Biology:Chromosome 1
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Short description: Human chromosome
| Chromosome 1 | |
|---|---|
 Human chromosome 1 pair after G-banding. One is from mother, one is from father. | |
 Chromosome 1 pair in human male karyogram. | |
| Features | |
| Length (bp) | 248,387,328 bp (CHM13) |
| No. of genes | 1,961 (CCDS)[1] |
| Type | Autosome |
| Centromere position | Metacentric[2] (123.4 Mbp[3]) |
| Complete gene lists | |
| CCDS | Gene list |
| HGNC | Gene list |
| UniProt | Gene list |
| NCBI | Gene list |
| External map viewers | |
| Ensembl | Chromosome 1 |
| Entrez | Chromosome 1 |
| NCBI | Chromosome 1 |
| UCSC | Chromosome 1 |
| Full DNA sequences | |
| RefSeq | NC_000001 (FASTA) |
| GenBank | CM000663 (FASTA) |
Chromosome 1 is the designation for the largest human chromosome. Humans have two copies of chromosome 1, as they do with all of the autosomes, which are the non-sex chromosomes. Chromosome 1 spans about 249 million nucleotide base pairs, which are the basic units of information for DNA.[4] It represents about 8% of the total DNA in human cells.[5]
It was the last completed chromosome, sequenced two decades after the beginning of the Human Genome Project.
Genes
Number of genes
The following are some of the gene count estimates of human chromosome 1. 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 | 1,961 | — | — | [1] | 2016-09-08 |
| HGNC | 1,993 | 707 | 1,113 | [7] | 2017-05-12 |
| Ensembl | 2,044 | 1,924 | 1,223 | [8] | 2017-03-29 |
| UniProt | 2,064 | — | — | [9] | 2018-02-28 |
| NCBI | 2,093 | 1,790 | 1,426 | [10][11][12] | 2017-05-19 |
Gene list
The following is a partial list of genes on human chromosome 1. For complete list, see the link in the infobox on the right.
- C1orf112: encoding protein Chromosome 1 open reading frame 112
- C1orf127: encoding protein Chromosome 1 open reading frame 127
- C1orf27: encoding protein Chromosome 1 open reading frame 27
- C1orf38: encoding protein Chromosome 1 open reading frame 38
- CCDC181: encoding protein Coiled-coil domain-containing protein 181
- DENN1B: hypothesized to be related to asthma
- FHAD1: encoding protein Forkhead-associated domain containing protein 1
- LOC100132287: uncharacterized protein
- LRRIQ3: encoding protein Leucine-rich repeats and IQ motif containing 3
- Shisa family member 4: encoding protein Shisa family member 4
- TINAGL1: encoding protein Tubulointerstitial nephritis antigen-like
p-arm
Partial list of the genes located on p-arm (short arm) of human chromosome 1:
q-arm
Partial list of the genes located on q-arm (long arm) of human chromosome 1:
Diseases and disorders
There are 890 known diseases related to this chromosome.[citation needed] Some of these diseases are hearing loss, Alzheimer's disease, glaucoma and breast cancer. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident.
Complete monosomy (only having one copy of the entire chromosome) is invariably lethal before birth.[13] Complete trisomy (having three copies of the entire chromosome) is lethal within days after conception.[13] Some partial deletions and partial duplications produce birth defects.
The following diseases are some of those related to genes on chromosome 1 (which contains the most known genetic diseases of any human chromosome):
- 1q21.1 deletion syndrome
- 1q21.1 duplication syndrome
- Alzheimer's disease
- Autosomal dominant Charcot-Marie-Tooth disease type 2 with giant axons
- Breast cancer
- Brooke Greenberg Disease (Syndrome X)
- Carnitine palmitoyltransferase II deficiency
- Charcot–Marie–Tooth disease, types 1 and 2
- collagenopathy, types II and XI
- congenital hypothyroidism
- Ehlers-Danlos syndrome
- Factor V Leiden thrombophilia
- Familial adenomatous polyposis
- galactosemia
- Gaucher disease
- Gaucher-like disease
- Gelatinous drop-like corneal dystrophy
- Glaucoma
- GLUT1 deficiency syndrome
- Hearing loss, autosomal recessive deafness 36
- Hemochromatosis
- Hepatoerythropoietic porphyria
- Homocystinuria
- Hutchinson Gilford progeria syndrome
- 3-hydroxy-3-methylglutaryl-CoA lyase deficiency
- Hypertrophic cardiomyopathy, autosomal dominant mutations of TNNT2; hypertrophy usually mild; restrictive phenotype may be present; may carry high risk of sudden cardiac death
- maple syrup urine disease
- medium-chain acyl-coenzyme A dehydrogenase deficiency
- Microcephaly
- Muckle–Wells syndrome
- Nonsyndromic deafness
- Oligodendroglioma
- Parkinson disease
- Pheochromocytoma
- porphyria
- porphyria cutanea tarda
- popliteal pterygium syndrome
- prostate cancer
- Stickler syndrome
- TAR syndrome
- trimethylaminuria
- Usher syndrome
- Usher syndrome type II
- Van der Woude syndrome
- Variegate porphyria
Cytogenetic band
G-banding ideograms of human chromosome 1
G-banding ideogram of human chromosome 1 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 1 in three different resolutions (400,[14] 550[15] and 850[3]). 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]
| Chr. | Arm[18] | Band[19] | ISCN start[20] |
ISCN stop[20] |
Basepair start |
Basepair stop |
Stain[21] | Density |
|---|---|---|---|---|---|---|---|---|
| 1 | p | 36.33 | 0 | 100 | 1 | 2,300,000 | gneg | |
| 1 | p | 36.32 | 100 | 244 | 2,300,001 | 5,300,000 | gpos | 25 |
| 1 | p | 36.31 | 244 | 344 | 5,300,001 | 7,100,000 | gneg | |
| 1 | p | 36.23 | 344 | 459 | 7,100,001 | 9,100,000 | gpos | 25 |
| 1 | p | 36.22 | 459 | 660 | 9,100,001 | 12,500,000 | gneg | |
| 1 | p | 36.21 | 660 | 861 | 12,500,001 | 15,900,000 | gpos | 50 |
| 1 | p | 36.13 | 861 | 1206 | 15,900,001 | 20,100,000 | gneg | |
| 1 | p | 36.12 | 1206 | 1321 | 20,100,001 | 23,600,000 | gpos | 25 |
| 1 | p | 36.11 | 1321 | 1521 | 23,600,001 | 27,600,000 | gneg | |
| 1 | p | 35.3 | 1521 | 1651 | 27,600,001 | 29,900,000 | gpos | 25 |
| 1 | p | 35.2 | 1651 | 1780 | 29,900,001 | 32,300,000 | gneg | |
| 1 | p | 35.1 | 1780 | 1895 | 32,300,001 | 34,300,000 | gpos | 25 |
| 1 | p | 34.3 | 1895 | 2210 | 34,300,001 | 39,600,000 | gneg | |
| 1 | p | 34.2 | 2210 | 2411 | 39,600,001 | 43,700,000 | gpos | 25 |
| 1 | p | 34.1 | 2411 | 2770 | 43,700,001 | 46,300,000 | gneg | |
| 1 | p | 33 | 2770 | 2986 | 46,300,001 | 50,200,000 | gpos | 75 |
| 1 | p | 32.3 | 2986 | 3273 | 50,200,001 | 55,600,000 | gneg | |
| 1 | p | 32.2 | 3273 | 3416 | 55,600,001 | 58,500,000 | gpos | 50 |
| 1 | p | 32.1 | 3416 | 3732 | 58,500,001 | 60,800,000 | gneg | |
| 1 | p | 31.3 | 3732 | 3976 | 60,800,001 | 68,500,000 | gpos | 50 |
| 1 | p | 31.2 | 3976 | 4206 | 68,500,001 | 69,300,000 | gneg | |
| 1 | p | 31.1 | 4206 | 4852 | 69,300,001 | 84,400,000 | gpos | 100 |
| 1 | p | 22.3 | 4852 | 5210 | 84,400,001 | 87,900,000 | gneg | |
| 1 | p | 22.2 | 5210 | 5440 | 87,900,001 | 91,500,000 | gpos | 75 |
| 1 | p | 22.1 | 5440 | 5741 | 91,500,001 | 94,300,000 | gneg | |
| 1 | p | 21.3 | 5741 | 5957 | 94,300,001 | 99,300,000 | gpos | 75 |
| 1 | p | 21.2 | 5957 | 6029 | 99,300,001 | 101,800,000 | gneg | |
| 1 | p | 21.1 | 6029 | 6244 | 101,800,001 | 106,700,000 | gpos | 100 |
| 1 | p | 13.3 | 6244 | 6459 | 106,700,001 | 111,200,000 | gneg | |
| 1 | p | 13.2 | 6459 | 6660 | 111,200,001 | 115,500,000 | gpos | 50 |
| 1 | p | 13.1 | 6660 | 6861 | 115,500,001 | 117,200,000 | gneg | |
| 1 | p | 12 | 6861 | 7048 | 117,200,001 | 120,400,000 | gpos | 50 |
| 1 | p | 11.2 | 7048 | 7119 | 120,400,001 | 121,700,000 | gneg | |
| 1 | p | 11.1 | 7119 | 7335 | 121,700,001 | 123,400,000 | acen | |
| 1 | q | 11 | 7335 | 7579 | 123,400,001 | 125,100,000 | acen | |
| 1 | q | 12 | 7579 | 8483 | 125,100,001 | 143,200,000 | gvar | |
| 1 | q | 21.1 | 8483 | 8756 | 143,200,001 | 147,500,000 | gneg | |
| 1 | q | 21.2 | 8756 | 8957 | 147,500,001 | 150,600,000 | gpos | 50 |
| 1 | q | 21.3 | 8957 | 9244 | 150,600,001 | 155,100,000 | gneg | |
| 1 | q | 22 | 9244 | 9459 | 155,100,001 | 156,600,000 | gpos | 50 |
| 1 | q | 23.1 | 9459 | 9832 | 156,600,001 | 159,100,000 | gneg | |
| 1 | q | 23.2 | 9832 | 10048 | 159,100,001 | 160,500,000 | gpos | 50 |
| 1 | q | 23.3 | 10048 | 10349 | 160,500,001 | 165,500,000 | gneg | |
| 1 | q | 24.1 | 10349 | 10507 | 165,500,001 | 167,200,000 | gpos | 50 |
| 1 | q | 24.2 | 10507 | 10679 | 167,200,001 | 170,900,000 | gneg | |
| 1 | q | 24.3 | 10679 | 10894 | 170,900,001 | 173,000,000 | gpos | 75 |
| 1 | q | 25.1 | 10894 | 11009 | 173,000,001 | 176,100,000 | gneg | |
| 1 | q | 25.2 | 11009 | 11196 | 176,100,001 | 180,300,000 | gpos | 50 |
| 1 | q | 25.3 | 11196 | 11598 | 180,300,001 | 185,800,000 | gneg | |
| 1 | q | 31.1 | 11598 | 11827 | 185,800,001 | 190,800,000 | gpos | 100 |
| 1 | q | 31.2 | 11827 | 11942 | 190,800,001 | 193,800,000 | gneg | |
| 1 | q | 31.3 | 11942 | 12172 | 193,800,001 | 198,700,000 | gpos | 100 |
| 1 | q | 32.1 | 12172 | 12617 | 198,700,001 | 207,100,000 | gneg | |
| 1 | q | 32.2 | 12617 | 12803 | 207,100,001 | 211,300,000 | gpos | 25 |
| 1 | q | 32.3 | 12803 | 13033 | 211,300,001 | 214,400,000 | gneg | |
| 1 | q | 41 | 13033 | 13320 | 214,400,001 | 223,900,000 | gpos | 100 |
| 1 | q | 42.11 | 13320 | 13406 | 223,900,001 | 224,400,000 | gneg | |
| 1 | q | 42.12 | 13406 | 13607 | 224,400,001 | 226,800,000 | gpos | 25 |
| 1 | q | 42.13 | 13607 | 13966 | 226,800,001 | 230,500,000 | gneg | |
| 1 | q | 42.2 | 13966 | 14153 | 230,500,001 | 234,600,000 | gpos | 50 |
| 1 | q | 42.3 | 14153 | 14397 | 234,600,001 | 236,400,000 | gneg | |
| 1 | q | 43 | 14397 | 14756 | 236,400,001 | 243,500,000 | gpos | 75 |
| 1 | q | 44 | 14756 | 15100 | 243,500,001 | 248,956,422 | gneg |
References
- ↑ 1.0 1.1 "Search results - 1[CHR] AND "Homo sapiens"[Organism] AND ("has ccds"[Properties] AND alive[prop]) - Gene". 2016-09-08. https://www.ncbi.nlm.nih.gov/gene?term=1%5BChr%5D%20AND%20%22Homo%20sapiens%22%5BOrganism%5D%20AND%20%28%22has%20ccds%22%5BProperties%5D%20AND%20alive%5Bprop%5D%29&cmd=DetailsSearch.
- ↑ Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2. https://books.google.com/books?id=dSwWBAAAQBAJ&pg=PA45.
- ↑ 3.0 3.1 3.2 Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
- ↑ http://vega.sanger.ac.uk/Homo_sapiens/mapview?chr=1 Chromosome size and number of genes derived from this database, retrieved 2012-03-11.
- ↑ "The DNA sequence and biological annotation of human chromosome 1". Nature 441 (7091): 315–21. May 2006. doi:10.1038/nature04727. PMID 16710414. Bibcode: 2006Natur.441..315G.
- ↑ 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. PMID 20441615.
- ↑ "Statistics & Downloads for chromosome 1". 2017-05-12. https://www.genenames.org/cgi-bin/statistics?c=1.
- ↑ "Chromosome 1: Chromosome summary - Homo sapiens". 2017-03-29. http://mar2017.archive.ensembl.org/Homo_sapiens/Location/Chromosome?r=1.
- ↑ "Human chromosome 1: entries, gene names and cross-references to MIM". 2018-02-28. https://www.uniprot.org/docs/humchr01.txt.
- ↑ "Search results - 1[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". 2017-05-19. https://www.ncbi.nlm.nih.gov/gene?term=1%5BCHR%5D%20AND%20%22Homo%20sapiens%22%5BOrganism%5D%20AND%20%28%22genetype%20protein%20coding%22%5BProperties%5D%20AND%20alive%5Bprop%5D%29&cmd=DetailsSearch.
- ↑ "Search results - 1[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". 2017-05-19. https://www.ncbi.nlm.nih.gov/gene?term=1%5BCHR%5D%20AND%20%22Homo%20sapiens%22%5BOrganism%5D%20AND%20%28%28%22genetype%20miscrna%22%5BProperties%5D%20OR%20%22genetype%20ncrna%22%5BProperties%5D%20OR%20%22genetype%20rrna%22%5BProperties%5D%20OR%20%22genetype%20trna%22%5BProperties%5D%20OR%20%22genetype%20scrna%22%5BProperties%5D%20OR%20%22genetype%20snrna%22%5BProperties%5D%20OR%20%22genetype%20snorna%22%5BProperties%5D%29%20NOT%20%22genetype%20protein%20coding%22%5BProperties%5D%20AND%20alive%5Bprop%5D%29&cmd=DetailsSearch.
- ↑ "Search results - 1[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". 2017-05-19. https://www.ncbi.nlm.nih.gov/gene?term=1%5BCHR%5D%20AND%20%22Homo%20sapiens%22%5BOrganism%5D%20AND%20%28%22genetype%20pseudo%22%5BProperties%5D%20AND%20alive%5Bprop%5D%29&cmd=DetailsSearch.
- ↑ 13.0 13.1 Gersen, Steven L.; Keagle, Martha B. (2013-03-26) (in en). The Principles of Clinical Cytogenetics. Springer Science & Business Media. pp. 278. ISBN 9781441916884. https://books.google.com/books?id=PT9DAAAAQBAJ&pg=PA278.
- ↑ 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. https://books.google.com/books?id=lGCLrh0DIwEC.
- ↑ 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. https://www.researchgate.net/publication/261304470.
- ↑ "p": Short arm; "q": Long arm.
- ↑ For cytogenetic banding nomenclature, see article locus.
- ↑ 20.0 20.1 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
- "The Origin of Human Chromosome 1 and Its Homologs in Placental Mammals". Genome Res 13 (8): 1880–8. 2003. doi:10.1101/gr.1022303. PMID 12869576.
- Revera, M.; Van Der Merwe, L et al. (2007). "Long-term follow-up of R403WMHY7 and R92WTNNT2 HCM families: mutations determine left ventricular dimensions but not wall thickness during disease progression". Cardiovascular Journal of Africa 18 (3): 146–153. PMID 17612745.
- "Report and abstracts of the sixth international workshop on human chromosome 1 mapping 2000. Iowa City, Iowa, USA. 30 September-3 October 2000". Cytogenet Cell Genet 92 (1–2): 23–41. 2001. doi:10.1159/000056867. PMID 11306795.
External links
- National Institutes of Health. "Chromosome 1". Genetics Home Reference. http://ghr.nlm.nih.gov/chromosome=1.
- "Final genome 'chapter' published". 2006-05-18. http://news.bbc.co.uk/2/hi/science/nature/4994088.stm.
- "Chromosome 1". http://web.ornl.gov/sci/techresources/Human_Genome/posters/chromosome/chromo01.shtml.
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