Chromosome 2

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)242,193,529 bp
(GRCh38)[1]
No. of genes1,194 (CCDS)[2]
TypeAutosome
Centromere positionSubmetacentric[3]
(93.9 Mbp[4])
Complete gene lists
CCDSGene list
HGNCGene list
UniProtGene list
NCBIGene list
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 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[5] and representing almost eight percent of the total DNA in human cells.

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

Evolution

Humans have only twenty-three pairs of chromosomes, while all other extant members of Hominidae have twenty-four pairs.[7] (It is believed that Neanderthals and Denisovans had twenty-three pairs.)[7] Human chromosome 2 is a result of an end-to-end fusion of two ancestral chromosomes.[8][9][10]

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.[11][12]
  • 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.[13]
  • 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.[14]

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[14]

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.[15]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS1,194—— [2] 2016-09-08
HGNC1,196450931 [16] 2017-05-12
Ensembl1,2921,5981,029 [17] 2017-03-29
UniProt1,274—— [18] 2018-02-28
NCBI1,2811,4461,207 [19][20][21] 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:

  • 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: Alstrom syndrome 1
  • ABCG5 and ABCG8: ATP-binding cassette, subfamily A, members 5 and 8
  • ASXL2: Additional sex combs like 2, transcriptional regulator
  • ATRAID: encoding protein Apoptosis-related protein 3
  • BCYRN1: BC200 lncRNA
  • C2orf16: unknown protein C2orf16
  • CAPG: capping acting protein
  • CCDC142: Coiled-Coil Domain Containing 142
  • CTLA4: cytotoxic T-Lymphocyte Antigen 4
  • CYTOR: Cytoskeleton regulator RNA
  • 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
  • GEN1 encoding protein GEN1, Holliday junction 5' flap endonuclease
  • GCKR: Glucokinase regulator
  • 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
  • NDUFAF7: Protein arginine methyltransferase NDUFAF7, mitochondrial
  • NRBP1: Nuclear receptor-binding protein 1
  • ODC1: Ornithine decarboxylase
  • OTOF: otoferlin
  • PAIP2B: Poly(a) binding protein interacting protein 2b
  • PARK3 encoding protein Parkinson disease 3 (autosomal dominant, Lewy body)
  • PCBP1-AS1: encoding protein PCBP1 antisense RNA 1
  • 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
  • SLC35F6: encoding protein Transmembrane protein SLC35F6
  • 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
  • WDCP: WD Repeat and Coiled Coil Containing Protein

q-arm

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

  • ABCA12: ATP-binding cassette, subfamily 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
  • BCS1L: GRACILE (Finnish heritage disease) related gene
  • BMPR2: bone morphogenetic protein receptor, type II (serine/threonine kinase)
  • C2orf54: Chromosome 2 open reading frame 54
  • CCDC138: Coiled-coil domain-containing protein 138
  • CCDC74A: Coiled-coil domain containing 74a
  • CCDC88A: Coiled-coil domain-containing protein 88A
  • CCDC93: Coiled-coil domain-containing protein 93
  • 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
  • LINC00607: Long intergenic non-protein coding RNA 607
  • LOC100287387: LOC100287387
  • 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
  • PARD3B encoding protein Partitioning defective 3 homolog B
  • PAX3: paired box gene 3 (Waardenburg syndrome 1)
  • PAX8: paired box gene 8
  • PID1: Phosphotyrosine interaction domain containing 1
  • POLR1B: DNA-directed RNA polymerase I subunit RPA2
  • PRR21: Proline-rich protein 21
  • PRSS56: Putative serine protease 56
  • RBM44: Rna binding motif protein 44
  • RFX8: Rfx family member 8, lacking rfx dna binding domain
  • RIF1: replication timing regulatory factor 1
  • RNU4ATAC: RNA, U4atac small nuclear (U12-dependent splicing)
  • RPL37A: encoding protein 60S ribosomal protein L37a
  • SATB2: Homeobox 2
  • SCARNA5: Small Cajal body-specific RNA 5
  • 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
  • TSGA10 encoding protein Testis specific 10
  • TTN: titin
  • TUBA4B: encoding protein Tubulin alpha 4b
  • 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

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

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,[23] 550[24] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[25] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[26]
G-bands of human chromosome 2 in resolution 850 bphs[4]
Chr. Arm[27] Band[28] ISCN
start[29]		 ISCN
stop[29]		 Basepair
start		 Basepair
stop		 Stain[30] Density
2p 25.3038814,400,000 gneg
2p 25.23885664,400,0016,900,000 gpos50
2p 25.15669546,900,00112,000,000 gneg
2p 24.3954119312,000,00116,500,000 gpos75
2p 24.21193131216,500,00119,000,000 gneg
2p 24.11312156519,000,00123,800,000 gpos75
2p 23.31565178923,800,00127,700,000 gneg
2p 23.21789190827,700,00129,800,000 gpos25
2p 23.11908202729,800,00131,800,000 gneg
2p 22.32027229631,800,00136,300,000 gpos75
2p 22.22296241536,300,00138,300,000 gneg
2p 22.12415260938,300,00141,500,000 gpos50
2p 212609296641,500,00147,500,000 gneg
2p 16.32966322047,500,00152,600,000 gpos100
2p 16.23220329452,600,00154,700,000 gneg
2p 16.13294354854,700,00161,000,000 gpos100
2p 153548375761,000,00163,900,000 gneg
2p 143757393563,900,00168,400,000 gpos50
2p 13.33935411468,400,00171,300,000 gneg
2p 13.24114424871,300,00173,300,000 gpos50
2p 13.14248435373,300,00174,800,000 gneg
2p 124353486074,800,00183,100,000 gpos100
2p 11.24860530783,100,00191,800,000 gneg
2p 11.15307554591,800,00193,900,000 acen
2q 11.15545572493,900,00196,000,000 acen
2q 11.25724602296,000,001102,100,000 gneg
2q 12.160226261102,100,001105,300,000 gpos50
2q 12.262616395105,300,001106,700,000 gneg
2q 12.363956559106,700,001108,700,000 gpos25
2q 1365596812108,700,001112,200,000 gneg
2q 14.168127036112,200,001118,100,000 gpos50
2q 14.270367334118,100,001121,600,000 gneg
2q 14.373347602121,600,001129,100,000 gpos50
2q 21.176027826129,100,001131,700,000 gneg
2q 21.278268050131,700,001134,300,000 gpos25
2q 21.380508169134,300,001136,100,000 gneg
2q 22.181698437136,100,001141,500,000 gpos100
2q 22.284378497141,500,001143,400,000 gneg
2q 22.384978646143,400,001147,900,000 gpos100
2q 23.186468735147,900,001149,000,000 gneg
2q 23.287358795149,000,001149,600,000 gpos25
2q 23.387959078149,600,001154,000,000 gneg
2q 24.190789361154,000,001158,900,000 gpos75
2q 24.293619585158,900,001162,900,000 gneg
2q 24.395859928162,900,001168,900,000 gpos75
2q 31.1992810435168,900,001177,100,000 gneg
2q 31.21043510599177,100,001179,700,000 gpos50
2q 31.31059910733179,700,001182,100,000 gneg
2q 32.11073311091182,100,001188,500,000 gpos75
2q 32.21109111225188,500,001191,100,000 gneg
2q 32.31122511538191,100,001196,600,000 gpos75
2q 33.11153811925196,600,001202,500,000 gneg
2q 33.21192512060202,500,001204,100,000 gpos50
2q 33.31206012283204,100,001208,200,000 gneg
2q 341228312641208,200,001214,500,000 gpos100
2q 351264113014214,500,001220,700,000 gneg
2q 36.11301413237220,700,001224,300,000 gpos75
2q 36.21323713297224,300,001225,200,000 gneg
2q 36.31329713595225,200,001230,100,000 gpos100
2q 37.11359513893230,100,001234,700,000 gneg
2q 37.21389313998234,700,001236,400,000 gpos50
2q 37.31399814400236,400,001242,193,529 gneg

References

  1. ↑ "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 24 December 2013. Retrieved 4 March 2017.
  2. 1 2 "Search results - 2[CHR] AND "Homo sapiens"[Organism] AND ("has ccds"[Properties] AND alive[prop]) - Gene". NCBI. CCDS Release 20 for Homo sapiens. 8 September 2016. Retrieved 28 May 2017.
  3. ↑ Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2.
  4. 1 2 3 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. 1 2 Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, 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. ↑ "Chromosome 2 in the Great Apes - YouTube". www.youtube.com. Archived from the original on 21 December 2021. Retrieved 24 July 2020.
  10. ↑ "Chromosome 2--Re-Upload - YouTube". www.youtube.com. Archived from the original on 21 December 2021. Retrieved 24 July 2020.
  11. ↑ 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.
  12. ↑ Human and Ape Chromosomes Archived 6 September 2017 at the Wayback Machine; accessed 8 September 2007.
  13. ↑ 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. S2CID 1441285.
  14. 1 2 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. Bibcode:1991PNAS...88.9051I. doi:10.1073/pnas.88.20.9051. PMC 52649. PMID 1924367.
  15. ↑ 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.
  16. ↑ "Statistics & Downloads for chromosome 2". HUGO Gene Nomenclature Committee. 12 May 2017. Retrieved 19 May 2017.
  17. ↑ "Chromosome 2: Chromosome summary - Homo sapiens". Ensembl Release 88. 29 March 2017. Retrieved 19 May 2017.
  18. ↑ "Human chromosome 2: entries, gene names and cross-references to MIM". UniProt. 28 February 2018. Retrieved 16 March 2018.
  19. ↑ "Search results - 2[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 19 May 2017. Retrieved 20 May 2017.
  20. ↑ "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. 19 May 2017. Retrieved 20 May 2017.
  21. ↑ "Search results - 2[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 19 May 2017. Retrieved 20 May 2017.
  22. ↑ Swaminathan, Nikhil. "Largest Ever Autism Study Identifies Two Genetic Culprits". Scientific American. Retrieved 25 January 2018.
  23. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  24. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  25. ↑ 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.
  26. ↑ Sethakulvichai, W.; Manitpornsut, S.; Wiboonrat, M.; Lilakiatsakun, W.; Assawamakin, A.; Tongsima, S. (2012). Estimation of band level resolutions of human chromosome images. In Computer Science and Software Engineering (JCSSE), 2012 International Joint Conference on. pp. 276–282. doi:10.1109/JCSSE.2012.6261965. ISBN 978-1-4673-1921-8. S2CID 16666470.
  27. ↑ "p": Short arm; "q": Long arm.
  28. ↑ For cytogenetic banding nomenclature, see article locus.
  29. 1 2 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.
  30. ↑ 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.
  • National Institutes of Health. "Chromosome 2". Genetics Home Reference. Archived from the original on 9 March 2016. Retrieved 6 May 2017.
  • "Chromosome 2". Human Genome Project Information Archive 1990–2003. Retrieved 6 May 2017.
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