Chromosome 4




































































Chromosome 4

Human male karyotpe high resolution - Chromosome 4 cropped.png
Human chromosome 4 pair after G-banding. One is from mother, one is from father.


Human male karyotpe high resolution - Chromosome 4.png
Chromosome 4 pair
in human male karyogram.

Features
Length (bp) 190,214,555 bp
(GRCh38)[1]

No. of genes
727 (CCDS)[2]
Type Autosome
Centromere position
Submetacentric[3]
(50.0 Mbp[4])
Complete gene lists
CCDS Gene list
HGNC Gene list
UniProt Gene list
NCBI Gene list
External map viewers
Ensembl Chromosome 4
Entrez Chromosome 4
NCBI Chromosome 4
UCSC Chromosome 4
Full DNA sequences
RefSeq NC_000004 (FASTA)
GenBank CM000666 (FASTA)

Chromosome 4 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 4 spans more than 186 million base pairs (the building material of DNA) and represents between 6 and 6.5 percent of the total DNA in cells.




Contents






  • 1 Genomics


  • 2 Genes


    • 2.1 Number of genes


    • 2.2 Gene list




  • 3 Diseases and disorders


  • 4 Cytogenetic band


  • 5 References


  • 6 Further reading


  • 7 External links





Genomics


The chromosome is ~191 megabases in length. In a 2012 paper, seven hundred and fifty seven protein-encoding genes were identified on this chromosome.[5] Two-hundred and eleven (27.9%) of these coding sequences did not have any experimental evidence at the protein level, in 2012. Two-hundred and seventy-one appear to be membrane proteins. Fifty-four have been classified as cancer-associated proteins.



Genes



Number of genes


The following are some of the gene count estimates of human chromosome 4. 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]



















































Estimated by

Protein-coding genes

Non-coding RNA genes

Pseudogenes
Source
Release date
CCDS 727
[2] 2016-09-08
HGNC 731 277 633
[7] 2017-05-12
Ensembl 746 993 727
[8] 2017-03-29
UniProt 765
[9] 2018-02-28
NCBI 769 934 819

[10][11][12]
2017-05-19


Gene list



The following is a partial list of genes on human chromosome 4. For complete list, see the link in the infobox on the right.





  • AASDH: aminoadipate-semialdehyde dehydrogenase


  • ACVR1: activin-like kinase 2 (ALK-2)


  • ACOX3: encoding enzyme Peroxisomal acyl-coenzyme A oxidase 3


  • AGPAT9: encoding enzyme Glycerol-3-phosphate acyltransferase 3 a.k.a. 1-acylglycerol-3-phosphate O-acyltransferase 9


  • ANK2: ankyrin 2, neuronal


  • APBB2: encoding protein Amyloid beta A4 precursor protein-binding family B member 2


  • ART3: encoding enzyme Ecto-ADP-ribosyltransferase 3


  • ASAHL: encoding enzyme N-acylethanolamine-hydrolyzing acid amidase


  • C4orf18: encoding protein Protein ENED


  • C4orf21: zinc-finger GRF-type containing 1


  • CCDC109B: Coiled-coil domain containing 109B


  • Complement Factor I: Complement Factor I


  • CRMP1: Collapsin response mediator protein 1, a member of CRMP family


  • CSN2: Beta-casein


  • CXCL1: chemokine (C-X-C motif) ligand 1, scyb1


  • CXCL2: chemokine (C-X-C motif) ligand 2, scyb2


  • CXCL3: chemokine (C-X-C motif) ligand 3, scyb3


  • CXCL4: chemokine (C-X-C motif) ligand 4, Platelet factor-4, PF-4, scyb4


  • CXCL5: chemokine (C-X-C motif) ligand 5, scyb5


  • CXCL6: chemokine (C-X-C motif) ligand 6, scyb6


  • CXCL7: chemokine (C-X-C motif) ligand 7, PPBP, scyb7


  • CXCL8: chemokine (C-X-C motif) ligand 8, interleukin 8 (IL-8), scyb8


  • CXCL9: chemokine (C-X-C motif) ligand 9, scyb9


  • CXCL10: chemokine (C-X-C motif) ligand 10, scyb10


  • CXCL11: chemokine (C-X-C motif) ligand 11, scyb11


  • CXCL13: chemokine (C-X-C motif) ligand 13, scyb13


  • CYTL1: Cytokine-like 1


  • DCUN1D4: Defective in cullin neddylation 1 domain containing 4


  • DHX15: DEAH-box helicase 15


  • DKK2: Dickkopf-related protein 2


  • DUX4: Thought to be inactive but 2010 research shows a key role in FSHD[13]


  • ELMOD2: Elmo domain-containing 2


  • EMCN: Endomucin


  • EVC: Ellis van Creveld syndrome


  • EVC2: Ellis van Creveld syndrome 2 (limbin)


  • Factor XI: Mutations cause Haemophilia C


  • FAM47E-STBD1: FAM47E-STBD1 readthrough


  • FAM114A1: Family with sequence similarity 114, member A1


  • FAM149A: Family with sequence similarity 149, member A


  • FAM193A: Family with sequence similarity 193, member A


  • FAM221B: Family with sequence similarity 221, member B


  • FGF2: Fibroblast growth factor 2 (basic fibroblast growth factor)


  • FGFR3: fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism, bladder cancer)


  • FGFRL1: fibroblast growth factor receptor-like 1


  • FRG1: FSHD region gene 1


  • GUF1: GUF1 homolog, GTPase


  • HCL2 (also called RHA or RHC): related to red hair


  • HTT (Huntingtin): huntingtin protein (Huntington's disease)


  • IGJ: linker protein for immunoglobulin alpha and mu polypeptides


  • INTS12: Integrator complex subunit 12


  • KDR: Kinase insert domain receptor (Vascular endothelial growth factor receptor 2)


  • KIAA1530: UV stimulated scaffold protein A


  • LCORL: Ligand dependent nuclear receptor corepressor like


  • LDB2: LIM domain-binding protein 2


  • LGI2: Leucine-rich repeat LGI family member 2


  • LOC100505912 encoding protein Uncharacterized LOC100505912


  • LSM6: U6 snRNA-associated Sm-like protein


  • LYAR: Cell growth-regulating nucleolar protein


  • MAB21L2: Mab-21-like 2


  • Marcksl1: encoding protein MARCKS-like 1


  • MAML3: Mastermind-like 3


  • MFSD7: encoding protein Major facilitator superfamily domain containing 7


  • MIR1269A: microRNA 1269a


  • MLF1IP: Centromere protein U


  • MMAA: methylmalonic aciduria (cobalamin deficiency) cblA type


  • MTHFD2L: NAD-dependent methylenetetrahydrofolate dehydrogenase 2-like protein


  • MYL5: Myosin light chain 5


  • NOA1: encoding protein Nitric oxide associated 1


  • NUDT6: nudix hydrolase 6


  • NUDT9: nudix hydrolase 9


  • OTUD4: OTU domain-containing protein 4


  • PABPC4L: encoding protein Poly(A) binding protein, cytoplasmic 4-like


  • PARM1: Prostate androgen-regulated mucin-like protein 1


  • PHOX2B: codes for a homeodomain transcription factor


  • PI4K2B: Phosphatidylinositol 4-kinase type 2-beta


  • PKD2: polycystic kidney disease 2 (autosomal dominant)


  • PLK4: Serine/threonine-protein kinase PLK4


  • PSAPL1: encoding protein Prosaposin-like 1 (gene/pseudogene)


  • QDPR: quinoid dihydropteridine reductase


  • RBM47: RNA binding motif protein 47


  • SDAD1: protein SDA1 homolog


  • SEC24B: Sec24 homolog B


  • SEC24D: Sec24 homolog D


  • SEPT11: Septin-11


  • SLC9B2: solute carrier family 9 member B2


  • SLC10A4: solute carrier family 10 member 4


  • SMIM20: encoding protein Small integral membrane protein 20


  • SNCA: synuclein, alpha (non A4 component of amyloid precursor)


  • SPATA5: Spermatogenesis-associated protein 5


  • STATH: gene with protein product


  • TACC3: Transforming acidic coiled-coil-containing protein 3


  • TENM3: Teneurin transmembrane protein 3


  • THAP6: THAP domain-containing protein 6


  • TMPRSS11D: Transmembrane protease, serine 11D


  • TNIP2: TNFAIP3-interaction protein 2


  • UCHL1: ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase)


  • UGT8: UDP glycosyltransferase 8


  • UNC5C: netrin receptor UNC5C


  • USP38: encoding protein Ubiquitin specific peptidase 38


  • USP53: ubiquitin specific peptidase 53


  • UTP3: small subunit processome component


  • WFS1: Wolfram syndrome 1 (wolframin)


  • ZNF621: encoding protein Zinc finger protein 621




Diseases and disorders


The following are some of the diseases related to genes located on chromosome 4:




  • Achondroplasia


  • Autosomal dominant polycystic kidney disease (PKD-2)

  • Bladder cancer

  • Crouzonodermoskeletal syndrome

  • Chronic lymphocytic leukemia

  • Congenital central hypoventilation syndrome

  • Ellis-van Creveld syndrome

  • Facioscapulohumeral muscular dystrophy


  • Fibrodysplasia ossificans progressiva (FOP)

  • Haemophilia C

  • Huntington's disease

  • Hemolytic uremic syndrome

  • Hereditary benign intraepithelial dyskeratosis

  • Hirschprung's disease

  • Hypochondroplasia

  • Methylmalonic acidemia

  • Mucopolysaccharidosis type I

  • Muenke syndrome

  • Nonsyndromic deafness

  • Nonsyndromic deafness, autosomal dominant

  • Parkinson's disease

  • Polycystic kidney disease

  • Romano-Ward syndrome

  • SADDAN

  • Tetrahydrobiopterin deficiency


  • Thanatophoric dysplasia

    • Type 1

    • Type 2



  • Wolfram syndrome

  • Wolf–Hirschhorn syndrome




Cytogenetic band


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G-banding ideograms of human chromosome 4



G-banding ideogram of human chromosome 4 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 4 in three different resolutions (400,[14] 550[15] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[16] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[17]

























































































































































































































































































































































































































































































































































G-bands of human chromosome 4 in resolution 850 bphs[18]
Chr.
Arm[19]
Band[20]
ISCN
start[21]
ISCN
stop[21]
Basepair
start
Basepair
stop
Stain[22]
Density
4 p
16.3 0 220 1 4500000
gneg
4 p
16.2 220 389 7006450000100000000♠4,500,001
7006600000000000000♠6,000,000
gpos 25
4 p
16.1 389 779 7006600000100000000♠6,000,001
7007113000000000000♠11,300,000
gneg
4 p
15.33 779 1066 7007113000010000000♠11,300,001
7007150000000000000♠15,000,000
gpos 50
4 p
15.32 1066 1286 7007150000010000000♠15,000,001
7007177000000000000♠17,700,000
gneg
4 p
15.31 1286 1557 7007177000010000000♠17,700,001
7007213000000000000♠21,300,000
gpos 75
4 p
15.2 1557 1811 7007213000010000000♠21,300,001
7007277000000000000♠27,700,000
gneg
4 p
15.1 1811 2166 7007277000010000000♠27,700,001
7007358000000000000♠35,800,000
gpos 100
4 p
14 2166 2505 7007358000010000000♠35,800,001
7007412000000000000♠41,200,000
gneg
4 p
13 2505 2742 7007412000010000000♠41,200,001
7007446000000000000♠44,600,000
gpos 50
4 p
12 2742 2877 7007446000010000000♠44,600,001
7007482000000000000♠48,200,000
gneg
4 p
11 2877 3046 7007482000010000000♠48,200,001
7007500000000000000♠50,000,000
acen
4 q
11 3046 3249 7007500000010000000♠50,000,001
7007518000000000000♠51,800,000
acen
4 q
12 3249 3571 7007518000010000000♠51,800,001
7007585000000000000♠58,500,000
gneg
4 q
13.1 3571 3910 7007585000010000000♠58,500,001
7007655000000000000♠65,500,000
gpos 100
4 q
13.2 3910 4062 7007655000010000000♠65,500,001
7007694000000000000♠69,400,000
gneg
4 q
13.3 4062 4333 7007694000010000000♠69,400,001
7007753000000000000♠75,300,000
gpos 75
4 q
21.1 4333 4502 7007753000010000000♠75,300,001
7007780000000000000♠78,000,000
gneg
4 q
21.21 4502 4671 7007780000010000000♠78,000,001
7007815000000000000♠81,500,000
gpos 50
4 q
21.22 4671 4739 7007815000010000000♠81,500,001
7007832000000000000♠83,200,000
gneg
4 q
21.23 4739 4874 7007832000010000000♠83,200,001
7007860000000000000♠86,000,000
gpos 25
4 q
21.3 4874 5145 7007860000010000000♠86,000,001
7007871000000000000♠87,100,000
gneg
4 q
22.1 5145 5517 7007871000010000000♠87,100,001
7007928000000000000♠92,800,000
gpos 75
4 q
22.2 5517 5636 7007928000010000000♠92,800,001
7007942000000000000♠94,200,000
gneg
4 q
22.3 5636 5890 7007942000010000000♠94,200,001
7007979000000000000♠97,900,000
gpos 75
4 q
23 5890 6059 7007979000010000000♠97,900,001
7008100100000000000♠100,100,000
gneg
4 q
24 6059 6347 7008100100001000000♠100,100,001
7008106700000000000♠106,700,000
gpos 50
4 q
25 6347 6685 7008106700001000000♠106,700,001
7008113200000000000♠113,200,000
gneg
4 q
26 6685 7040 7008113200001000000♠113,200,001
7008119900000000000♠119,900,000
gpos 75
4 q
27 7040 7277 7008119900001000000♠119,900,001
7008122800000000000♠122,800,000
gneg
4 q
28.1 7277 7565 7008122800001000000♠122,800,001
7008127900000000000♠127,900,000
gpos 50
4 q
28.2 7565 7734 7008127900001000000♠127,900,001
7008130100000000000♠130,100,000
gneg
4 q
28.3 7734 8259 7008130100001000000♠130,100,001
7008138500000000000♠138,500,000
gpos 100
4 q
31.1 8259 8581 7008138500001000000♠138,500,001
7008140600000000000♠140,600,000
gneg
4 q
31.21 8581 8733 7008140600001000000♠140,600,001
7008145900000000000♠145,900,000
gpos 25
4 q
31.22 8733 8851 7008145900001000000♠145,900,001
7008147500000000000♠147,500,000
gneg
4 q
31.23 8851 9004 7008147500001000000♠147,500,001
7008150200000000000♠150,200,000
gpos 25
4 q
31.3 9004 9207 7008150200001000000♠150,200,001
7008154600000000000♠154,600,000
gneg
4 q
32.1 9207 9545 7008154600001000000♠154,600,001
7008160800000000000♠160,800,000
gpos 100
4 q
32.2 9545 9681 7008160800001000000♠160,800,001
7008163600000000000♠163,600,000
gneg
4 q
32.3 9681 9985 7008163600001000000♠163,600,001
7008169200000000000♠169,200,000
gpos 100
4 q
33 9985 10087 7008169200001000000♠169,200,001
7008171000000000000♠171,000,000
gneg
4 q
34.1 10087 10341 7008171000001000000♠171,000,001
7008175400000000000♠175,400,000
gpos 75
4 q
34.2 10341 10408 7008175400001000000♠175,400,001
7008176600000000000♠176,600,000
gneg
4 q
34.3 10408 10628 7008176600001000000♠176,600,001
7008182300000000000♠182,300,000
gpos 100
4 q
35.1 10628 10967 7008182300001000000♠182,300,001
7008186200000000000♠186,200,000
gneg
4 q
35.2 10967 11170 7008186200001000000♠186,200,001
7008190214555000000♠190,214,555
gpos 25


References





  1. ^ "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04..mw-parser-output cite.citation{font-style:inherit}.mw-parser-output .citation q{quotes:"""""""'""'"}.mw-parser-output .citation .cs1-lock-free a{background:url("//upload.wikimedia.org/wikipedia/commons/thumb/6/65/Lock-green.svg/9px-Lock-green.svg.png")no-repeat;background-position:right .1em center}.mw-parser-output .citation .cs1-lock-limited a,.mw-parser-output .citation .cs1-lock-registration a{background:url("//upload.wikimedia.org/wikipedia/commons/thumb/d/d6/Lock-gray-alt-2.svg/9px-Lock-gray-alt-2.svg.png")no-repeat;background-position:right .1em center}.mw-parser-output .citation .cs1-lock-subscription a{background:url("//upload.wikimedia.org/wikipedia/commons/thumb/a/aa/Lock-red-alt-2.svg/9px-Lock-red-alt-2.svg.png")no-repeat;background-position:right .1em center}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration{color:#555}.mw-parser-output .cs1-subscription span,.mw-parser-output .cs1-registration span{border-bottom:1px dotted;cursor:help}.mw-parser-output .cs1-ws-icon a{background:url("//upload.wikimedia.org/wikipedia/commons/thumb/4/4c/Wikisource-logo.svg/12px-Wikisource-logo.svg.png")no-repeat;background-position:right .1em center}.mw-parser-output code.cs1-code{color:inherit;background:inherit;border:inherit;padding:inherit}.mw-parser-output .cs1-hidden-error{display:none;font-size:100%}.mw-parser-output .cs1-visible-error{font-size:100%}.mw-parser-output .cs1-maint{display:none;color:#33aa33;margin-left:0.3em}.mw-parser-output .cs1-subscription,.mw-parser-output .cs1-registration,.mw-parser-output .cs1-format{font-size:95%}.mw-parser-output .cs1-kern-left,.mw-parser-output .cs1-kern-wl-left{padding-left:0.2em}.mw-parser-output .cs1-kern-right,.mw-parser-output .cs1-kern-wl-right{padding-right:0.2em}


  2. ^ ab "Search results - 4[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. ^ ab Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.


  5. ^ Chen LC, Liu MY, Hsiao YC, Choong WK, Wu HY, Hsu WL, Liao PC, Sung TY, Tsai SF, Yu JS, Chen YJ (2012) Decoding the disease-associated proteins encoded in the human chromosome 4. J Proteome Res


  6. ^ 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.


  7. ^ "Statistics & Downloads for chromosome 4". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.


  8. ^ "Chromosome 4: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.


  9. ^ "Human chromosome 4: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.


  10. ^ "Search results - 4[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.


  11. ^ "Search results - 4[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.


  12. ^ "Search results - 4[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.


  13. ^ Lemmers RJ, van der Vliet PJ, Klooster R, Sacconi S, Camaño P, Dauwerse JG, Snider L, Straasheijm KR, van Ommen GJ, Padberg GW, Miller DG, Tapscott SJ, Tawil R, Frants RR, van der Maarel SM (September 2010). "A unifying genetic model for facioscapulohumeral muscular dystrophy". Science. 329 (5999): 1650–3. Bibcode:2010Sci...329.1650L. doi:10.1126/science.1189044. PMC 4677822. PMID 20724583.


  14. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.


  15. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.


  16. ^ 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.


  17. ^ 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.


  18. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.


  19. ^ "p": Short arm; "q": Long arm.


  20. ^ For cytogenetic banding nomenclature, see article locus.


  21. ^ ab 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.


  22. ^ 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


.mw-parser-output .refbegin{font-size:90%;margin-bottom:0.5em}.mw-parser-output .refbegin-hanging-indents>ul{list-style-type:none;margin-left:0}.mw-parser-output .refbegin-hanging-indents>ul>li,.mw-parser-output .refbegin-hanging-indents>dl>dd{margin-left:0;padding-left:3.2em;text-indent:-3.2em;list-style:none}.mw-parser-output .refbegin-100{font-size:100%}


  • Goldfrank D, Schoenberger E, Gilbert F (2003). "Disease genes and chromosomes: disease maps of the human genome. Chromosome 4". Genet Test. 7 (4): 351–72. doi:10.1089/109065703322783752. PMID 15000816.


  • Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, Minx P, et al. (April 2005). "Generation and annotation of the DNA sequences of human chromosomes 2 and 4". Nature. 434 (7034): 724–31. Bibcode:2005Natur.434..724H. doi:10.1038/nature03466. PMID 15815621.





External links








  • National Institutes of Health. "Chromosome 4". Genetics Home Reference. Retrieved 2017-05-06.


  • "Chromosome 4". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.










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