Biology:Chromosome 16
From HandWiki
Short description: Human chromosome
| Chromosome 16 | |
|---|---|
 Human chromosome 16 pair after G-banding. One is from mother, one is from father. | |
 Chromosome 16 pair in human male karyogram. | |
| Features | |
| Length (bp) | 96,330,374 bp (CHM13) |
| No. of genes | 795 (CCDS)[1] |
| Type | Autosome |
| Centromere position | Metacentric[2] (36.8 Mbp[3]) |
| Complete gene lists | |
| CCDS | Gene list |
| HGNC | Gene list |
| UniProt | Gene list |
| NCBI | Gene list |
| External map viewers | |
| Ensembl | Chromosome 16 |
| Entrez | Chromosome 16 |
| NCBI | Chromosome 16 |
| UCSC | Chromosome 16 |
| Full DNA sequences | |
| RefSeq | NC_000016 (FASTA) |
| GenBank | CM000678 (FASTA) |
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 (the building material of DNA) and represents just under 3% of the total DNA in cells.
Genes
Number of genes
The following are some of the gene count estimates of human chromosome 16. 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.[4]
| Estimated by | Protein-coding genes | Non-coding RNA genes | Pseudogenes | Source | Release date |
|---|---|---|---|---|---|
| CCDS | 795 | — | — | [1] | 2016-09-08 |
| HGNC | 802 | 251 | 365 | [5] | 2017-05-12 |
| Ensembl | 865 | 1,046 | 462 | [6] | 2017-03-29 |
| UniProt | 838 | — | — | [7] | 2018-02-28 |
| NCBI | 912 | 652 | 502 | [8][9][10] | 2017-05-19 |
Gene list
The following is a partial list of genes on human chromosome 16. For complete list, see the link in the infobox on the right.
Diseases and disorders
- Attention deficit hyperactivity disorder (ADHD)
- Asperger syndrome
- Autism spectrum disorder[11][12]
- Autosomal dominant polycystic kidney disease (PKD-1)
- Batten disease
- Combined malonic and methylmalonic aciduria (CMAMMA)
- Familial Mediterranean fever (FMF)
- Synesthesia
- Thalassemia
- Trisomy 16
- Morquio syndrome
Associated traits
- Red hair
Cytogenetic band
G-banding ideograms of human chromosome 16
G-banding ideogram of human chromosome 16 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 16 in three different resolutions (400,[13] 550[14] and 850[3]). Band length in this diagram is based on the ideograms from ISCN (2013).[15] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[16]
| Chr. | Arm[18] | Band[19] | ISCN start[20] |
ISCN stop[20] |
Basepair start |
Basepair stop |
Stain[21] | Density |
|---|---|---|---|---|---|---|---|---|
| 16 | p | 13.3 | 0 | 352 | 1 | 7,800,000 | gneg | |
| 16 | p | 13.2 | 352 | 596 | 7,800,001 | 10,400,000 | gpos | 50 |
| 16 | p | 13.13 | 596 | 813 | 10,400,001 | 12,500,000 | gneg | |
| 16 | p | 13.12 | 813 | 948 | 12,500,001 | 14,700,000 | gpos | 50 |
| 16 | p | 13.11 | 948 | 1070 | 14,700,001 | 16,700,000 | gneg | |
| 16 | p | 12.3 | 1070 | 1246 | 16,700,001 | 21,200,000 | gpos | 50 |
| 16 | p | 12.2 | 1246 | 1409 | 21,200,001 | 24,200,000 | gneg | |
| 16 | p | 12.1 | 1409 | 1558 | 24,200,001 | 28,500,000 | gpos | 50 |
| 16 | p | 11.2 | 1558 | 1856 | 28,500,001 | 35,300,000 | gneg | |
| 16 | p | 11.1 | 1856 | 2045 | 35,300,001 | 36,800,000 | acen | |
| 16 | q | 11.1 | 2045 | 2194 | 36,800,001 | 38,400,000 | acen | |
| 16 | q | 11.2 | 2194 | 2709 | 38,400,001 | 47,000,000 | gvar | |
| 16 | q | 12.1 | 2709 | 2953 | 47,000,001 | 52,600,000 | gneg | |
| 16 | q | 12.2 | 2953 | 3142 | 52,600,001 | 56,000,000 | gpos | 50 |
| 16 | q | 13 | 3142 | 3346 | 56,000,001 | 57,300,000 | gneg | |
| 16 | q | 21 | 3346 | 3657 | 57,300,001 | 66,600,000 | gpos | 100 |
| 16 | q | 22.1 | 3657 | 4023 | 66,600,001 | 70,800,000 | gneg | |
| 16 | q | 22.2 | 4023 | 4118 | 70,800,001 | 72,800,000 | gpos | 50 |
| 16 | q | 22.3 | 4118 | 4294 | 72,800,001 | 74,100,000 | gneg | |
| 16 | q | 23.1 | 4294 | 4551 | 74,100,001 | 79,200,000 | gpos | 75 |
| 16 | q | 23.2 | 4551 | 4659 | 79,200,001 | 81,600,000 | gneg | |
| 16 | q | 23.3 | 4659 | 4768 | 81,600,001 | 84,100,000 | gpos | 50 |
| 16 | q | 24.1 | 4768 | 4930 | 84,100,001 | 87,000,000 | gneg | |
| 16 | q | 24.2 | 4930 | 5025 | 87,000,001 | 88,700,000 | gpos | 25 |
| 16 | q | 24.3 | 5025 | 5120 | 88,700,001 | 90,338,345 | gneg |
References
- ↑ 1.0 1.1 "Search results - 16[CHR] AND "Homo sapiens"[Organism] AND ("has ccds"[Properties] AND alive[prop]) - Gene". 2016-09-08. https://www.ncbi.nlm.nih.gov/gene?term=16%5BChr%5D%20AND%20%22Homo%20sapiens%22%5BOrganism%5D%20AND%20%28%22has%20ccds%22%5BProperties%5D%20AND%20alive%5Bprop%5D%29&cmd=DetailsSearch.
- ↑ Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2. https://books.google.com/books?id=dSwWBAAAQBAJ&pg=PA45.
- ↑ 3.0 3.1 Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
- ↑ 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. PMID 20441615.
- ↑ "Statistics & Downloads for chromosome 16". 2017-05-12. https://www.genenames.org/cgi-bin/statistics?c=16.
- ↑ "Chromosome 16: Chromosome summary - Homo sapiens". 2017-03-29. http://mar2017.archive.ensembl.org/Homo_sapiens/Location/Chromosome?r=16.
- ↑ "Human chromosome 16: entries, gene names and cross-references to MIM". 2018-02-28. https://www.uniprot.org/docs/humchr16.txt.
- ↑ "Search results - 16[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". 2017-05-19. https://www.ncbi.nlm.nih.gov/gene?term=16%5BCHR%5D%20AND%20%22Homo%20sapiens%22%5BOrganism%5D%20AND%20%28%22genetype%20protein%20coding%22%5BProperties%5D%20AND%20alive%5Bprop%5D%29&cmd=DetailsSearch.
- ↑ "Search results - 16[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". 2017-05-19. https://www.ncbi.nlm.nih.gov/gene?term=16%5BCHR%5D%20AND%20%22Homo%20sapiens%22%5BOrganism%5D%20AND%20%28%28%22genetype%20miscrna%22%5BProperties%5D%20OR%20%22genetype%20ncrna%22%5BProperties%5D%20OR%20%22genetype%20rrna%22%5BProperties%5D%20OR%20%22genetype%20trna%22%5BProperties%5D%20OR%20%22genetype%20scrna%22%5BProperties%5D%20OR%20%22genetype%20snrna%22%5BProperties%5D%20OR%20%22genetype%20snorna%22%5BProperties%5D%29%20NOT%20%22genetype%20protein%20coding%22%5BProperties%5D%20AND%20alive%5Bprop%5D%29&cmd=DetailsSearch.
- ↑ "Search results - 16[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". 2017-05-19. https://www.ncbi.nlm.nih.gov/gene?term=16%5BCHR%5D%20AND%20%22Homo%20sapiens%22%5BOrganism%5D%20AND%20%28%22genetype%20pseudo%22%5BProperties%5D%20AND%20alive%5Bprop%5D%29&cmd=DetailsSearch.
- ↑ Maillard, A M (25 November 2014). "The 16p11.2 locus modulates brain structures common to autism, schizophrenia and obesity". Molecular Psychiatry 20 (1): 140–147. doi:10.1038/mp.2014.145. PMID 25421402.
- ↑ Richter, M (21 February 2018). "Altered TAOK2 activity causes autism-related neurodevelopmental and cognitive abnormalities through RhoA signaling". Molecular Psychiatry 24 (9): 1329–1350. doi:10.1038/s41380-018-0025-5. PMID 29467497.
- ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
- ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
- ↑ 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. https://books.google.com/books?id=lGCLrh0DIwEC.
- ↑ 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. https://www.researchgate.net/publication/261304470.
- ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
- ↑ "p": Short arm; "q": Long arm.
- ↑ For cytogenetic banding nomenclature, see article locus.
- ↑ 20.0 20.1 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.
- ↑ 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.
- Gilbert F (1999). "Disease genes and chromosomes: disease maps of the human genome. Chromosome 16". Genet Test 3 (2): 243–54. doi:10.1089/gte.1999.3.243. PMID 10464676.
- Martin J et al. (2004). "The sequence and analysis of duplication-rich human chromosome 16". Nature 432 (7020): 988–94. doi:10.1038/nature03187. PMID 15616553. Bibcode: 2004Natur.432..988M. https://digital.library.unt.edu/ark:/67531/metadc788092/m2/1/high_res_d/842679.pdf.
- Miller, David T; Nasir, Ramzi; Sobeih, Magdi M; Shen, Yiping; Wu, Bai-Lin; Hanson, Ellen (2011-10-27). "16p11.2 Recurrent Microdeletion". 16p11.2 Microdeletion. University of Washington, Seattle. NBK11167. https://www.ncbi.nlm.nih.gov/books/NBK11167/. In Adam, M. P.; Everman, D. B.; Mirzaa, G. M.; Pagon, R. A.; Wallace, S. E.; Bean LJH; Gripp, K. W.; Amemiya, A. (1993). GeneReviews [Internet]. Seattle WA: University of Washington, Seattle. https://www.ncbi.nlm.nih.gov/books/n/gene/TOC/.
- http://omim.org/search?index=geneMap&search=16p13.3
External links
- National Institutes of Health. "Chromosome 16". Genetics Home Reference. http://ghr.nlm.nih.gov/chromosome=16.
- "Chromosome 16". http://web.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/chromo16.shtml.
 |  |
