Chromosome 19

Last updated
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)61,707,364 bp
(CHM13)
No. of genes 1,357 (CCDS) [1]
Type Autosome
Centromere position Metacentric [2]
(26.2 Mbp [3] )
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 61.7 million base pairs, the building material of DNA. It is considered the most gene-rich chromosome containing roughly 1,500 genes, despite accounting for only 2 percent of the human genome. [4] [5]

Contents

Genes

Number of genes

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. [6]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes SourceRelease date
CCDS 1,357—— [1] 2016-09-08
HGNC 1,372299413 [7] 2017-05-12
Ensembl 1,469894514 [8] 2017-03-29
UniProt 1,435—— [9] 2018-02-28
NCBI 1,430604528 [10] [11] [12] 2017-05-19

Gene list

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

  • 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
  • ZNF121: Zinc finger protein 121. 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
  • 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

  • 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 [13]
  • 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. [14]
  • 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. [14]
  • MORT (Mortal Obligate RNA Transcript, lincRNA): Gene map locus 19q13.43

Diseases and disorders

The following diseases are some of those related to genes on chromosome 19: [15]

Cytogenetic band

G-banding ideograms of human chromosome 19
Human chromosome 19 ideogram vertical.svg
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).
Human chromosome 19 - 400 550 850 bphs.png
G-banding patterns of human chromosome 19 in three different resolutions (400, [18] 550 [19] and 850 [3] ). Band length in this diagram is based on the ideograms from ISCN (2013). [20] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process. [21]
G-bands of human chromosome 19 in resolution 850 bphs [22]
Chr.Arm [23] Band [24] ISCN
start [25] 		ISCN
stop [25] 		Basepair
start		Basepair
stop		Stain [26] Density
19p13.3057816,900,000gneg
19p13.25788706,900,00112,600,000gpos25
19p13.13870103412,600,00113,800,000gneg
19p13.121034121613,800,00116,100,000gpos25
19p13.111216158116,100,00119,900,000gneg
19p121581180919,900,00124,200,000gvar
19p111809199224,200,00126,200,000acen
19q111992215926,200,00128,100,000acen
19q122159237228,100,00131,900,000gvar
19q13.112372256931,900,00135,100,000gneg
19q13.122569273735,100,00137,800,000gpos25
19q13.132737294937,800,00138,200,000gneg
19q13.22949310138,200,00142,900,000gpos25
19q13.313101319342,900,00144,700,000gneg
19q13.323193339044,700,00147,500,000gpos25
19q13.333390364947,500,00150,900,000gneg
19q13.413649377050,900,00153,100,000gpos25
19q13.423770393853,100,00155,800,000gneg
19q13.433938412055,800,00158,617,616gpos25

Related Research Articles

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<span class="mw-page-title-main">Chromosome 21</span> Human chromosome

Chromosome 21 is one of the 23 pairs of chromosomes in humans. Chromosome 21 is both the smallest human autosome and chromosome, with 45 million base pairs representing about 1.5 percent of the total DNA in cells. Most people have two copies of chromosome 21, while those with three copies of chromosome 21 have Down syndrome, also called "trisomy 21".

<span class="mw-page-title-main">Chromosome 1</span> Human chromosome

Chromosome 1 is the designation for the largest human chromosome. Humans have two copies of chromosome 1, as they do with all of the autosomes, which are the non-sex chromosomes. Chromosome 1 spans about 249 million nucleotide base pairs, which are the basic units of information for DNA. It represents about 8% of the total DNA in human cells.

<span class="mw-page-title-main">Chromosome 6</span> Human chromosome

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<span class="mw-page-title-main">Chromosome 13</span> Human chromosome

Chromosome 13 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 13 spans about 113 million base pairs and represents between 3.5 and 4% of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 2</span> Human chromosome

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 and representing almost eight percent of the total DNA in human cells.

<span class="mw-page-title-main">Chromosome 3</span> Human chromosome

Chromosome 3 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 3 spans 201 million base pairs and represents about 6.5 percent of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 4</span> Human chromosome

Chromosome 4 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 4 spans more than 193 million base pairs and represents between 6 and 6.5 percent of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 5</span> Human chromosome

Chromosome 5 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 5 spans about 182 million base pairs and represents almost 6% of the total DNA in cells. Chromosome 5 is the 5th largest human chromosome, yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of non-coding and syntenic conservation with non-mammalian vertebrates, suggesting they are functionally constrained.

<span class="mw-page-title-main">Chromosome 7</span> Human chromosome

Chromosome 7 is one of the 23 pairs of chromosomes in humans, who normally have two copies of this chromosome. Chromosome 7 spans about 160 million base pairs and represents between 5 and 5.5 percent of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 8</span> Human chromosome

Chromosome 8 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 8 spans about 146 million base pairs and represents between 4.5 and 5.0% of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 9</span> Human chromosome

fChromosome 9 is one of the 23 pairs of chromosomes in humans. Humans normally have two copies of this chromosome, as they normally do with all chromosomes. Chromosome 9 spans about 150 million base pairs of nucleic acids and represents between 4.0 and 4.5% of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 10</span> Human chromosome

Chromosome 10 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 10 spans about 134 million base pairs and represents between 4 and 4.5 percent of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 12</span> Human chromosome

Chromosome 12 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 12 spans about 133 million base pairs and represents between 4 and 4.5 percent of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 14</span> Human chromosome

Chromosome 14 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 14 spans about 101 million base pairs and represents between 3 and 3.5% of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 15</span> Human chromosome

Chromosome 15 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 15 spans about 99.7 million base pairs and represents between 3% and 3.5% of the total DNA in cells. Chromosome 15 is an acrocentric chromosome, with a very small short arm, which contains few protein coding genes among its 19 million base pairs. It has a larger long arm that is gene rich, spanning about 83 million base pairs.

<span class="mw-page-title-main">Chromosome 16</span> Human chromosome

Chromosome 16 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 16 spans about 96 million base pairs and represents just under 3% of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 17</span> Human chromosome

Chromosome 17 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 17 spans more than 84 million base pairs and represents between 2.5 and 3% of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 18</span> Human chromosome

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 and represents about 2.5 percent of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 20</span> Human chromosome

Chromosome 20 is one of the 23 pairs of chromosomes in humans. Chromosome 20 spans around 66 million base pairs 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. Since then, due to sequencing improvements and fixes, the length of chromosome 20 has been updated to just over 66 million base pairs.

References

  1. 1 2 "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.
  2. ↑ Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN   978-1-136-84407-2.
  3. 1 2 Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  4. ↑ Ucciferri, Charles (2004-03-31). "Gene-Rich Human Chromosome 19 Sequence Completed". DOE Joint Genome Institute. Retrieved 2022-12-10.
  5. ↑ Sehgal, N.; Fritz, A. J.; Morris, K.; Torres, I.; Chen, Z.; Xu, J.; Berezney, R. (2014). "Gene Density and Chromosome Territory Shape". Chromosoma. 123 (5): 499–513. doi:10.1007/s00412-014-0480-y. PMC   5726871 . PMID   25106753.
  6. ↑ 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.
  7. ↑ "Statistics & Downloads for chromosome 19". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.
  8. ↑ "Chromosome 19: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
  9. ↑ "Human chromosome 19: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.
  10. ↑ "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.
  11. ↑ "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.
  12. ↑ "Search results - 19[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  13. ↑ 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   3376086 . PMID   11409409.
  14. 1 2 Dean, L. (2005). "Ch. 5: The ABO blood group". Blood Groups and Red Cell Antigens. Bethesda MD: National Center for Biotechnology Information. NBK2261.
  15. ↑ 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.
  16. ↑ "OMIM Entry - # 613845 - HYPERURICEMIA, PULMONARY HYPERTENSION, RENAL FAILURE, AND ALKALOSIS SYNDROME; HUPRAS". www.omim.org. Retrieved 20 January 2017.
  17. ↑ 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.
  18. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  19. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  20. ↑ 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.
  21. ↑ Sethakulvichai, W.; Manitpornsut, S.; Wiboonrat, M.; Lilakiatsakun, W.; Assawamakin, A.; Tongsima, S. (2012). "Estimation of band level resolutions of human chromosome images". 2012 Ninth International Conference on Computer Science and Software Engineering (JCSSE). pp. 276–282. doi:10.1109/JCSSE.2012.6261965. ISBN   978-1-4673-1921-8. S2CID   16666470.
  22. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  23. ↑ "p": Short arm; "q": Long arm.
  24. ↑ For cytogenetic banding nomenclature, see article locus.
  25. 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.
  26. ↑ 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.
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