Chromosome 5

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Chromosome 5
File:Human male karyotpe high resolution - Chromosome 5 cropped.png
Human chromosome 5 pair after G-banding.
One is from mother, one is from father.
File:Human male karyotpe high resolution - Chromosome 5.png
Chromosome 5 pair
in human male karyogram.
Features
Length (bp)181,538,259 bp
(GRCh38)[1]
No. of genes839 (CCDS)[2]
TypeAutosome
Centromere positionSubmetacentric[3]
(48.8 Mbp[4])
Complete gene lists
CCDSGene list
HGNCGene list
UniProtGene list
NCBIGene list
External map viewers
EnsemblChromosome 5
EntrezChromosome 5
NCBIChromosome 5
UCSCChromosome 5
Full DNA sequences
RefSeqNC_000005 (FASTA)
GenBankCM000667 (FASTA)

Chromosome 5 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 5 spans about 181 million base pairs (the building blocks of DNA) 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.[5]

Because chromosome 5 is responsible for many forms of growth and development (cell divisions) changes may cause cancers. One example would be acute myeloid leukemia (AML).[6]

Genes

Number of genes

The following are some of the gene count estimates of human chromosome 5. 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.[7]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS 839 — — [2] 2016-09-08
HGNC 790 355 574 [8] 2017-05-12
Ensembl 882 1,207 707 [9] 2017-03-29
UniProt 875 — — [10] 2018-02-28
NCBI 886 981 785 [11][12][13] 2017-05-19

Gene list

See also: Category:Genes on human chromosome 5.

The following is a partial list of genes on human chromosome 5. For complete list, see the link in the infobox on the right.

  • ABLIM3: encoding protein Actin-binding LIM protein 3
  • ADAMTS2: ADAM metallopeptidase with thrombospondin type 1 motif, 2
  • AGXT2: Alanine-glyoxylate aminotransferase 2
  • ANKRD31: encoding protein Ankyrin repeat domain 31
  • APBB3: encoding protein Amyloid beta A4 precursor protein-binding family B member 3
  • APC: adenomatosis polyposis coli
  • ARL15: encoding protein ADP-ribosylation factor-like 15
  • BRIX1: Ribosome biogenesis protein BRX1 homolog (also BXDC2)
  • C1QTNF3: Complement C1q tumor necrosis factor-related protein 3
  • C5orf3: encoding protein FAM114A2
  • C5orf13: Neuronal regeneration related protein
  • C5orf21/FAM172A: encoding protein UPF0528 protein FAM172A
  • C5orf42: Chromosome 5 open reading frame 42
  • CAST: Calpastatin
  • CPLX2: Complexin-2
  • CREBRF: encoding protein CREB3 regulatory factor
  • CXXC5: CXXC-type zing finger protein 5
  • DPYSL3: Dihydropyrimidinase-like protein 3
  • EGR1: early growth response protein 1
  • ERAP1: endoplasmic reticulum aminopeptidase 1 (previously called ARTS-1)
  • ERAP2: endoplasmic reticulum aminopeptidase 2
  • ESM1: Endothelial cell-specific molecule 1
  • DTDST: diastrophic dysplasia sulfate transporter
  • EIF4E1B: encoding protein Eukaryotic translation initiation factor 4E family member 1B
  • ERCC8: excision repair cross-complementing rodent repair deficiency, complementation group 8
  • FAM71B: encoding protein Family with sequence similarity 71 member B
  • FAM105B: encoding protein Family with sequence similarity 105, member B
  • FASTKD3: FAST kinase domain-containing protein 3
  • FBXL7: F-box/LRR-repeat protein 7
  • FCHSD1: FCH and double SH3 domain protein 1
  • FGF1: fibroblast growth factor 1 (acidic fibroblast growth factor)
  • FGFR4: fibroblast growth factor receptor 4
  • GM2A: GM2 ganglioside activator
  • GNPDA1: Glucosamine-6-phosphate isomerase 1
  • GPBP1: Vasculin
  • HEXB: hexosaminidase B (beta polypeptide)
  • HMGXB3: encoding protein HMG-box containing 3
  • IK: Protein Red
  • IRX1: Iroquois-class homeodomain protein (human)
  • LARP1: La-related protein 1
  • LMAN2: Lectin mannose binding 2
  • LNCR3 encoding protein Lung cancer susceptibility 3
  • LPCAT1: Lysophosphatidylcholine acyltransferase 1
  • LYSMD3: LysM and putative peptidoglycan-binding domain-containing protein 3
  • MAN2A1: Alpha-mannosidase 2
  • MASS1: monogenic, audiogenic seizure susceptibility 1 homolog (mouse)
  • MCC: Colorectal mutant cancer protein
  • MCCC2: methylcrotonoyl-Coenzyme A carboxylase 2 (beta)
  • MEF2C: Myocyte-specific enhancer factor 2C
  • MEF2C-AS1: encoding protein MEF2C antisense RNA 1
  • MGAT1: Mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase
  • MIR146A: microRNA 146a
  • MTRR: 5-methyltetrahydrofolate-homocysteine methyltransferase reductase
  • MZB1: Marginal zone B and B1 cell-specific protein
  • NIPBL: Nipped-B homolog (Drosophila)
  • NSA2 encoding protein TGF beta-inducible nuclear protein 1
  • NSD1: Transcription coregulator protein
  • NSUN2: NOP2/Sun domain family, member 2
  • NUDCD2: NudC domain-containing protein 2
  • P4HA2: Prolyl 4-hydroxylase subunit alpha-2
  • PCBD2: Pterin-4-alpha-carbinolamine dehydratase 2
  • PELO: Pelota homolog
  • PHAX: Phosphorylated adapter for RNA export
  • Pikachurin: Responsible for the functioning of the ribbon synapses; allows the eye to track moving objects
  • PFDN1: Prefoldin subunit 1
  • POLR3G: encoding protein Polymerase (RNA) III (DNA directed) polypeptide G (32kD)
  • PPIP5K2: Diphosphoinositol pentakisphosphate kinase 2
  • PRCC1: Proline-rich coiled coil 1
  • PURA: Purine-rich element-binding protein A
  • PWWP2A: encoding protein PWWP domain containing 2A
  • RANBP3L: encoding protein RAN binding protein 3-like
  • RMND5B: Required for meiotic nuclear division 5 homolog B
  • SFXN1: Sideroflexin-1
  • SKIV2L2: Ski2 like RNA helicase 2
  • SLC22A5: solute carrier family 22 (organic cation transporter), member 5
  • SLC26A2: solute carrier family 26 (sulfate transporter), member 2
  • SH3TC2: domain and tetratricopeptide repeats 2
  • SLCO4C1: Solute carrier organic anion transporter family member 4c1
  • SLU7: pre-mRNA-splicing factor SLU7
  • SMN1: survival motor neuron 1, telomeric
  • SMN2: survival motor neuron 2, centromeric
  • SNCAIP: synuclein, alpha interacting protein (synphilin)
  • SPEF2: Sperm flagellar protein 2
  • SPINK5: serine protease inhibitor Kazal-type 5 (LEKTI)
  • SPINK6: serine protease inhibitor Kazal-type 6
  • SPINK9: serine protease inhibitor Kazal-type 9 (LEKTI-2)
  • SPZ1: Spermatogenic leucine zipper protein 1
  • STC2: Stanniocalcin-2
  • TBCA: Tubulin-specific chaperone A
  • TCOF1: Treacher Collins-Franceschetti syndrome 1
  • TGFBI: keratoepithelin
  • THG1L: Probable tRNA(His) guanylyltransferase
  • TICAM2: TIR domain-containing adapter molecule 2
  • TNFAIP8: Tumor necrosis factor, alpha-induced protein 8
  • TTC37: Tetratricopeptide repeat domain 37
  • UPF0488: encodes G protein-coupled receptor protein signaling pathway
  • YIPF5: Yip1 domain family member 5
  • YTHDC2: encoding protein YTH domain containing 2
  • ZBED3: Zinc finger BED domain-containing protein 3
  • ZNF608: encoding protein Zinc finger protein 608

Diseases and disorders

The following are some of the diseases related to genes located on chromosome 5:

Chromosomal conditions

The following conditions are caused by changes in the structure or number of copies of chromosome 5:

  • Cri-du-chat syndrome is caused by a deletion of the end of the short (p) arm of chromosome 5. This chromosomal change is written as 5p-. The signs and symptoms of cri-du-chat syndrome are probably related to the loss of multiple genes in this region. Researchers have not identified all of these genes or determined how their loss leads to the features of the disorder. They have discovered, however, that a larger deletion tends to result in more severe mental retardation and developmental delays in people with cri-du-chat syndrome.[14][15][16]
Researchers have defined narrow regions of the short arm of chromosome 5 that are associated with particular features of cri-du-chat syndrome. A specific region designated 5p15.3 is associated with a cat-like cry, and a nearby region called 5p15.2 is associated with mental retardation, small head (microcephaly), and distinctive facial features.
  • Familial Adenomatous Polyposis is caused by a deletion of the APC tumor suppressor gene on the long (q) arm of chromosome 5. This chromosomal change results in thousands of colonic polyps which gives the patient a 100% risk of colon cancer if total colectomy is not done.
  • Chromosome 5q deletion syndrome is caused by the deletion of the q arm (long arm) of chromosome 5. This deletion has been linked to several blood related disorders including Myelodysplastic syndrome and Erythroblastopenia. This is a different condition than Cri-du-chat which was mentioned above.
  • Other changes in the number or structure of chromosome 5 can have a variety of effects, including delayed growth and development, distinctive facial features, birth defects, and other medical problems. Changes to chromosome 5 include an extra segment of the short (p) or long (q) arm of the chromosome in each cell (partial trisomy 5p or 5q), a missing segment of the long arm of the chromosome in each cell (partial monosomy 5q), and a circular structure called ring chromosome 5. A ring chromosome occurs when both ends of a broken chromosome are reunited.

Cytogenetic band

G-banding ideograms of human chromosome 5
File:Human chromosome 5 ideogram vertical.svg
G-banding ideogram of human chromosome 5 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).
File:Human chromosome 05 - 400 550 850 bphs.png
G-banding patterns of human chromosome 5 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 5 in resolution 850 bphs[21]
Chr. Arm[22] Band[23] ISCN
start[24] 		ISCN
stop[24] 		Basepair
start 		Basepair
stop 		Stain[25] Density
5 p 15.33 0 278 1 4,400,000 gneg
5 p 15.32 278 401 4,400,001 6,300,000 gpos 25
5 p 15.31 401 555 6,300,001 9,900,000 gneg
5 p 15.2 555 802 9,900,001 15,000,000 gpos 50
5 p 15.1 802 972 15,000,001 18,400,000 gneg
5 p 14.3 972 1234 18,400,001 23,300,000 gpos 100
5 p 14.2 1234 1281 23,300,001 24,600,000 gneg
5 p 14.1 1281 1543 24,600,001 28,900,000 gpos 100
5 p 13.3 1543 1836 28,900,001 33,800,000 gneg
5 p 13.2 1836 2068 33,800,001 38,400,000 gpos 25
5 p 13.1 2068 2253 38,400,001 42,500,000 gneg
5 p 12 2253 2407 42,500,001 46,100,000 gpos 50
5 p 11 2407 2592 46,100,001 48,800,000 acen
5 q 11.1 2592 2839 48,800,001 51,400,000 acen
5 q 11.2 2839 3271 51,400,001 59,600,000 gneg
5 q 12.1 3271 3518 59,600,001 63,600,000 gpos 75
5 q 12.2 3518 3580 63,600,001 63,900,000 gneg
5 q 12.3 3580 3765 63,900,001 67,400,000 gpos 75
5 q 13.1 3765 4012 67,400,001 69,100,000 gneg
5 q 13.2 4012 4197 69,100,001 74,000,000 gpos 50
5 q 13.3 4197 4397 74,000,001 77,600,000 gneg
5 q 14.1 4397 4752 77,600,001 82,100,000 gpos 50
5 q 14.2 4752 4907 82,100,001 83,500,000 gneg
5 q 14.3 4907 5400 83,500,001 93,000,000 gpos 100
5 q 15 5400 5678 93,000,001 98,900,000 gneg
5 q 21.1 5678 5879 98,900,001 103,400,000 gpos 100
5 q 21.2 5879 5987 103,400,001 105,100,000 gneg
5 q 21.3 5987 6295 105,100,001 110,200,000 gpos 100
5 q 22.1 6295 6419 110,200,001 112,200,000 gneg
5 q 22.2 6419 6527 112,200,001 113,800,000 gpos 50
5 q 22.3 6527 6666 113,800,001 115,900,000 gneg
5 q 23.1 6666 6943 115,900,001 122,100,000 gpos 100
5 q 23.2 6943 7267 122,100,001 127,900,000 gneg
5 q 23.3 7267 7468 127,900,001 131,200,000 gpos 100
5 q 31.1 7468 7807 131,200,001 136,900,000 gneg
5 q 31.2 7807 8008 136,900,001 140,100,000 gpos 25
5 q 31.3 8008 8316 140,100,001 145,100,000 gneg
5 q 32 8316 8625 145,100,001 150,400,000 gpos 75
5 q 33.1 8625 8887 150,400,001 153,300,000 gneg
5 q 33.2 8887 9072 153,300,001 156,300,000 gpos 50
5 q 33.3 9072 9304 156,300,001 160,500,000 gneg
5 q 34 9304 9690 160,500,001 169,000,000 gpos 100
5 q 35.1 9690 9952 169,000,001 173,300,000 gneg
5 q 35.2 9952 10183 173,300,001 177,100,000 gpos 25
5 q 35.3 10183 10600 177,100,001 181,538,259 gneg

References

  1. ↑ "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04.
  2. ↑ 2.0 2.1 "Search results - 5[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. ↑ 4.0 4.1 Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  5. ↑ Home - Homo sapiens
  6. ↑ "Chromosome 5". Genetics Home Reference. Lister Hill National Center for Biomedical Communications. U.S. National Library of Medicine. December 2014.
  7. ↑ 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.
  8. ↑ "Statistics & Downloads for chromosome 5". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.
  9. ↑ "Chromosome 5: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
  10. ↑ "Human chromosome 5: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.
  11. ↑ "Search results - 5[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  12. ↑ "Search results - 5[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.
  13. ↑ "Search results - 5[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  14. ↑ Cornish K, Bramble D; Bramble (2002). "Cri du chat syndrome: genotype-phenotype correlations and recommendations for clinical management". Dev Med Child Neurol. 44 (7): 494–7. doi:10.1017/S0012162201002419. PMID 12162388.
  15. ↑ Wu Q, Niebuhr E, Yang H, Hansen L (2005). "Determination of the 'critical region' for cat-like cry of Cri-du-chat syndrome and analysis of candidate genes by quantitative PCR". Eur J Hum Genet. 13 (4): 475–85. doi:10.1038/sj.ejhg.5201345. PMID 15657623.
  16. ↑ Zhang X, Snijders A, Segraves R, Zhang X, Niebuhr A, Albertson D, Yang H, Gray J, Niebuhr E, Bolund L, Pinkel D (2005). "High-resolution mapping of genotype-phenotype relationships in cri du chat syndrome using array comparative genomic hybridization". Am J Hum Genet. 76 (2): 312–26. doi:10.1086/427762. PMC 1196376. PMID 15635506.
  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. ↑ 24.0 24.1 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.
  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.

Further reading

External links

  • National Institutes of Health. "Chromosome 5". Genetics Home Reference. Retrieved 2017-05-06.
  • "Chromosome 5". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.
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