Chromosome 4

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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.

Genomics[edit]

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[edit]

Number of genes[edit]

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[edit]

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

Diseases and disorders[edit]

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

Cytogenetic band[edit]

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 4,500,001 6,000,000 gpos 25
4 p 16.1 389 779 6,000,001 11,300,000 gneg
4 p 15.33 779 1066 11,300,001 15,000,000 gpos 50
4 p 15.32 1066 1286 15,000,001 17,700,000 gneg
4 p 15.31 1286 1557 17,700,001 21,300,000 gpos 75
4 p 15.2 1557 1811 21,300,001 27,700,000 gneg
4 p 15.1 1811 2166 27,700,001 35,800,000 gpos 100
4 p 14 2166 2505 35,800,001 41,200,000 gneg
4 p 13 2505 2742 41,200,001 44,600,000 gpos 50
4 p 12 2742 2877 44,600,001 48,200,000 gneg
4 p 11 2877 3046 48,200,001 50,000,000 acen
4 q 11 3046 3249 50,000,001 51,800,000 acen
4 q 12 3249 3571 51,800,001 58,500,000 gneg
4 q 13.1 3571 3910 58,500,001 65,500,000 gpos 100
4 q 13.2 3910 4062 65,500,001 69,400,000 gneg
4 q 13.3 4062 4333 69,400,001 75,300,000 gpos 75
4 q 21.1 4333 4502 75,300,001 78,000,000 gneg
4 q 21.21 4502 4671 78,000,001 81,500,000 gpos 50
4 q 21.22 4671 4739 81,500,001 83,200,000 gneg
4 q 21.23 4739 4874 83,200,001 86,000,000 gpos 25
4 q 21.3 4874 5145 86,000,001 87,100,000 gneg
4 q 22.1 5145 5517 87,100,001 92,800,000 gpos 75
4 q 22.2 5517 5636 92,800,001 94,200,000 gneg
4 q 22.3 5636 5890 94,200,001 97,900,000 gpos 75
4 q 23 5890 6059 97,900,001 100,100,000 gneg
4 q 24 6059 6347 100,100,001 106,700,000 gpos 50
4 q 25 6347 6685 106,700,001 113,200,000 gneg
4 q 26 6685 7040 113,200,001 119,900,000 gpos 75
4 q 27 7040 7277 119,900,001 122,800,000 gneg
4 q 28.1 7277 7565 122,800,001 127,900,000 gpos 50
4 q 28.2 7565 7734 127,900,001 130,100,000 gneg
4 q 28.3 7734 8259 130,100,001 138,500,000 gpos 100
4 q 31.1 8259 8581 138,500,001 140,600,000 gneg
4 q 31.21 8581 8733 140,600,001 145,900,000 gpos 25
4 q 31.22 8733 8851 145,900,001 147,500,000 gneg
4 q 31.23 8851 9004 147,500,001 150,200,000 gpos 25
4 q 31.3 9004 9207 150,200,001 154,600,000 gneg
4 q 32.1 9207 9545 154,600,001 160,800,000 gpos 100
4 q 32.2 9545 9681 160,800,001 163,600,000 gneg
4 q 32.3 9681 9985 163,600,001 169,200,000 gpos 100
4 q 33 9985 10087 169,200,001 171,000,000 gneg
4 q 34.1 10087 10341 171,000,001 175,400,000 gpos 75
4 q 34.2 10341 10408 175,400,001 176,600,000 gneg
4 q 34.3 10408 10628 176,600,001 182,300,000 gpos 100
4 q 35.1 10628 10967 182,300,001 186,200,000 gneg
4 q 35.2 10967 11170 186,200,001 190,214,555 gpos 25

References[edit]

  1. ^ "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04. 
  2. ^ a b "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. ^ 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.
  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 2898077Freely accessible. 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 4677822Freely accessible. 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. ^ 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.
  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[edit]

  • 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. doi:10.1038/nature03466. PMID 15815621. 


External links[edit]

  • 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.