Chromosome 19

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Chromosome 19
Human male karyotpe high resolution - Chromosome 19 cropped.png
Human chromosome 19 pair after G-banding.
One is from mother, one is from father.
Human male karyotpe high resolution - Chromosome 19.png
Chromosome 19 pair
in human male karyogram.
Features
Length (bp) 58,617,616 bp
(GRCh38)[1]
No. of genes 1,357 (CCDS)[2]
Type Autosome
Centromere position Metacentric[3]
(26.2 Mbp[4])
Complete gene lists
CCDS Gene list
HGNC Gene list
UniProt Gene list
NCBI Gene list
External map viewers
Ensembl Chromosome 19
Entrez Chromosome 19
NCBI Chromosome 19
UCSC Chromosome 19
Full DNA sequences
RefSeq NC_000019 (FASTA)
GenBank CM000681 (FASTA)

Chromosome 19 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 19 spans more than 58.6 million base pairs, the building material of DNA.

Genes[edit]

Number of genes[edit]

The following are some of the gene count estimates of human chromosome 19. 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 1,357 - - [2] 2016-09-08
HGNC 1,372 299 413 [6] 2017-05-12
Ensembl 1,469 894 514 [7] 2017-03-29
UniProt 1,435 - - [8] 2018-02-28
NCBI 1,430 604 528 [9][10][11] 2017-05-19

Gene list[edit]

The following is a partial list of genes on human chromosome 19. For complete list, see the link in the infobox on the right.

Short arm[edit]

  • CACNA1A: Calcium channel, voltage-dependent, P/Q type, alpha 1A subunit (Familial hemiplegic migraine Type I). Gene map locus 19p13
  • COMP: Cartilage oligomeric matrix protein. Gene map locus 19p13.1
  • NOTCH3: Notch homolog 3 (Drosophila): Gene map locus 19p13.1-p13.2
  • GCDH: Glutaryl-Coenzyme A dehydrogenase. Gene map locus 19p13.2
  • BSG: Basigin (Ok blood group)/Extracellular matrix metalloproteinase inducer/CD147. Gene map locus 19p13.3
  • ICAM4: Landsteiner and Weiner glycoprotein. Gene map locus 19p13.3
  • NRTN: Neurturin, associated with Hirschsprung's disease: Gene locus map 19p13.3
  • HCL1: Hair Colour 1; Brown hair colour; BRHC. Gene map locus 19p13.1-q13.11 OMIM: 113750
  • EYCL1: Eye Colour 1; Eye colour, green/blue; GEY. Gene map locus 19p13.1-q13.11 OMIM: 227240
  • GTPBP3: GTP binding protein 3 19p13.11
  • KLF2: Krüppel-like factor 2, also known as Lung Krüppel-like factor. Gene map locus 19p13.11 OMIM: 602016
  • FAM32A: family with sequence similarity 32 member A 19q13.11
  • DDX39: DExD-box helicase 39. Gene map locus 19p13.12

Long arm[edit]

  • GAPDHS: glyceraldehyde-3-phosphate dehydrogenase, spermatogenic 19q13.12
  • HAMP: Hepcidin antimicrobial peptide. Gene map locus 19q13.12
  • BCKDHA: Branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease). Gene map location 19q13.1-q13.2
  • APOE: Apolipoprotein E, gene associated with Alzheimer's disease. Gene map locus 19q13.2
  • CIC: Capicua transcriptional repressor. Gene map locus 19q13.2
  • FCGBP: Fc fragment of IgG binding protein
  • SARS2: seryl-tRNA synthetase 2, mitochondrial. Gene map locus 19q13.2
  • ATP1A3: ATPase. Gene map locus 19q13.31
  • DMWD: DM1 locus, WD repeat containing. Gene map locus 19q13.32
  • PNMA8A: paraneoplastic Ma antigen family member 8A 19q13.32
  • DMPK: Dystrophia myotonica-protein kinase. Gene map locus 19q13.32
  • GLTSCR2: Glioma tumor suppressor candidate region gene 2 protein 19q13.33
  • A1BG: Plasma glycoprotein, unknown function. Gene map locus 19q13.43
  • LRC: The Leukocyte Receptor Complex is a family of immunoreceptors expressed predominantly on monocytes and B cells and at lower levels on dendritic cells and natural killer (NK) cells. The LRC also includes the KIR locus. Gene map locus 19q13.4 OMIM: 604812
  • KPTN: Kaptin (actin binding protein) at the tips of stereocilia. Gene map locus 19q13.4[12]
  • FUT1: The H locus is located on chromosome 19 at 19q13.3. It contains three exons that span more than 5 kb of genomic DNA, and it encodes a fucosyltransferase that produces the H antigen on RBCs.[13]
  • FUT2: The Se locus is located on chromosome 19 at 19q13.3. It contains two exons that span about 25 kb of genomic DNA. The Se locus encodes a specific fucosyltransferase that is expressed in the epithelia of secretory tissues, such as salivary glands, the gastrointestinal tract, and the respiratory tract. The enzyme it encodes catalyzes the production of H antigen.[13]
  • MORT (Mortal Obligate RNA Transcript, lincRNA): Gene map locus 19q13.43

Diseases and disorders[edit]

The following diseases are some of those related to genes on chromosome 19:[14]

Cytogenetic band[edit]

G-banding ideograms of human chromosome 19
G-banding ideogram of human chromosome 19 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 19 in three different resolutions (400,[17] 550[18] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[19] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[20]
G-bands of human chromosome 19 in resolution 850 bphs[21]
Chr. Arm[22] Band[23] ISCN
start[24]
ISCN
stop[24]
Basepair
start
Basepair
stop
Stain[25] Density
19 p 13.3 0 578 1 6,900,000 gneg
19 p 13.2 578 870 6,900,001 12,600,000 gpos 25
19 p 13.13 870 1034 12,600,001 13,800,000 gneg
19 p 13.12 1034 1216 13,800,001 16,100,000 gpos 25
19 p 13.11 1216 1581 16,100,001 19,900,000 gneg
19 p 12 1581 1809 19,900,001 24,200,000 gvar
19 p 11 1809 1992 24,200,001 26,200,000 acen
19 q 11 1992 2159 26,200,001 28,100,000 acen
19 q 12 2159 2372 28,100,001 31,900,000 gvar
19 q 13.11 2372 2569 31,900,001 35,100,000 gneg
19 q 13.12 2569 2737 35,100,001 37,800,000 gpos 25
19 q 13.13 2737 2949 37,800,001 38,200,000 gneg
19 q 13.2 2949 3101 38,200,001 42,900,000 gpos 25
19 q 13.31 3101 3193 42,900,001 44,700,000 gneg
19 q 13.32 3193 3390 44,700,001 47,500,000 gpos 25
19 q 13.33 3390 3649 47,500,001 50,900,000 gneg
19 q 13.41 3649 3770 50,900,001 53,100,000 gpos 25
19 q 13.42 3770 3938 53,100,001 55,800,000 gneg
19 q 13.43 3938 4120 55,800,001 58,617,616 gpos 25

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 - 19[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. ^ 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. 
  6. ^ "Statistics & Downloads for chromosome 19". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19. 
  7. ^ "Chromosome 19: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19. 
  8. ^ "Human chromosome 19: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16. 
  9. ^ "Search results - 19[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20. 
  10. ^ "Search results - 19[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. 
  11. ^ "Search results - 19[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20. 
  12. ^ Bearer EL, Chen AF, Chen AH, Li Z, Mark HF, Smith RJ, Jackson CL (2000). "2E4/Kaptin (KPTN)—a candidate gene for the hearing loss locus, DFNA4". Ann Hum Genet. 64 (3): 189–196. doi:10.1046/j.1469-1809.2000.6430189.x. PMC 3376086Freely accessible. PMID 11409409. 
  13. ^ a b Dean, L. (2005). "Ch. 5: The ABO blood group". Blood Groups and Red Cell Antigens. Bethesda MD: National Center for Biotechnology Information. NBK2261. 
  14. ^ Gilbert F (1997). "Disease genes and chromosomes: disease maps of the human genome. Chromosome 19". Genet Test. 1 (2): 145–9. doi:10.1089/gte.1997.1.145. PMID 10464639. 
  15. ^ "OMIM Entry - # 613845 - HYPERURICEMIA, PULMONARY HYPERTENSION, RENAL FAILURE, AND ALKALOSIS SYNDROME; HUPRAS". www.omim.org. Retrieved 20 January 2017. 
  16. ^ Moss, K (Spring 2001). "Leber's Congenital Amaurosis". Texas Deafblind Outreach. Texas School for the Blind and Visually Impaired. Archived from the original on November 19, 2013. 
  17. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  18. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  19. ^ 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. 
  20. ^ 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. 
  21. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  22. ^ "p": Short arm; "q": Long arm.
  23. ^ For cytogenetic banding nomenclature, see article locus.
  24. ^ 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.
  25. ^ 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.
  • Grimwood J, Gordon LA, Olsen A, Terry A, Schmutz J, Lamerdin J, Hellsten U, Goodstein D, Couronne O, Tran-Gyamfi M, Aerts A, Altherr M, Ashworth L, Bajorek E, Black S, Branscomb E, Caenepeel S, Carrano A, Caoile C, Chan YM, Christensen M, Cleland CA, Copeland A, Dalin E, Dehal P, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Garcia C, Georgescu AM, Glavina T, Gomez M, Gonzales E, Groza M, Hammon N, Hawkins T, Haydu L, Ho I, Huang W, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Larionov V, Leem SH, Lopez F, Lou Y, Lowry S, Malfatti S, Martinez D, McCready P, Medina C, Morgan J, Nelson K, Nolan M, Ovcharenko I, Pitluck S, Pollard M, Popkie AP, Predki P, Quan G, Ramirez L, Rash S, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, She X, Smith D, Slezak T, Solovyev V, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wagner M, Wheeler J, Wu K, Xie G, Yang J, Dubchak I, Furey TS, DeJong P, Dickson M, Gordon D, Eichler EE, Pennacchio LA, Richardson P, Stubbs L, Rokhsar DS, Myers RM, Rubin EM, Lucas SM (2004). "The DNA sequence and biology of human chromosome 19". Nature. 428 (6982): 529–35. doi:10.1038/nature02399. PMID 15057824. 
  • Human Proteome Project Launch website~ https://web.archive.org/web/20110726163128/http://www.hupo.org/research/hpp/HPP_legrain_sep_2010.pdf

External links[edit]

  • National Institutes of Health. "Chromosome 19". Genetics Home Reference. Retrieved 2017-05-06. 
  • "Chromosome 19". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.