing 1
  • TGOLN2: Trans-Golgi network integral membrane protein 2
  • THADA: encoding protein Thyroid adenoma associated
  • TIA1: TIA1 cytotoxic granule-associated RNA binding protein
  • TMEM150: Transmembrane protein 150A
  • TP53I3: Putative quinone oxidoreducatse
  • TPO: thyroid peroxidase
  • TTC7A: familial multiple intestinal atresia
  • WBP1: WW domain-binding protein 1
  • WDR35 (IFT121: TULP4): intraflagellar transport 121

q-arm

The following are some of the genes located on q-arm (long arm) of human chromosome 2:

  • ABCA12: ATP-binding cassette, sub-family A (ABC1), member 12
  • ACTR1B: encoding protein Beta-centractin
  • AGXT: alanine-glyoxylate aminotransferase (oxalosis I; hyperoxaluria I; glycolicaciduria; serine-pyruvate aminotransferase)
  • ALS2: amyotrophic lateral sclerosis 2 (juvenile)
  • ALS2CR8: encoding protein Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8 protein also known as calcium-response factor (CaRF)
  • ARMC9: encoding protein LisH domain-containing protein ARMC9
  • B3GNT7: encoding protein UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7
  • BMPR2: bone morphogenetic protein receptor, type II (serine/threonine kinase)
  • CCDC88A: Coiled-coil domain-containing protein 88A
  • CCDC93: Coiled-coil domain-containing protein 93
  • CCDC138: Coiled-coil domain-containing protein 138
  • CDCA7: Cell division cycle associated protein 1
  • CHPF: Chondroitin sulfate synthase 2
  • COL3A1: collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant)
  • COL4A3: collagen, type IV, alpha 3 (Goodpasture antigen)
  • COL4A4: collagen, type IV, alpha 4
  • COL5A2: collagen, type V, alpha 2
  • DIS3L2: DIS3 mitotic control homolog-like 2
  • ECEL1: Endothelin converting enzyme like 1
  • EPC2: Enhancer of polycomb homolog 2
  • EPB41L5: encoding protein Erythrocyte membrane protein band 4.1 like 5
  • ERICH2: encoding protein Glutamate rich protein 2
  • FASTKD1: FAST kinase domain-containing protein 1
  • IMP4: U3 small nucleolar ribonucleoprotein
  • INPP1: Inositol polyphosphate 1-phosphatase
  • INPP4A: inositol polyphosphate-4-phosphatase type A
  • ITM2C: Integral membrane protein 2C
  • KANSL3: KAT8 regulatory NSL complex subunit 3
  • KIAA1211L: Uncharacterized Protein KIAA1211- Like
  • LANCL1: LanC like 1
  • MALL: MAL-like protein
  • MGAT5: mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase
  • NABP1: Nucleic acid binding protein 1
  • NEURL3: encoding protein Neuralized E3 ubiquitin protein ligase 3
  • NCL: Nucleolin
  • NR4A2: nuclear receptor subfamily 4, group A, member 2
  • OLA1: Obg-like ATPase 1
  • PAX3: paired box gene 3 (Waardenburg syndrome 1)
  • PAX8: paired box gene 8
  • POLR1B: DNA-directed RNA polymerase I subunit RPA2
  • PRR21: Proline-rich protein 21
  • PRSS56: Putative serine protease 56
  • RIF1: replication timing regulatory factor 1
  • RNU4ATAC: RNA, U4atac small nuclear (U12-dependent splicing)
  • RPL37A: encoding protein 60S ribosomal protein L37a
  • SATB2: Homeobox 2
  • SDPR: Serum deprivation-response protein
  • SGOL2: Shugoshin-like 2
  • SH3BP4: SH3 domain-binding protein 4
  • SLC9A4: solute carrier family 9 member A4
  • SLC40A1: solute carrier family 40 (iron-regulated transporter), member 1
  • SMPD4: Sphingomyelin phosphodiesterase 4
  • SP140: encoding protein SP140 nuclear body protein
  • SPATS2L: spermatogenesis associated, serine-rich 2-like protein
  • SSB: Sjogren syndrome antigen B
  • SSFA2: Sperm-specific antigen 2
  • TBR1: T-box, brain, 1
  • THAP4: THAP domain-containing protein 4
  • TMBIM1: Transmembrane BAX inhibitor motif-containing protein 1
  • TNRC15: PERQ amino acid-rich with GYF domain-containing protein 2
  • TTN: titin
  • UBXD2: UBX domain-containing protein 4
  • UXS1: UDP-glucuronic acid decarboxylase 1
  • XIRP2: Xin actin-binding repeat-containing protein 2
  • ZNF142: zinc finger protein 142

Related diseases and traits

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

Cytogenetic band

G-banding ideograms of human chromosome 2
File:Human chromosome 2 ideogram vertical.svg
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).
File:Human chromosome 02 - 400 550 850 bphs.png
G-banding patterns of human chromosome 2 in three different resolutions (400,[20] 550[21] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[22] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[23]
G-bands of human chromosome 2 in resolution 850 bphs[4]
Chr. Arm[24] Band[25] ISCN
start[26] 		ISCN
stop[26] 		Basepair
start 		Basepair
stop 		Stain[27] 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. ↑ "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04.
  2. ↑ 2.0 2.1 "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. Retrieved 2017-05-28.
  3. ↑ Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2.
  4. ↑ 4.0 4.1 4.2 Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  5. ↑ Hillier; et al. (2005). "Generation and annotation of the DNAD sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724–31. Bibcode:2005Natur.434..724H. doi:10.1038/nature03466. PMID 15815621.
  6. ↑ Vega Homo sapiens genome browser: HoxD cluster on Chromosome 2
  7. ↑ 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; Kircher; Gansauge; Li; Racimo; Mallick; Schraiber; Jay; Prüfer; De Filippo; Sudmant; Alkan; Fu; Do; Rohland; Tandon; Siebauer; Green; Bryc; Briggs; Stenzel; Dabney; Shendure; Kitzman; Hammer; Shunkov; Derevianko; Patterson; Andrés; et al. (October 2012). "A high-coverage genome sequence from an archaic Denisovan individual". Science. 338 (6104): 222–6. Bibcode:2012Sci...338..222M. doi:10.1126/science.1224344. PMC 3617501. PMID 22936568.
  8. ↑ It has been hypothesized that Human Chromosome 2 is a fusion of two ancestral chromosomes by Alec MacAndrew; accessed 18 May 2006.
  9. ↑ Evidence of Common Ancestry: Human Chromosome 2 (video) 2007
  10. ↑ Yunis and Prakash; Prakash, O (1982). "The origin of man: a chromosomal pictorial legacy". Science. 215 (4539): 1525–30. Bibcode:1982Sci...215.1525Y. doi:10.1126/science.7063861. PMID 7063861.
  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; et al. (1991). "Origin of human chromosome 2: an ancestral telomere-telomere fusion". Proc. Natl. Acad. Sci. U.S.A. 88 (20): 9051–5. Bibcode:1991PNAS...88.9051I. doi:10.1073/pnas.88.20.9051. PMC 52649. PMID 1924367.
  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. PMC 2898077. PMID 20441615.
  15. ↑ "Statistics & Downloads for chromosome 2". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.
  16. ↑ "Chromosome 2: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
  17. ↑ "Search results - 2[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  18. ↑ "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. Retrieved 2017-05-20.
  19. ↑ "Search results - 2[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  20. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  21. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  22. ↑ 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.
  23. ↑ 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.
  24. ↑ "p": Short arm; "q": Long arm.
  25. ↑ For cytogenetic banding nomenclature, see article locus.
  26. ↑ 26.0 26.1 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.
  27. ↑ 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. Retrieved 2017-05-06.
  • "Chromosome 2". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.
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