Chromosome 7

Chromosome 7
Human chromosome 7 pair after G-banding.
One is from mother, one is from father.
Chromosome 7 pair
in human male karyogram.
Features
Length (bp) 159,345,973 bp
(GRCh38)[1]
No. of genes 862 (CCDS)[2]
Type Autosome
Centromere position Submetacentric[3]
(60.1 Mbp[4])
Complete gene lists
CCDS Gene list
HGNC Gene list
UniProt Gene list
NCBI Gene list
External map viewers
Ensembl Chromosome 7
Entrez Chromosome 7
NCBI Chromosome 7
UCSC Chromosome 7
Full DNA sequences
RefSeq NC_000007 (FASTA)
GenBank CM000669 (FASTA)

Chromosome 7 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 7 spans about 159 million[5] base pairs (the building material of DNA) and represents between 5 and 5.5 percent of the total DNA in cells.

Genes

Number of genes

The following are some of the gene count estimates of human chromosome 7. 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 byProtein-coding genesNon-coding RNA genesPseudogenesSourceRelease date
CCDS862-- [2] 2016-09-08
HGNC870245703 [7] 2017-05-12
Ensembl984973889 [8] 2017-03-29
UniProt944-- [9] 2018-02-28
NCBI948905933 [10][11][12] 2017-05-19

Gene list

The following is a partial list of genes on human chromosome 7. For complete list, see the link in the infobox on the right.

  • ACTR3B: actin-related protein 3B
  • AEBP1: AE binding protein 1
  • AGK: encoding enzyme mitochondrial acylglycerol kinase
  • AASS: encoding enzyme Alpha-aminoadipic semialdehyde synthase, mitochondrial
  • ARHGEF35: encoding protein Rho guanine nucleotide exchange factor (GEF) 35
  • BCAP29: B-cell receptor-associated protein 29
  • BRAT1: BRCA1-associated ATM activator 1
  • C7orf20: encoding protein UPF0363 protein C7orf20
  • C7orf25: protein UPF0415
  • C7orf31: chromosome 7 open reading frame 31
  • C7orf43: encoding protein
  • CALU: Calumenin
  • CDCA7L: Cell division cycle-associated 7-like protein
  • CNOT4: CCR4-NOT transcription complex, subunit 4
  • CPED1: cadherin like and PC-esterase domain containing 1
  • CPVL: carboxypeptidase, vitellogenic like
  • CROT: Peroxisomal carnitine O-octanoyltransferase
  • DDX56: DEAD-box helicase 56
  • DMTF1: Cyclin D binding myb like transcription factor 1
  • ECOP: EGFR-coamplified and overexpressed protein
  • EZH2: encoding enzyme histone-lysine N-methyltransferase for histone h3 lysine 27
  • FAM71F2: family with sequence similarity 71 member F2
  • FAM185A: family with sequence similarity 185 member A
  • FAM200A: family with sequence similarity 200 member A
  • FBXO24: F-box only protein 24
  • GBAS: Glioblastoma amplified sequence; Protein NipSnap homolog 2
  • GLCCI1: Glucocorticoid-induced transcript 1 protein
  • ICA1: islet cell autoantigen 1
  • ING3: inhibitor of growth protein 3
  • INTS1: encoding protein Integrator complex subunit 1
  • IQCE: IQ domain-containing protein E
  • KDM7A: encoding protein Lysine demethylase 7A
  • LRRC17: leucine-rich repeat containing protein 17
  • LSM5: U6 small nuclear RNA and mRNA degradation associated
  • LUC7L2: putative RNA-binding protein Luc7-like 2
  • MDFIC: MyoD family inhibitor domain containing
  • METTL2B: methyltransferase-like protein 2B
  • MINDY4: MINDY lysine 48 deubiquitinase 4
  • MIR96: microRNA 96
  • MOSPD3: motile sperm domain containing 3
  • MTERF: mitochondrial transcription termination factor 1
  • NOM1: nucleolar protein with MIF4G domain 1
  • NUDCD3: NudC domain-containing protein 3
  • NUPL2: nucleoporin-like 2
  • NXPH1: neurexophilin-1
  • PDAP1: PDGFA associated protein 1
  • PHTF2: putative homeodomain transcription factor 2
  • PLOD3: procollagen-lysine,2-oxoglutarate 5-dioxygenase 3
  • POM121: POM121 transmembrane nucleoporin
  • POP7: ribonuclease P protein subunit p20
  • PPP1R17: protein phosphatase 1 regulatory subunit 17
  • PSPH: phosphoserine phosphatase
  • PURB: purine-rich element binding protein B
  • PVRIG: encoding protein Poliovirus receptor related immunoglobulin domain containing
  • RADIL: ras-associating and dilute domain-containing protein
  • RCP9: DNA-directed RNA polymerase III subunit RCP9
  • REPIN1: replication initiator 1
  • RNF216-IT1: encoding protein RNF216 intronic transcript 1
  • SCIN: scinderin
  • SCRN1: secernin 1
  • SOSTDC1: sclerostin domain containing 1
  • SPDYE1: speedy/RINGO cell cycle regulator family member E1
  • SSC4D: scavenger receptor cysteine rich family member with 4 domains
  • STEAP1: six transmembrane epithelial antigen of the prostate 1
  • STEAP2: six transmembrane epithelial antigen of the prostate 2
  • STEAP4: six transmembrane epithelial antigen of the prostate 4
  • STYXL1: serine/threonine/tyrosine-interacting-like protein 1
  • SUMF2: sulatase-modifying factor 2
  • SYPL1: synaptophysin-like protein 1
  • TARP: TCR gamma alternate reading frame protein
  • TBRG4: transforming growth factor beta regulator 4
  • TECPR1 encoding protein Tectonin beta-propeller repeat containing 1
  • TMED4: transmembrane emp24 domain-containing protein 4
  • TMEM130: transmembrane protein 130
  • TMEM196 encoding protein Transmembrane protein 196
  • TRBC1 encoding protein T cell receptor beta constant 1
  • TRBC2 encoding protein T cell receptor beta constant 2
  • TRIL: TRL4 interactor with leucine rich repeats
  • URG4: up-regulated gene 4
  • WBSCR17: polypeptide N-acetylgalactosaminyltransferase 17
  • WDR91 encoding protein WD repeat domain 91
  • ZC3HAV1: zinc finger CCCH-type containing
  • ZC3HC1: zinc finger C3HC-type containing 1
  • ZKSCAN1: zinc finger protein with KRAB and SCAN domains 1
  • ZKSCAN5: zinc finger protein with KRAB and SCAN domains 5
  • ZMIZ2: zinc finger MIZ domain-containing protein 2
  • ZNF277P: zinc finger protein 277
  • ZNF394: zinc finger protein 394
  • ZNF398: zinc finger protein 398
  • ZNF727: encoding protein Zinc finger protein 727
  • ZNF786: encoding protein Zinc finger protein 786
  • ZRF1: DnaJ heat shock protein family (Hsp40) member C2
  • ZSCAN21: zinc finger and SCAN domain-containing protein 21

Diseases and disorders

The following diseases are some of those related to genes on chromosome 7:

Chromosomal disorders

The following conditions are caused by changes in the structure or number of copies of chromosome 7:

  • Williams syndrome is caused by the deletion of genetic material from a portion of the long (q) arm of chromosome 7. The deleted region, which is located at position 11.23 (written as 7q11.23), is designated as the Williams syndrome critical region. This region includes more than 20 genes, and researchers believe that the characteristic features of Williams syndrome are probably related to the loss of multiple genes in this region.

While a few of the specific genes related to Williams syndrome have been identified, the relationship between most of the genes in the deleted region and the signs and symptoms of Williams syndrome is unknown.

  • Other changes in the number or structure of chromosome 7 can cause delayed growth and development, mental disorder, characteristic facial features, skeletal abnormalities, delayed speech, and other medical problems. These changes include an extra copy of part of chromosome 7 in each cell (partial trisomy 7) or a missing segment of the chromosome in each cell (partial monosomy 7). In some cases, several DNA building blocks (nucleotides) are deleted or duplicated in part of chromosome 7. A circular structure called ring chromosome 7 is also possible. A ring chromosome occurs when both ends of a broken chromosome are reunited.[23]

Cytogenetic band

G-banding ideograms of human chromosome 7
G-banding ideogram of human chromosome 7 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 7 in three different resolutions (400,[24] 550[25] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[26] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[27]
G-bands of human chromosome 7 in resolution 850 bphs[4]
Chr. Arm[28] Band[29] ISCN
start[30]		 ISCN
stop[30]		 Basepair
start		 Basepair
stop		 Stain[31] Density
7p 22.3022712,800,000 gneg
7p 22.22273972,800,0014,500,000 gpos25
7p 22.13976104,500,0017,200,000 gneg
7p 21.36109087,200,00113,700,000 gpos100
7p 21.290896513,700,00116,500,000 gneg
7p 21.1965112116,500,00120,900,000 gpos100
7p 15.31121141920,900,00125,500,000 gneg
7p 15.21419158925,500,00127,900,000 gpos50
7p 15.11589181627,900,00128,800,000 gneg
7p 14.31816198628,800,00134,900,000 gpos75
7p 14.21986204334,900,00137,100,000 gneg
7p 14.12043232737,100,00143,300,000 gpos75
7p 132327263943,300,00145,400,000 gneg
7p 12.32639283845,400,00149,000,000 gpos75
7p 12.22838290949,000,00150,500,000 gneg
7p 12.12909309350,500,00153,900,000 gpos75
7p 11.23093330653,900,00158,100,000 gneg
7p 11.13306344858,100,00160,100,000 acen
7q 11.13448368960,100,00162,100,000 acen
7q 11.213689397362,100,00167,500,000 gneg
7q 11.223973417167,500,00172,700,000 gpos50
7q 11.234171459772,700,00177,900,000 gneg
7q 21.114597499477,900,00186,700,000 gpos100
7q 21.124994510886,700,00188,500,000 gneg
7q 21.135108529288,500,00191,500,000 gpos75
7q 21.25292540691,500,00193,300,000 gneg
7q 21.35406566193,300,00198,400,000 gpos75
7q 22.15661612998,400,001104,200,000 gneg
7q 22.261296300104,200,001104,900,000 gpos50
7q 22.363006470104,900,001107,800,000 gneg
7q 31.164706683107,800,001115,000,000 gpos75
7q 31.266836867115,000,001117,700,000 gneg
7q 31.3168677094117,700,001121,400,000 gpos75
7q 31.3270947208121,400,001124,100,000 gneg
7q 31.3372087364124,100,001127,500,000 gpos75
7q 32.173647449127,500,001129,600,000 gneg
7q 32.274497576129,600,001130,800,000 gpos25
7q 32.375767803130,800,001132,900,000 gneg
7q 3378038031132,900,001138,500,000 gpos50
7q 3480318371138,500,001143,400,000 gneg
7q 3583718612143,400,001148,200,000 gpos75
7q 36.186128910148,200,001152,800,000 gneg
7q 36.289109080152,800,001155,200,000 gpos25
7q 36.390809350155,200,001159,345,973 gneg

Novels

In the novel Performance Anomalies, researchers at Stanford University identify mutations in the long (q) arm of chromosome 7 as underlying the accelerated nervous system of the spy protagonist Cono,[32] who receives the moniker Cono 7Q

References

  1. ↑ "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04.
  2. 1 2 "Search results - 1[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. 1 2 3 Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  5. ↑ What is chromosome 7, "Genetics Home Reference" of U.S. National Library of Medicine. April 2008. [2014-05-14].
  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 7". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.
  8. ↑ "Chromosome 7: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
  9. ↑ "Human chromosome 7: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.
  10. ↑ "Search results - 7[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 - 7[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 - 7[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  13. 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 Scherer SW, Cheung J, MacDonald JR, Osborne LR, Nakabayashi K, Herbrick JA, Carson AR, Parker-Katiraee L, Skaug J, Khaja R, Zhang J, Hudek AK, Li M, Haddad M, Duggan GE, Fernandez BA, Kanematsu E, Gentles S, Christopoulos CC, Choufani S, Kwasnicka D, Zheng XH, Lai Z, Nusskern D, Zhang Q, Gu Z, Lu F, Zeesman S, Nowaczyk MJ, Teshima I, Chitayat D, Shuman C, Weksberg R, Zackai EH, Grebe TA, Cox SR, Kirkpatrick SJ, Rahman N, Friedman JM, Heng HH, Pelicci PG, Lo-Coco F, Belloni E, Shaffer LG, Pober B, Morton CC, Gusella JF, Bruns GA, Korf BR, Quade BJ, Ligon AH, Ferguson H, Higgins AW, Leach NT, Herrick SR, Lemyre E, Farra CG, Kim HG, Summers AM, Gripp KW, Roberts W, Szatmari P, Winsor EJ, Grzeschik KH, Teebi A, Minassian BA, Kere J, Armengol L, Pujana MA, Estivill X, Wilson MD, Koop BF, Tosi S, Moore GE, Boright AP, Zlotorynski E, Kerem B, Kroisel PM, Petek E, Oscier DG, Mould SJ, Döhner H, Döhner K, Rommens JM, Vincent JB, Venter JC, Li PW, Mural RJ, Adams MD, Tsui LC (May 2003). "Human chromosome 7: DNA sequence and biology". Science. 300 (5620): 767–72. Bibcode:2003Sci...300..767S. doi:10.1126/science.1083423. PMC 2882961. PMID 12690205.
  14. ↑ Nagamani SC, Erez A, Lee B (May 2012). "Argininosuccinate lyase deficiency". Genetics in Medicine. 14 (5): 501–7. doi:10.1038/gim.2011.1. PMC 3709024. PMID 22241104.
  15. 1 2 3 4 Gilbert F (2002). "Chromosome 7". Genetic Testing. 6 (2): 141–61. doi:10.1089/10906570260199429. PMID 12215256.
  16. 1 2 Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK (Jul 2003). "The DNA sequence of human chromosome 7". Nature. 424 (6945): 157–64. Bibcode:2003Natur.424..157H. doi:10.1038/nature01782. PMID 12853948. </bn>Lichtenbelt KD, Hochstenbach R, van Dam WM, Eleveld MJ, Poot M, Beemer FA (Jan 2005). "Supernumerary ring chromosome 7 mosaicism: case report, investigation of the gene content, and delineation of the phenotype" (PDF). American Journal of Medical Genetics Part A. 132A (1): 93–100. doi:10.1002/ajmg.a.30408. PMID 15580634.
  17. 1 2 Newbury DF, Monaco AP (Oct 2010). "Genetic advances in the study of speech and language disorders". Neuron. 68 (2): 309–20. doi:10.1016/j.neuron.2010.10.001. PMC 2977079. PMID 20955937.
  18. ↑ Solé F, Espinet B, Sanz GF, Cervera J, Calasanz MJ, Luño E, Prieto F, Granada I, Hernández JM, Cigudosa JC, Diez JL, Bureo E, Marqués ML, Arranz E, Ríos R, Martínez Climent JA, Vallespí T, Florensa L, Woessner S (Feb 2000). "Incidence, characterization and prognostic significance of chromosomal abnormalities in 640 patients with primary myelodysplastic syndromes. Grupo Cooperativo Español de Citogenética Hematológica". British Journal of Haematology. 108 (2): 346–356. doi:10.1046/j.1365-2141.2000.01868.x. PMID 10691865.
  19. ↑ Lossin C, George AL (2008). "Myotonia congenita". Advances in Genetics. Advances in Genetics. 63: 25–55. doi:10.1016/S0065-2660(08)01002-X. ISBN 9780123745279. PMID 19185184.
  20. ↑ Grimaldi R, Capuano P, Miranda N, Wagner C, Capasso G (2007). "[Pendrin: physiology, molecular biology and clinical importance]". Giornale Italiano Di Nefrologia (in Italian). 24 (4): 288–94. PMID 17659500.
  21. ↑ Eggermann T, Begemann M, Binder G, Spengler S (2010). "Silver-Russell syndrome: genetic basis and molecular genetic testing". Orphanet Journal of Rare Diseases. 5: 19. doi:10.1186/1750-1172-5-19. PMC 2907323. PMID 20573229.
  22. ↑ Zarchi O, Attias J, Gothelf D (2010). "Auditory and visual processing in Williams syndrome". The Israel Journal of Psychiatry and Related Sciences. 47 (2): 125–31. PMID 20733255.
  23. ↑ Velagaleti GV, Jalal SM, Kukolich MK, Lockhart LH, Tonk VS (Mar 2002). "De novo supernumerary ring chromosome 7: first report of a non-mosaic patient and review of the literature". Clinical Genetics. 61 (3): 202–6. doi:10.1034/j.1399-0004.2002.610306.x. PMID 12000362.
  24. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  25. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  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.
  27. ↑ 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.
  28. ↑ "p": Short arm; "q": Long arm.
  29. ↑ For cytogenetic banding nomenclature, see article locus.
  30. 1 2 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.
  31. ↑ 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.
  32. ↑ Lee, Victor Robert (2013-01-15). Performance Anomalies: A Novel. Perimeter Six Press. ISBN 9781938409202.

Further reading

  • Rodríguez L, López F, Paisán L, de la Red Mdel M, Ruiz AM, Blanco M, Antelo Cortizas J, Martínez-Frías ML (Nov 2002). "Pure partial trisomy 7q: two new patients and review". American Journal of Medical Genetics. 113 (2): 218–24. doi:10.1002/ajmg.10719. PMID 12407716.
  • National Institutes of Health. "Chromosome 7". Genetics Home Reference. Retrieved 2017-05-06.
  • "Chromosome 7". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.
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