Chromosome 17 (human)

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Chromosome 17 (human)
Human male karyotpe high resolution - Chromosome 17 cropped.png
Human chromosome 17 pair after G-banding.
One is from mother, one is from father.
Human male karyotpe high resolution - Chromosome 17.png
Chromosome 17 pair
in human male karyogram.
Features
Length (bp) 83,257,441 bp
(GRCh38)[1]
No. of genes 1,124 (CCDS)[2]
Type Autosome
Centromere position Submetacentric[3]
(25.1 Mbp[4])
External map viewers
Ensembl Chromosome 17
Entrez Chromosome 17
NCBI Chromosome 17
UCSC Chromosome 17
Full DNA sequences
RefSeq NC_000017 (FASTA)
GenBank CM000679 (FASTA)

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 83 million base pairs (the building material of DNA) and represents between 2.5 and 3% of the total DNA in cells.

Chromosome 17 contains the Homeobox B gene cluster.

Genes[edit]

The following are some of the gene count estimates of human chromosome 17. 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]

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 1,124 - - [2] 2016-09-08
HGNC 1,132 325 458 [6] 2017-05-12
Ensembl 1,184 1,199 535 [7] 2017-03-29
NCBI 1,199 757 566 [8][9][10] 2017-05-19

The following are some of the genes and their corresponding Cytogenetic location on chromosome 17:

q-arm[edit]

  • CCDC55: Coiled-coil domain-containing protein 55 (17q11.2)
  • FLOT2: flotillin 2 (17q11.2)
  • NF1: neurofibromin 1 (neurofibromatosis, von Recklinghausen disease, Watson disease) (17q11.2)
  • SLC6A4: Serotonin transporter linked to Obsessive Compulsive Disorder (OCD) [11] (17q11.2)
  • CCL4L1: C-C motif chemokine ligand 4 like 1 (17q12)
  • DDX52: DExD-box helicase 52 (17q12)
  • ERBB2 loca leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian) (17q12)
  • GRB7: Growth factor Receptor-Bound protein 7 (17q12)
  • BRCA1: breast cancer 1, early onset (17q21)
  • GFAP: glial fibrillary acidic protein (17q21)
  • RARA or RAR-alpha: Retinoic acid receptor Alpha (involved in t(15,17) with PML) (17q21)
  • MAPT gene coding for encoding tau protein (17q21.1)
  • NAGLU: N-acetyl glucosaminidase, Sanfilippo B syndrome (17q21.2)
  • SLC4A1: Band 3 anion transporter protein. Solute carrier family 4, member 1 (17q21.31)
  • CBX1: chromobox homolog 1 (17q21.32)
  • COL1A1: collagen, type I, alpha 1 (17q21.33)
  • LUC7L3: LUC7 like 3 pre-mRNA splicing factor (17q21.33)
  • NOG: Noggin protein (17q22)
  • RPS6KB1 or S6K: Ribosomal protein S6-kinase (17q23.1)
  • FTSJ3: FtsJ homolog 3 (17q23.3)
  • SCN4A: Voltage-Gated Sodium Channel Subunit Alpha Nav1.4 (17q23.3)
  • GALK1: galactokinase 1 (17q24)
  • KCNJ2: potassium inwardly-rectifying channel, subfamily J, member 2 (17q24.3)
  • ACTG1: actin, gamma 1 (17q25)
  • CDC42EP4: CDC42 effector protein 4 (17q25.1)
  • USH1G: Usher syndrome 1G (autosomal recessive) (17q25.1)
  • CANT1: Calcium-activated nucleotidase 1 (17q25.3)
  • CHMP6: Charged multivesicular body protein 6 (17q25.3)
  • ENPP7: ectonucleotide pyrophosphatase/phosphodiesterase 7 (17q25.3)
  • RHBDF2: Rhomboid family member 2 (17q25.3)
  • TMC6 and TMC8: Transmembrane channel-like 6 and 8 (epidermodysplasia verruciformis) (17q25.3)

p-arm[edit]

  • FLCN: folliculin (17p11.2)
  • MYO15A: myosin XVA (17p11.2)
  • RAI1: retinoic acid induced 1 (17p11.2)
  • PMP22: peripheral myelin protein 22 (17p12)
  • CTNS: cystinosin, the lysosomal cystine transporter (17p13)
  • USP6: Ubiquitin carboxyl-terminal hydrolase 6 linked to Aneurysmal bone cyst (17p13)
  • ACADVL: acyl-coenzyme A dehydrogenase, very long chain (17p13.1)
  • SHBG: Sex hormone binding globulin (17p13.1)
  • TP53: tumor suppressor protein p53 (Li-Fraumeni syndrome), tumor suppressor gene (17p13.1)
  • ASPA: aspartoacylase (Canavan disease) (17p13.3)
  • GLOD4: glyoxalase domain containing 4 (17p13.3)

Diseases and disorders[edit]

Inactivating PH mutation in either the EVER1 or EVER2 genes, which are located adjacent to one another on chromosome 17 causes Epidermodysplasia verruciformis.

The following diseases are related to genes on chromosome 17:

Cytogenetic band[edit]

G-banding ideograms of human chromosome 17
G-banding ideogram of human chromosome 17 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 17 in three different resolutions (400,[12] 550[13] and 850[4]). 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 17 in resolution 850 bphs[16]
Chr. Arm[17] Band[18] ISCN
start[19]
ISCN
stop[19]
Basepair
start
Basepair
stop
Stain[20] Density
17 p 13.3 0 385 1 3,400,000 gneg
17 p 13.2 385 550 3,400,001 6,500,000 gpos 50
17 p 13.1 550 784 6,500,001 10,800,000 gneg
17 p 12 784 990 10,800,001 16,100,000 gpos 75
17 p 11.2 990 1499 16,100,001 22,700,000 gneg
17 p 11.1 1499 1664 22,700,001 25,100,000 acen
17 q 11.1 1664 1815 25,100,001 27,400,000 acen
17 q 11.2 1815 2104 27,400,001 33,500,000 gneg
17 q 12 2104 2255 33,500,001 39,800,000 gpos 50
17 q 21.1 2255 2461 39,800,001 40,200,000 gneg
17 q 21.2 2461 2599 40,200,001 42,800,000 gpos 25
17 q 21.31 2599 2874 42,800,001 46,800,000 gneg
17 q 21.32 2874 3025 46,800,001 49,300,000 gpos 25
17 q 21.33 3025 3176 49,300,001 52,100,000 gneg
17 q 22 3176 3383 52,100,001 59,500,000 gpos 75
17 q 23.1 3383 3451 59,500,001 60,200,000 gneg
17 q 23.2 3451 3658 60,200,001 63,100,000 gpos 75
17 q 23.3 3658 3781 63,100,001 64,600,000 gneg
17 q 24.1 3781 3850 64,600,001 66,200,000 gpos 50
17 q 24.2 3850 4001 66,200,001 69,100,000 gneg
17 q 24.3 4001 4166 69,100,001 72,900,000 gpos 75
17 q 25.1 4166 4400 72,900,001 76,800,000 gneg
17 q 25.2 4400 4510 76,800,001 77,200,000 gpos 25
17 q 25.3 4510 4950 77,200,001 83,257,441 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 - 17[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. PMC 2898077Freely accessible. PMID 20441615. doi:10.1186/gb-2010-11-5-206. 
  6. ^ "Statistics & Downloads for chromosome 17". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19. 
  7. ^ "Chromosome 17: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19. 
  8. ^ "Search results - 17[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20. 
  9. ^ "Search results - 9[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. 
  10. ^ "Search results - 17[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20. 
  11. ^ "Obsessive Compulsive Disorder". An Online Catalog of Human Genes and Genetic Disorders. 
  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.

External links[edit]

  • National Institutes of Health. "Chromosome 17". Genetics Home Reference. Retrieved 2017-05-06. 
  • "Chromosome 17". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.