Chromosome 5
Human chromosome
Chromosome 5 is one of the 23 pairs of chromosomes in humans . People normally have two copies of this chromosome. Chromosome 5 spans about 182 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.[ 4]
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).[ 5]
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.[ 6]
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
C5orf47 : encoding protein Chromosome 5 open reading frame 47
C5orf49 : encoding protein Chromosome 5 open reading frame 49
CAST : Calpastatin
CDO1 : encoding protein Cysteine dioxygenase type 1
CPLANE1 : Ciliogenesis And Planar Polarity Effector 1
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
MINAR2 : encoding protein Kiaa1024 like
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
NSG2 : encoding protein Hmp19 protein
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
RASGEF1C : encoding protein RasGEF domain family member 1C
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
TSSK1B : encoding protein Testis specific serine kinase 1b
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.[ 13] [ 14] [ 15]
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 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,
[ 16] 550
[ 17] and 850
[ 3] ). Band length in this diagram is based on the ideograms from ISCN (2013).
[ 18] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the
mitotic process .
[ 19]
G-bands of human chromosome 5 in resolution 850 bphs[ 20]
Chr.
Arm[ 21]
Band[ 22]
ISCN start[ 23]
ISCN stop[ 23]
Basepair start
Basepair stop
Stain[ 24]
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
^ a b "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 .
^ Tom Strachan, Andrew Read (2 April 2010). Human Molecular Genetics . Garland Science. p. 45. ISBN 978-1-136-84407-2 .
^ 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.
^ "Home - Homo sapiens" . Archived from the original on 2015-04-02. Retrieved 2007-02-07 .
^ "Chromosome 5" . Genetics Home Reference . Lister Hill National Center for Biomedical Communications. U.S. National Library of Medicine. December 2014.
^ 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 .
^ "Statistics & Downloads for chromosome 5" . HUGO Gene Nomenclature Committee . 2017-05-12. Archived from the original on 2017-06-29. Retrieved 2017-05-19 .
^ "Chromosome 5: Chromosome summary - Homo sapiens" . Ensembl Release 88 . 2017-03-29. Retrieved 2017-05-19 .
^ "Human chromosome 5: entries, gene names and cross-references to MIM" . UniProt . 2018-02-28. Retrieved 2018-03-16 .
^ "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 .
^ "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 .
^ "Search results - 5[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene" . NCBI . 2017-05-19. Retrieved 2017-05-20 .
^
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 .
^ 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 .
^
^ 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 .
^ 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 . S2CID 16666470 .
^ 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 .
^ 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 .
^ 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
Mainardi PC, Perfumo C, Cali A, Coucourde G, Pastore G, Cavani S, et al. (2001). "Clinical and molecular characterisation of 80 patients with 5p deletion: genotype–phenotype correlation" . J Med Genet . 38 (3): 151–8. doi :10.1136/jmg.38.3.151 . PMC 1734829 . PMID 11238681 .
Schafer IA, Robin NH, Posch JJ, Clark BA, Izumo S, Schwartz S (2001). "Distal 5q deletion syndrome: phenotypic correlations". Am J Med Genet . 103 (1): 63–8. doi :10.1002/ajmg.1513 . PMID 11562936 .
Schmutz J, Martin J, Terry A, Couronne O, Grimwood J, Lowry S, et al. (September 2004). "The DNA sequence and comparative analysis of human chromosome 5" . Nature . 431 (7006): 268–74. Bibcode :2004Natur.431..268S . doi :10.1038/nature02919 . PMID 15372022 .
Siddiqi R, Gilbert F (2003). "Chromosome 5". Genet Test . 7 (2): 169–87. doi :10.1089/109065703322146902 . PMID 12885343 .
External links
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 .
Basic concepts Types Processes and evolution Structures
See also