Chromosome 5

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]

Chromosome 5
Human chromosome 5 pair after G-banding.
One is from mother, one is from father.
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)

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
CCDS839—— [2] 2016-09-08
HGNC790355574 [8] 2017-05-12
Ensembl8821,207707 [9] 2017-03-29
UniProt875—— [10] 2018-02-28
NCBI886981785 [11][12][13] 2017-05-19

Gene list

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
  • C5orf45: Chromosome 5 open reading frame 45
  • CPLANE1: Ciliogenesis And Planar Polarity Effector 1
  • 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
  • FAF2: encoding protein Fas associated factor family member 2
  • FAM172A: encoding protein UPF0528 protein FAM172A
  • FAM105B: encoding protein Family with sequence similarity 105, member B
  • FAM114A2: encoding protein FAM114A2
  • FAM71B: encoding protein Family with sequence similarity 71 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
  • LYRM7: encoding protein LYR motif containing 7
  • 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)
  • MCEF: transcription factor AF4/FMR2 family, member 4
  • 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
  • MIR1271: encoding MicroRNA 1271
  • MIR146A: microRNA 146a
  • MTRR: 5-methyltetrahydrofolate-homocysteine methyltransferase reductase
  • MZB1: Marginal zone B and B1 cell-specific protein
  • NIPBL: Nipped-B homolog (Drosophila)
  • NREP: Neuronal regeneration related protein
  • NSA2 encoding protein TGF beta-inducible nuclear protein 1
  • NSD1: Transcription coregulator protein
  • NSUN2: NOP2/Sun domain family, member 2
  • NR2F1: Nuclear hormone receptor
  • NUDCD2: NudC domain-containing protein 2
  • P4HA2: Prolyl 4-hydroxylase subunit alpha-2
  • PCBD2: Pterin-4-alpha-carbinolamine dehydratase 2
  • PELO: Pelota homolog
  • PGGT1B: encoding protein Protein geranylgeranyltransferase type I subunit beta
  • 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
  • PRR16: encoding protein Proline-rich protein 16
  • 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
  • TMEM171: encoding protein Transmembrane protein 171
  • 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
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).
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
5p 15.33027814,400,000 gneg
5p 15.322784014,400,0016,300,000 gpos25
5p 15.314015556,300,0019,900,000 gneg
5p 15.25558029,900,00115,000,000 gpos50
5p 15.180297215,000,00118,400,000 gneg
5p 14.3972123418,400,00123,300,000 gpos100
5p 14.21234128123,300,00124,600,000 gneg
5p 14.11281154324,600,00128,900,000 gpos100
5p 13.31543183628,900,00133,800,000 gneg
5p 13.21836206833,800,00138,400,000 gpos25
5p 13.12068225338,400,00142,500,000 gneg
5p 122253240742,500,00146,100,000 gpos50
5p 112407259246,100,00148,800,000 acen
5q 11.12592283948,800,00151,400,000 acen
5q 11.22839327151,400,00159,600,000 gneg
5q 12.13271351859,600,00163,600,000 gpos75
5q 12.23518358063,600,00163,900,000 gneg
5q 12.33580376563,900,00167,400,000 gpos75
5q 13.13765401267,400,00169,100,000 gneg
5q 13.24012419769,100,00174,000,000 gpos50
5q 13.34197439774,000,00177,600,000 gneg
5q 14.14397475277,600,00182,100,000 gpos50
5q 14.24752490782,100,00183,500,000 gneg
5q 14.34907540083,500,00193,000,000 gpos100
5q 155400567893,000,00198,900,000 gneg
5q 21.15678587998,900,001103,400,000 gpos100
5q 21.258795987103,400,001105,100,000 gneg
5q 21.359876295105,100,001110,200,000 gpos100
5q 22.162956419110,200,001112,200,000 gneg
5q 22.264196527112,200,001113,800,000 gpos50
5q 22.365276666113,800,001115,900,000 gneg
5q 23.166666943115,900,001122,100,000 gpos100
5q 23.269437267122,100,001127,900,000 gneg
5q 23.372677468127,900,001131,200,000 gpos100
5q 31.174687807131,200,001136,900,000 gneg
5q 31.278078008136,900,001140,100,000 gpos25
5q 31.380088316140,100,001145,100,000 gneg
5q 3283168625145,100,001150,400,000 gpos75
5q 33.186258887150,400,001153,300,000 gneg
5q 33.288879072153,300,001156,300,000 gpos50
5q 33.390729304156,300,001160,500,000 gneg
5q 3493049690160,500,001169,000,000 gpos100
5q 35.196909952169,000,001173,300,000 gneg
5q 35.2995210183173,300,001177,100,000 gpos25
5q 35.31018310600177,100,001181,538,259 gneg

References
  1. "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04.
  2. "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. 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". Archived from the original on 2015-04-02. Retrieved 2007-02-07.
  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". In Computer Science and Software Engineering (JCSSE), 2012 International Joint Conference on: 276–282. doi:10.1109/JCSSE.2012.6261965. ISBN 978-1-4673-1921-8. S2CID 16666470.
  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. 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
Wikimedia Commons has media related to Human chromosome 5.
  • National Institutes of Health. "Chromosome 5". Genetics Home Reference. Archived from the original on October 14, 2004. Retrieved 2017-05-06.
  • "Chromosome 5". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.
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