Chromosome 15 (human)

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Chromosome 15 (human)
Human male karyotpe high resolution - Chromosome 15 cropped.png
Human chromosome 15 pair after G-banding.
One is from mother, one is from father.
Human male karyotpe high resolution - Chromosome 15.png
Chromosome 15 pair
in human male karyogram.
Features
Length (bp) 101,991,189 bp
(GRCh38)[1]
No. of genes 561 (CCDS)[2]
559 (HGNC)[3]
605 (Ensembl)[4]
629 (NCBI)[5]
Type Autosome
Centromere position Acrocentric[6]
(19.0 Mbp[7])
External map viewers
Ensembl Chromosome 15
Entrez Chromosome 15
NCBI Chromosome 15
UCSC Chromosome 15
Full DNA sequences
RefSeq NC_000015 (FASTA)
GenBank CM000677 (FASTA)

Chromosome 15 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 15 spans about 101 million base pairs (the building material of DNA) and represents between 3% and 3.5% of the total DNA in cells.

The human leukocyte antigen gene for β2-microglobulin is found at chromosome 15.

Genes[edit]

The following are some of the gene count estimates of human chromosome 15. 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).

When simply saying "number of genes", in most cases, it refers only to "number of protein-coding genes".

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS 561 - - [2] 2016-09-08
HGNC 559 328 433 [3] 2017-05-12
Ensembl 605 992 508 [4] 2017-03-29
NCBI 629 716 594 [5][8][9] 2017-05-19

The following are some of the genes located on chromosome 15:

  • AAGAB: alpha- and gamma-adaptin binding protein
  • ACSBG1: encoding enzyme Acyl-CoA Synthetase, Bubblegum Family, member 1
  • ARPP-19: encoding protein cAMP-regulated phosphoprotein 19
  • C15orf15/RSL24D1: encoding protein Probable ribosome biogenesis protein RLP24
  • C15orf29: encoding protein Uncharacterized protein C15orf29
  • CAPN3: Calpain 3 (limb-girdle muscular dystrophy type 2A)
  • CHP: Calcium binding protein P22
  • CHSY1: Chondroitin sulfate synthase 1
  • CLK3: CDC like kinase 3
  • CPEB1: Cytoplasmic polyladenylation element binding protein 1
  • FAH: fumarylacetoacetate hydrolase (fumarylacetoacetase)
  • FBN1: fibrillin 1 (Marfan syndrome)
  • GATM: Glycine aminotransferase, mitochondrial
  • GCHFR: GTP cyclohydrolase 1 feedback regulatory protein
  • GLCE: D-glucuronyl C5-epimerase
  • HEXA: hexosaminidase A (alpha polypeptide)(Tay-Sachs disease)
  • IVD: isovaleryl Coenzyme A dehydrogenase
  • MCPH4: microcephaly, primary autosomal recessive 4
  • OCA2: oculocutaneous albinism II (pink-eye dilution homolog, mouse)
  • RAD51: RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae)
  • STRC: stereocilin
  • UBE3A: ubiquitin protein ligase E3A (human papilloma virus E6-associated protein, Angelman syndrome)
  • PML: promyelocytic leukemia protein (involved in t(15,17) with RARalpha, predominant cause of acute promyelocytic leukemia.
  • SLC24A5: the gene responsible for at least 1/3 of the skin color differences between races, expressed in the brain and the nervous system
  • EYCL3 Eye color 3, BROWN & BLUE - location: 15q11-q15 (note eye color is a polygenic trait) [1]
  • EYCL2 Eye color 2, Determines the positioning of melanocytes on the iris (note eye color is a polygenic trait)
  • UNC13C: encoding protein unc-13 homolog C

Chromosomal conditions[edit]

The following conditions are caused by mutations in chromosome 15. Two of the conditions (Angelman syndrome and Prader-Willi syndrome) involve a loss of gene activity in the same part of chromosome 15, the 15q11.2-q13.1 region. This discovery provided the first evidence in humans that something beyond genes could determine how the genes are expressed.[10]

Angelman syndrome[edit]

The main characteristics of Angelman syndrome are severe mental retardation, ataxia, lack of speech, and excessively happy demeanor. Angelman syndrome results from a loss of gene activity in a specific part of chromosome 15, the 15q11-q13 region. This region contains a gene called UBE3A that, when mutated or absent, likely causes the characteristic features of this condition. People normally have two copies of the UBE3A gene, one from each parent. Both copies of this gene are active in many of the body's tissues. In the brain, however, only the copy inherited from a person's mother (the maternal copy) is active. If the maternal copy is lost because of a chromosomal change or a gene mutation, a person will have no working copies of the UBE3A gene in the brain.

In most cases (about 70%)[citation needed], people with Angelman syndrome have a deletion in the maternal copy of chromosome 15. This chromosomal change deletes the region of chromosome 15 that includes the UBE3A gene. Because the copy of the UBE3A gene inherited from a person's father (the paternal copy) is normally inactive in the brain, a deletion in the maternal chromosome 15 results in no active copies of the UBE3A gene in the brain.

In 3% to 7% of cases,[citation needed] Angelman syndrome occurs when a person has two copies of the paternal chromosome 15 instead of one copy from each parent. This phenomenon is called paternal uniparental disomy (UPD). People with paternal UPD for chromosome 15 have two copies of the UBE3A gene, but they are both inherited from the father and are therefore inactive in the brain.

About 10% of Angelman syndrome cases are caused by a mutation in the UBE3A gene, and another 3% result from a defect in the DNA region that controls the activation of the UBE3A gene and other genes on the maternal copy of chromosome 15. In a small percentage of cases, Angelman syndrome may be caused by a chromosomal rearrangement called a translocation or by a mutation in a gene other than UBE3A. These genetic changes can abnormally inactivate the UBE3A gene.

Angelman syndrome can be hereditary, as evidenced by one case where a patient became pregnant with a daughter who also had the condition.[11]

Prader-Willi syndrome[edit]

The main characteristics of this condition include polyphagia (extreme, insatiable appetite), mild to moderate developmental delay, hypogonadism resulting in delayed to no puberty, and hypotonia. Prader-Willi syndrome is caused by the loss of active genes in a specific part of chromosome 15, the 15q11-q13 region. People normally have two copies of this chromosome in each cell, one copy from each parent. Prader-Willi syndrome occurs when the paternal copy is partly or entirely missing.

In about 70% of cases,[citation needed] Prader-Willi syndrome occurs when the 15q11-q13 region of the paternal chromosome 15 is deleted. The genes in this region are normally active on the paternal copy of the chromosome and are inactive on the maternal copy. Therefore, a person with a deletion in the paternal chromosome 15 will have no active genes in this region.

In about 25% of cases, a person with Prader-Willi syndrome has two maternal copies of chromosome 15 in each cell instead of one copy from each parent. This phenomenon is called maternal uniparental disomy. Because some genes are normally active only on the paternal copy of this chromosome, a person with two maternal copies of chromosome 15 will have no active copies of these genes.

In a small percentage of cases, Prader-Willi syndrome is not caused by a chromosomal rearrangement called a trans location. Rarely, the condition is caused by an abnormality in the DNA region that controls the activity of genes on the paternal chromosome 15. Because patients almost always have difficulty reproducing, Prader-Willi syndrome is generally not hereditary.

Isodicentric chromosome 15[edit]

A specific chromosomal change called an isodicentric chromosome 15 (previously called[when?] an inverted duplication 15) can affect growth and development. The patient possesses an "extra" or "marker" chromosome. This small extra chromosome is made up of genetic material from chromosome 15 that has been abnormally duplicated (copied) and attached end-to-end. In some cases, the extra chromosome is very small and has no effect on a person's health. A larger isodicentric chromosome 15 can result in weak muscle tone (hypotonia), mental retardation, seizures, and behavioral problems.[citation needed] Signs and symptoms of autism (a developmental disorder that affects communication and social interaction) have also been associated with the presence of an isodicentric chromosome 15.

Other chromosomal conditions[edit]

Other changes in the number or structure of chromosome 15 can cause mental retardation, delayed growth and development, hypotonia, and characteristic facial features.[citation needed] These changes include an extra copy of part of chromosome 15 in each cell (partial trisomy 15) or a missing segment of the chromosome in each cell (partial monosomy 15). In some cases, several of the chromosome's DNA building blocks (nucleotides) are deleted or duplicated.

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

Cytogenetic band[edit]

G-banding ideograms of human chromosome 15
G-banding ideogram of human chromosome 15 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 15 in three different resolutions (400,[12] 550[13] and 850[7]). 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 15 in resolution 850 bphs[16]
Chr. Arm[17] Band[18] ISCN
start[19]
ISCN
stop[19]
Basepair
start
Basepair
stop
Stain[20] Density
15 p 13 0 270 1 4,200,000 gvar
15 p 12 270 631 4,200,001 9,700,000 stalk
15 p 11.2 631 1142 9,700,001 17,500,000 gvar
15 p 11.1 1142 1382 17,500,001 19,000,000 acen
15 q 11.1 1382 1487 19,000,001 20,500,000 acen
15 q 11.2 1487 1773 20,500,001 25,500,000 gneg
15 q 12 1773 1968 25,500,001 27,800,000 gpos 50
15 q 13.1 1968 2164 27,800,001 30,000,000 gneg
15 q 13.2 2164 2284 30,000,001 30,900,000 gpos 50
15 q 13.3 2284 2524 30,900,001 33,400,000 gneg
15 q 14 2524 2765 33,400,001 39,800,000 gpos 75
15 q 15.1 2765 2975 39,800,001 42,500,000 gneg
15 q 15.2 2975 3065 42,500,001 43,300,000 gpos 25
15 q 15.3 3065 3245 43,300,001 44,500,000 gneg
15 q 21.1 3245 3471 44,500,001 49,200,000 gpos 75
15 q 21.2 3471 3621 49,200,001 52,600,000 gneg
15 q 21.3 3621 3846 52,600,001 58,800,000 gpos 75
15 q 22.1 3846 3982 58,800,001 59,000,000 gneg
15 q 22.2 3982 4087 59,000,001 63,400,000 gpos 25
15 q 22.31 4087 4252 63,400,001 66,900,000 gneg
15 q 22.32 4252 4357 66,900,001 67,000,000 gpos 25
15 q 22.33 4357 4507 67,000,001 67,200,000 gneg
15 q 23 4507 4613 67,200,001 72,400,000 gpos 25
15 q 24.1 4613 4748 72,400,001 74,900,000 gneg
15 q 24.2 4748 4808 74,900,001 76,300,000 gpos 25
15 q 24.3 4808 4928 76,300,001 78,000,000 gneg
15 q 25.1 4928 5048 78,000,001 81,400,000 gpos 50
15 q 25.2 5048 5169 81,400,001 84,700,000 gneg
15 q 25.3 5169 5379 84,700,001 88,500,000 gpos 50
15 q 26.1 5379 5649 88,500,001 93,800,000 gneg
15 q 26.2 5649 5860 93,800,001 98,000,000 gpos 50
15 q 26.3 5860 6070 98,000,001 101,991,189 gneg

References[edit]

Specific references:

  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 - 15[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. ^ a b "Statistics & Downloads for chromosome 15". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19. 
  4. ^ a b "Chromosome 15: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19. 
  5. ^ a b "Search results - 15[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20. 
  6. ^ Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2. 
  7. ^ 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.
  8. ^ "Search results - 15[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. 
  9. ^ "Search results - 15[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20. 
  10. ^ "Teacher's Guide". Ghost in Your Genes (season 35). Nova (TV series). October 16, 2007. Retrieved 2009-09-26. The program...recounts how one scientist determined how the deletion of a key sequence of DNA on human chromosome 15 could lead to two different syndromes depending on whether the deletion originated from the mother or the father [and] explains that this was the first human evidence that something other than genes themselves could determine how genes are expressed. 
  11. ^ Lossie A, Driscoll D (1999). "Transmission of Angelman syndrome by an affected mother". Genet Med. 1 (6): 262–6. PMID 11258627. doi:10.1097/00125817-199909000-00004. 
  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. ^ 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.
  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.

General references:

External links[edit]

  • National Institutes of Health. "Chromosome 15". Genetics Home Reference. Retrieved 2017-05-06. 
  • "Chromosome 15". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.