Chromosome 20 (human)

From Wikipedia, the free encyclopedia
  (Redirected from Chromosome 20)
Jump to: navigation, search
Chromosome 20 (human)
Human male karyotpe high resolution - Chromosome 20 cropped.png
Human chromosome 20 pair after G-banding.
One is from mother, one is from father.
Human male karyotpe high resolution - Chromosome 20.png
Chromosome 20 pair
in human male karyogram.
Features
Length (bp) 64,444,167 bp
(GRCh38)[1]
No. of genes 516 (CCDS)[2]
Type Autosome
Centromere position Metacentric[3]
(28.1 Mbp[4])
External map viewers
Ensembl Chromosome 20
Entrez Chromosome 20
NCBI Chromosome 20
UCSC Chromosome 20
Full DNA sequences
RefSeq NC_000020 (FASTA)
GenBank CM000682 (FASTA)

Chromosome 20 is one of the 23 pairs of chromosomes in humans. Chromosome 20 spans around 63 million base pairs (the building material of DNA) and represents between 2 and 2.5 percent of the total DNA in cells. Chromosome 20 was fully sequenced in 2001 and was reported to contain over 59 million base pairs representing 99.4% of the euchromatic DNA.[5] Since then, due to sequencing improvements and fixes, the length of chromosome 20 has been updated to just over 63 million base pairs.[6]

Genes[edit]

The following are some of the gene count estimates of human chromosome 20. 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.[7]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS 516 - - [2] 2016-09-08
HGNC 519 191 297 [8] 2017-05-12
Ensembl 540 594 247 [9] 2017-03-29
NCBI 555 487 333 [10][11][12] 2017-05-19

The following are some of the genes located on chromosome 20:

  • ADA: Adenosine Deaminase (Adenosine Deaminase Deficiency)
  • ANDP: encoding protein Activity-dependent neuroprotector homeobox
  • AHCY: S-adenosylhomocysteine hydrolase
  • ARFGEF2: ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)
  • BCAS1: Breast carcinoma-amplified sequence 1
  • BLCAP: Bladder cancer associated protein
  • BMP2: Bone Morphogenetic Protein 2 (osteoblast differentiation)
  • BPIFB1: encoding protein BPI fold containing family B, member 1
  • BPIFB4: encoding protein BPI fold containing family B, member 4
  • C20orf132: encoding protein Uncharacterized protein C20orf132
  • C20orf27: encoding protein UPF0687 protein C20orf27
  • C20orf3: encoding protein Adipocyte plasma membrane-associated protein
  • C20orf43: encoding protein UPF0549 protein C20orf43
  • CSRP2BP: encoding protein CSRP2 binding protein
  • CST9L: Cystatin-9-like
  • CSTL1: Cystatin-like 1
  • CTCFL: CCCTC-binding factor-like
  • CTNNBL1: Beta-catenin-like protein 1
  • DBNDD2: Dysbindin domain-containing protein 2
  • DDX27: DEAD box polypeptide 27
  • DEFB118, DEFB119, DEFB126, DEFB127, DEFB129: Beta-defensin genes
  • DLGAP4: Disks large-associated protein 4
  • DNAJC5: Cysteine string protein
  • EDEM2: ER degradation-enhancing alpha-mannosidase-like 2
  • EDN3: endothelin 3
  • ENTPD6: Ectonucleoside triphosphate diphosphohydrolase 6
  • ESF1: ESF1 nucleolar pre-rRNA processing protein homolog
  • FASTKD5: encoding protein FAST kinase domain-containing protein 5 (FASTKD5)
  • FITM2: encoding protein Fat storage-inducing transmembrane protein 2
  • GZF1: encoding protein GDNF-inducible zinc finger protein 1
  • GMEB2: Glucocorticoid modulatory element-binding protein 2
  • GNAS1: Gs alpha subunit (membrane G-protein)
  • GSS: glutathione synthetase
  • ITPA: encoding enzyme Inosine triphosphate pyrophosphatase
  • JAG1: jagged 1 (Alagille syndrome)
  • JPH2: encoding protein Junctophilin 2
  • KIZ: encoding protein Kizuna centrosomal protein
  • Kua-UEV:
  • LIME1: encoding protein Lck-interacting transmembrane adapter 1
  • LZTS3: encoding protein Leucine zipper, putative tumor suppressor family member 3
  • NAPB: encoding protein Beta-soluble NSF attachment protein
  • NOL5A: encoding protein Nucleolar protein 56
  • NRSN2: encoding protein Neurensin-2
  • OTOR: encoding protein Otoraplin
  • PANK2: pantothenate kinase 2 (Hallervorden-Spatz syndrome)
  • PKIG: encoding protein cAMP-dependent protein kinase inhibitor gamma
  • PLAGL2: encoding protein Zinc finger protein PLAGL2
  • POLR3F: encoding enzyme DNA-directed RNA polymerase III subunit RPC6
  • PRIC285:
  • PRNP: prion protein (p27-30) (Creutzfeldt–Jakob disease, Gerstmann-Strausler-Scheinker syndrome, fatal familial insomnia)
  • PXMP4: encoding protein Peroxisomal membrane protein 4
  • R3HDML: encoding protein R3H domain containing-like
  • SALL4: sal-like 4 (Drosophila)
  • SERINC3: encoding protein Serine incorporator 3
  • SLC2A4RG: encoding protein SLC2A4 regulator
  • SLX4IP: encoding protein SLX4 interacting protein
  • SPATA2: encoding protein Spermatogenesis-associated protein 2
  • SPEF1: encoding protein Sperm flagellar protein 1
  • SRXN1: encoding protein Sulfiredoxin-1
  • STAU1: encoding protein Double-stranded RNA-binding protein Staufen homolog 1
  • STK35L1: encoding protein STK35L1
  • SUN5: encoding protein SUN domain-containing protein 5
  • TASP1: encoding enzyme Threonine aspartase 1
  • tTG: tissue transglutaminase (auto antigen of Celiac disease)
  • TMEPAI: encoding protein Transmembrane prostate androgen-induced protein
  • TTPAL: encoding protein Tocopherol (alpha) transfer protein-like
  • UCKL1: encoding enzyme Uridine-cytidine kinase-like 1
  • UQCC: encoding enzyme Ubiquinol-cytochrome c reductase complex chaperone CBP3 homolog
  • VAPB: VAMP (vesicle-associated membrane protein)-associated protein B and C
  • YTHDF1: encoding protein YTH domain family, member 1
  • ZFP64 encoding protein Zinc finger protein 64 homolog, isoforms 1 and 2
  • ZGPAT: encoding protein Zinc finger CCCH-type with G patch domain-containing protein
  • ZHX3: encoding protein Zinc fingers and homeoboxes protein 3
  • ZNF334: encoding protein Zinc finger protein 334
  • ZNF343: encoding protein Zinc finger protein 343
  • ZSWIM3: encoding protein Zinc finger SWIM-type containing 3
  • ZMYND8: encoding enzyme Protein kinase C-binding protein 1
  • ZNF133: encoding protein Zinc finger protein 133

Diseases and disorders[edit]

The following diseases are some of those related to genes on chromosome 20:[13]

Cytogenetic band[edit]

G-banding ideograms of human chromosome 20
G-banding ideogram of human chromosome 20 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 20 in three different resolutions (400,[14] 550[15] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[16] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[17]
G-bands of human chromosome 20 in resolution 850 bphs[18]
Chr. Arm[19] Band[20] ISCN
start[21]
ISCN
stop[21]
Basepair
start
Basepair
stop
Stain[22] Density
20 p 13 0 333 1 5,100,000 gneg
20 p 12.3 333 513 5,100,001 9,200,000 gpos 75
20 p 12.2 513 624 9,200,001 12,000,000 gneg
20 p 12.1 624 915 12,000,001 17,900,000 gpos 75
20 p 11.23 915 1164 17,900,001 21,300,000 gneg
20 p 11.22 1164 1275 21,300,001 22,300,000 gpos 25
20 p 11.21 1275 1441 22,300,001 25,700,000 gneg
20 p 11.1 1441 1608 25,700,001 28,100,000 acen
20 q 11.1 1608 1774 28,100,001 30,400,000 acen
20 q 11.21 1774 1927 30,400,001 33,500,000 gneg
20 q 11.22 1927 2051 33,500,001 35,800,000 gpos 25
20 q 11.23 2051 2232 35,800,001 39,000,000 gneg
20 q 12 2232 2439 39,000,001 43,100,000 gpos 75
20 q 13.11 2439 2578 43,100,001 43,500,000 gneg
20 q 13.12 2578 2758 43,500,001 47,800,000 gpos 25
20 q 13.13 2758 3077 47,800,001 51,200,000 gneg
20 q 13.2 3077 3299 51,200,001 56,400,000 gpos 75
20 q 13.31 3299 3382 56,400,001 57,800,000 gneg
20 q 13.32 3382 3493 57,800,001 59,700,000 gpos 50
20 q 13.33 3493 3770 59,700,001 64,444,167 gneg

References[edit]

  1. ^ "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04. 
  2. ^ a b "Search results - 20[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. ^ a b Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  5. ^ Deloukas P; et al. (2001). "The DNA sequence and comparative analysis of human chromosome 20". Nature. 414 (6866): 865–871. doi:10.1038/414865a. PMID 11780052. 
  6. ^ "Homo sapiens chromosome 20, GRCh37.p13 Primary Assembly". National Center for Biotechnology Information. Retrieved October 17, 2013. 
  7. ^ 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 2898077Freely accessible. PMID 20441615. 
  8. ^ "Statistics & Downloads for chromosome 20". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19. 
  9. ^ "Chromosome 20: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19. 
  10. ^ "Search results - 20[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20. 
  11. ^ "Search results - 20[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. 
  12. ^ "Search results - 20[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20. 
  13. ^ Gilbert F (1997). "Disease genes and chromosomes: disease maps of the human genome". Genet Test. 1 (3): 225–229. doi:10.1089/gte.1997.1.225. PMID 10464650. 
  14. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  15. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  16. ^ 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. 
  17. ^ 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. 
  18. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  19. ^ "p": Short arm; "q": Long arm.
  20. ^ For cytogenetic banding nomenclature, see article locus.
  21. ^ a b 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.
  22. ^ 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[edit]

  • National Institutes of Health. "Chromosome 20". Genetics Home Reference. Retrieved 2017-05-06. 
  • "Chromosome 20". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.