Chromosome 18 (human)

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Chromosome 18 (human)
File:Human male karyotpe high resolution - Chromosome 18 cropped.png
Human chromosome 18 pair after G-banding.
One is from mother, one is from father.
File:Human male karyotpe high resolution - Chromosome 18.png
Chromosome 18 pair
in human male karyogram.
Features
Length (bp)80,373,285 bp
(GRCh38)[1]
No. of genes261 (CCDS)[2]
TypeAutosome
Centromere positionSubmetacentric[3]
(18.5 Mbp[4])
Complete gene lists
CCDS?
HGNC?
UniProt?
NCBI?
External map viewers
EnsemblChromosome 18
EntrezChromosome 18
NCBIChromosome 18
UCSCChromosome 18
Full DNA sequences
RefSeqNC_000018 (FASTA)
GenBankCM000680 (FASTA)

Chromosome 18 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 18 spans about 80 million base pairs (the building material of DNA) and represents about 2.5 percent of the total DNA in cells.

Genes

See also: Category:Genes on human chromosome 18.

The following are some of the gene count estimates of human chromosome 18. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies (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.[5]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS 261 - - [2] 2016-09-08
HGNC 262 138 241 [6] 2017-05-12
Ensembl 268 608 247 [7] 2017-03-29
NCBI 285 432 304 [8][9][10] 2017-05-19

The following are some of the genes located in chromosome 18:

  • ASXL3: encoding protein Additional sex combs like 3 (Drosophila)
  • CABLES1: encoding protein CDK5 and ABL1 enzyme substrate 1
  • CABYR: Calcium-binding tyrosine phosphorylation-regulated protein
  • CHMP1B: Charged multivesicular body protein 1b
  • CXXC1: CXXC-type zinc finger protein 1
  • DCC: Deleted in Colorectal Cancer
  • ELAC1: elaC ribonuclease Z 1
  • ESCO1: encoding protein Establishment of sister chromatid cohesion N-acetyltransferase 1
  • FAM69C: encoding protein Family with sequence similarity 69, member C
  • FECH: ferrochelatase (protoporphyria)
  • GREB1L: encoding protein Growth regulation by estrogen in breast cancer-like
  • HAUS1: HAUS augmin-like complex subunit 1
  • HDHD2: encoding enzyme Haloacid dehalogenase-like hydrolase domain-containing protein 2
  • IER3IP1: encoding protein Immediate early response 3-interacting protein 1
  • KC6: Keratoconus gene 6, discovery reported in 2005;
  • MIR133A1: encoding microRNA MicroRNA 133a-1
  • MIR187: encoding protein MicroRNA 187
  • MRCL3: encoding protein Myosin regulatory light chain 12A
  • NAPG: encoding protein Gamma-soluble NSF attachment protein
  • NOL4: encoding protein Nucleolar protein 4
  • NPC1: Niemann-Pick disease, type C1
  • PIGN: encoding protein Phosphatidylinositol glycan anchor biosynthesis, class N
  • PSTPIP2: encoding enzyme Proline-serine-threonine phosphatase-interacting protein 2
  • RP11-267C16.1: encoding protein Uncharacterized LOC100287225
  • SERPINB10: encoding protein Serpin peptidase inhibitor, clade B (ovalbumin), member 10
  • SIGLEC15: encoding protein Sialic acid binding Ig-like lectin 15
  • SMAD4: SMAD, mothers against DPP homolog 4 (Drosophila)
  • TMEM241: encoding protein Transmembrane protein 241
  • TTC39C: encoding protein Tetratricopeptide repeat protein 39C
  • TWSG1: encoding protein Twisted gastrulation protein homolog 1
  • ZCCHC2: encoding protein Zinc finger CCHC domain-containing protein 2
  • ZFP161: encoding protein Zinc finger protein 161 homolog
  • ZNF236: encoding protein Zinc finger protein 236
  • ZNF516: encoding protein Zinc finger protein 516
  • ZNF521: encoding protein Zinc finger protein 521
  • ZNF532: encoding protein Zinc finger protein 532

Diseases and disorders

The following diseases are some of those related to genes on chromosome 18:

Cytogenetic band

G-banding ideograms of human chromosome 18
File:Human chromosome 18 ideogram vertical.svg
G-banding ideogram of human chromosome 18 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 18 - 400 550 850 bphs.png
G-banding patterns of human chromosome 18 in three different resolutions (400,[12] 550[13] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[14] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[15]
G-bands of human chromosome 18 in resolution 850 bphs[16]
Chr. Arm[17] Band[18] ISCN
start[19] 		ISCN
stop[19] 		Basepair
start 		Basepair
stop 		Stain[20] Density
18 p 11.32 0 159 1 2,900,000 gneg
18 p 11.31 159 430 2,900,001 7,200,000 gpos 50
18 p 11.23 430 526 7,200,001 8,500,000 gneg
18 p 11.22 526 685 8,500,001 10,900,000 gpos 25
18 p 11.21 685 1035 10,900,001 15,400,000 gneg
18 p 11.1 1035 1290 15,400,001 18,500,000 acen
18 q 11.1 1290 1561 18,500,001 21,500,000 acen
18 q 11.2 1561 1847 21,500,001 27,500,000 gneg
18 q 12.1 1847 2229 27,500,001 35,100,000 gpos 100
18 q 12.2 2229 2436 35,100,001 39,500,000 gneg
18 q 12.3 2436 2755 39,500,001 45,900,000 gpos 75
18 q 21.1 2755 3153 45,900,001 50,700,000 gneg
18 q 21.2 3153 3392 50,700,001 56,200,000 gpos 75
18 q 21.31 3392 3519 56,200,001 58,600,000 gneg
18 q 21.32 3519 3663 58,600,001 61,300,000 gpos 50
18 q 21.33 3663 3758 61,300,001 63,900,000 gneg
18 q 22.1 3758 4077 63,900,001 69,100,000 gpos 100
18 q 22.2 4077 4204 69,100,001 71,000,000 gneg
18 q 22.3 4204 4411 71,000,001 75,400,000 gpos 25
18 q 23 4411 4650 75,400,001 80,373,285 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 - 18[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 Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  5. ↑ 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.
  6. ↑ "Statistics & Downloads for chromosome 18". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.
  7. ↑ "Chromosome 18: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
  8. ↑ "Search results - 18[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  9. ↑ "Search results - 18[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.
  10. ↑ "Search results - 18[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  11. ↑ "chromosome18". www.chromosome18.org. Retrieved 2017-01-19.
  12. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  13. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  14. ↑ 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.
  15. ↑ 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.
  16. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  17. ↑ "p": Short arm; "q": Long arm.
  18. ↑ For cytogenetic banding nomenclature, see article locus.
  19. ↑ 19.0 19.1 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.
  20. ↑ 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.
  • Nusbaum C, Zody MC, Borowsky ML, Kamal M, Kodira CD, Taylor TD, Whittaker CA, Chang JL, Cuomo CA, Dewar K, FitzGerald MG, Yang X, Abouelleil A, Allen NR, Anderson S, Bloom T, Bugalter B, Butler J, Cook A, DeCaprio D, Engels R, Garber M, Gnirke A, Hafez N, Hall JL, Norman CH, Itoh T, Jaffe DB, Kuroki Y, Lehoczky J, Lui A, Macdonald P, Mauceli E, Mikkelsen TS, Naylor JW, Nicol R, Nguyen C, Noguchi H, O'Leary SB, O'Neill K, Piqani B, Smith CL, Talamas JA, Topham K, Totoki Y, Toyoda A, Wain HM, Young SK, Zeng Q, Zimmer AR, Fujiyama A, Hattori M, Birren BW, Sakaki Y, Lander ES (2005). "DNA sequence and analysis of human chromosome 18". Nature. 437 (7058): 551–5. doi:10.1038/nature03983. PMID 16177791.
  • Chen H, Wang N, Huo Y, Sklar P, MacKinnon DF, Potash JB, McMahon FJ, Antonarakis SE, DePaulo JR Jr, Ross CA, McInnis MG (2003). "Trapping and sequence analysis of 1138 putative exons from human chromosome 18". Mol Psychiatry. 8 (6): 619–23. doi:10.1038/sj.mp.4001288. PMID 12851638.
  • Gilbert F (1997). "Disease genes and chromosomes: disease maps of the human genome. Chromosome 18". Genet Test. 1 (1): 69–71. PMID 10464628.

External links

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