Chromosome 13 (human)
| Chromosome 13 (human) | |
|---|---|
 Human chromosome 13 pair after G-banding. One is from mother, one is from father. | |
 Chromosome 13 pair in human male karyogram. | |
| Features | |
| Length (bp) |
114,364,328 bp (GRCh38)[1] |
| No. of genes | 308 (CCDS)[2] |
| Type | Autosome |
| Centromere position |
Acrocentric[3] (17.7 Mbp[4]) |
| External map viewers | |
| Ensembl | Chromosome 13 |
| Entrez | Chromosome 13 |
| NCBI | Chromosome 13 |
| UCSC | Chromosome 13 |
| Full DNA sequences | |
| RefSeq | NC_000013 (FASTA) |
| GenBank | CM000675 (FASTA) |
Chromosome 13 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 13 spans about 114 million base pairs (the building material of DNA) and represents between 3.5 and 4% of the total DNA in cells.
Genes
The following are some of the gene count estimates of human chromosome 13. 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.[5]
When simply saying "number of genes", in most cases, it refers only to "number of protein-coding genes".
| Estimated by | Protein-coding genes | Non-coding RNA genes | Pseudogenes | Source | Release date |
| CCDS | 308 | - | - | [2] | 2016-09-08 |
| HGNC | 309 | 323 | 469 | [6] | 2017-05-12 |
| Ensembl | 324 | 586 | 373 | [7] | 2017-03-29 |
| NCBI | 343 | 622 | 481 | [8][9][10] | 2017-05-19 |
The following are some of the genes located on chromosome 13:
- ARGLU1: encoding protein Arginine and glutamate-rich protein 1
- ATP7B: ATPase, Cu++ transporting, beta polypeptide (Wilson disease)
- BRCA2: breast cancer 2, early onset
- CAB39L: encoding protein Calcium-binding protein 39-like
- CARKD: Carbohydrate Kinase Domain Containing Protein (Unknown Function)
- CCDC70: Coiled-coil domain-containing protein 70
- CHAMP1: Chromosome alignment-maintaining phosphoprotein 1
- CKAP2: Cytoskeleton-associated protein 2
- DLEU1: a long non-coding RNA
- DLEU2: Deleted in lymphocytic leukemia 1
- DZIP1: DAZ interacting zinc finger protein 1
- EDNRB: endothelin receptor type B
- ELF1: encoding protein E74-like factor 1 (ets domain transcription factor)
- ESD: S-formylglutathione hydrolase
- FAM155A: encoding protein Family with sequence similarity 155, member A
- FLT1: Fms related tyrosine kinase 1 (Vascular endothelial growth factor receptor 1)
- GJB2: gap junction protein, beta 2, 26kDa (connexin 26)
- GJB6: gap junction protein, beta 6 (connexin 30)
- Glypican 5: encoding protein Glypican-5
- HTR2A: 5-HT2A receptor
- INTS6: encoding protein Integrator complex subunit 6
- GPALPP1: encoding protein KIAA1704
- MBNL2: encoding protein Muscleblind-like protein 2
- MIPEP: encoding enzyme Mitochondrial intermediate peptidase
- MIRH1: encoding protein Putative microRNA host gene 1 protein
- MTRF1:
- NDFIP2: encoding protein NEDD4 family-interacting protein 2
- NUPL1: encoding protein Nucleoporin p58/p45
- PCCA: propionyl Coenzyme A carboxylase, alpha polypeptide
- RB1: retinoblastoma 1 (including osteosarcoma)
- RCBTB1: encoding protein RCC1 and BTB domain-containing protein 1
- RCBTB2: encoding protein RCC1 and BTB domain-containing protein 2
- RGCC: encoding protein Regulator of cell cycle RGCC
- SCEL: encoding protein Sciellin
- SLC46A3: encoding protein Solute carrier family 46, member 3
- SLITRK1: encoding protein SLIT and NTRK-like protein 1
- SLITRK1: mutation in this gene causes some (although very few) cases of Tourette syndrome and trichotillomania
- SLITRK5: encoding protein SLIT and NTRK-like protein 5
- SLITRK6: encoding protein SLIT and NTRK-like protein 6
- SOX21: Transcription factor SOX-21 is a protein that in humans is encoded by the SOX21; its disruption can lead to types of alopecia in mice.
- SPRYD7: encoding protein SPRY domain-containing protein 7
- SUPT20H: SPT20 homolog
- TDRD3: encoding protein Tudor domain-containing protein 3
- TM9SF2: encoding protein Transmembrane 9 superfamily member 2
- TPT1: Translationally controlled tumor protein (TCTP)
- TSC22D1: encoding protein TSC22 domain family protein 1
- UBL3: encoding protein Ubiquitin-like protein 3
- WBP4: encoding protein WW domain-binding protein 4
- XPO4: encoding protein Exportin-4
- ZC3H13: encoding protein Zinc finger CCCH domain-containing protein 13
- ZMYM2: encoding protein Zinc finger MYM-type protein 2
Diseases and disorders
The following diseases and disorders are some of those related to genes on chromosome 13:
- 13q deletion syndrome
- Bladder cancer
- Breast cancer
- Heterochromia
- Hirschsprung's disease
- Maturity onset diabetes of the young type 4
- Nonsyndromic deafness
- Nonsyndromic deafness, autosomal dominant
- Nonsyndromic deafness, autosomal recessive
- Propionic acidemia
- Retinoblastoma
- Schizophrenia
- Waardenburg syndrome
- Wilson's disease
- Patau syndrome
- Chronic Lymphocytic Leukemia (Acquired defect)
- Young–Madders syndrome
Chromosomal conditions
The following conditions are caused by changes in the structure or number of copies of chromosome 13:
- Retinoblastoma: A small percentage of retinoblastoma cases are caused by deletions in the region of chromosome 13 (13q14) containing the RB1 gene. Children with these chromosomal deletions may also have mental retardation, slow growth, and characteristic facial features (such as prominent eyebrows, a broad nasal bridge, a short nose, and ear abnormalities). Researchers have not determined which other genes are located in the deleted region, but a loss of several genes is likely responsible for these developmental problems.
- Trisomy 13: Trisomy 13 occurs when each cell in the body has three copies of chromosome 13 instead of the usual two copies. Trisomy 13 can also result from an extra copy of chromosome 13 in only some of the body's cells (mosaic trisomy 13). In a small percentage of cases, trisomy 13 is caused by a rearrangement of chromosomal material between chromosome 13 and another chromosome. As a result, a person has the two usual copies of chromosome 13, plus extra material from chromosome 13 attached to another chromosome. These cases are called translocation trisomy 13. Extra material from chromosome 13 disrupts the course of normal development, causing the characteristic signs and symptoms of trisomy 13. Researchers are not yet certain how this extra genetic material leads to the features of the disorder, which include severely abnormal cerebral functions, a small cranium, retardation, non functional eyes and heart defects.
- Other chromosomal conditions: Partial monosomy 13q is a rare chromosomal disorder that results when a piece of the long arm (q) of chromosome 13 is missing (monosomic). Infants born with partial monosomy 13q may exhibit low birth weight, malformations of the head and face (craniofacial region), skeletal abnormalities (especially of the hands and feet), and other physical abnormalities. Mental retardation is characteristic of this condition. The mortality rate during infancy is high among individuals born with this disorder. Almost all cases of partial monosomy 13q occur randomly for no apparent reason (sporadic).
Cytogenetic band
G-banding ideograms of human chromosome 13
G-banding ideogram of human chromosome 13 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 13 in three different resolutions (400,[11] 550[12] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[13] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[14]
| Chr. | Arm[16] | Band[17] | ISCN start[18] |
ISCN stop[18] |
Basepair start |
Basepair stop |
Stain[19] | Density |
|---|---|---|---|---|---|---|---|---|
| 13 | p | 13 | 0 | 282 | 1 | 4,600,000 | gvar | |
| 13 | p | 12 | 282 | 620 | 4,600,001 | 10,100,000 | stalk | |
| 13 | p | 11.2 | 620 | 1015 | 10,100,001 | 16,500,000 | gvar | |
| 13 | p | 11.1 | 1015 | 1198 | 16,500,001 | 17,700,000 | acen | |
| 13 | q | 11 | 1198 | 1353 | 17,700,001 | 18,900,000 | acen | |
| 13 | q | 12.11 | 1353 | 1536 | 18,900,001 | 22,600,000 | gneg | |
| 13 | q | 12.12 | 1536 | 1635 | 22,600,001 | 24,900,000 | gpos | 25 |
| 13 | q | 12.13 | 1635 | 1790 | 24,900,001 | 27,200,000 | gneg | |
| 13 | q | 12.2 | 1790 | 1888 | 27,200,001 | 28,300,000 | gpos | 25 |
| 13 | q | 12.3 | 1888 | 2114 | 28,300,001 | 31,600,000 | gneg | |
| 13 | q | 13.1 | 2114 | 2255 | 31,600,001 | 33,400,000 | gpos | 50 |
| 13 | q | 13.2 | 2255 | 2367 | 33,400,001 | 34,900,000 | gneg | |
| 13 | q | 13.3 | 2367 | 2649 | 34,900,001 | 39,500,000 | gpos | 75 |
| 13 | q | 14.11 | 2649 | 2931 | 39,500,001 | 44,600,000 | gneg | |
| 13 | q | 14.12 | 2931 | 3030 | 44,600,001 | 45,200,000 | gpos | 25 |
| 13 | q | 14.13 | 3030 | 3128 | 45,200,001 | 46,700,000 | gneg | |
| 13 | q | 14.2 | 3128 | 3311 | 46,700,001 | 50,300,000 | gpos | 50 |
| 13 | q | 14.3 | 3311 | 3537 | 50,300,001 | 54,700,000 | gneg | |
| 13 | q | 21.1 | 3537 | 3762 | 54,700,001 | 59,000,000 | gpos | 100 |
| 13 | q | 21.2 | 3762 | 3889 | 59,000,001 | 61,800,000 | gneg | |
| 13 | q | 21.31 | 3889 | 4058 | 61,800,001 | 65,200,000 | gpos | 75 |
| 13 | q | 21.32 | 4058 | 4199 | 65,200,001 | 68,100,000 | gneg | |
| 13 | q | 21.33 | 4199 | 4439 | 68,100,001 | 72,800,000 | gpos | 100 |
| 13 | q | 22.1 | 4439 | 4565 | 72,800,001 | 74,900,000 | gneg | |
| 13 | q | 22.2 | 4565 | 4678 | 74,900,001 | 76,700,000 | gpos | 50 |
| 13 | q | 22.3 | 4678 | 4791 | 76,700,001 | 78,500,000 | gneg | |
| 13 | q | 31.1 | 4791 | 5087 | 78,500,001 | 87,100,000 | gpos | 100 |
| 13 | q | 31.2 | 5087 | 5171 | 87,100,001 | 89,400,000 | gneg | |
| 13 | q | 31.3 | 5171 | 5355 | 89,400,001 | 94,400,000 | gpos | 100 |
| 13 | q | 32.1 | 5355 | 5510 | 94,400,001 | 97,500,000 | gneg | |
| 13 | q | 32.2 | 5510 | 5636 | 97,500,001 | 98,700,000 | gpos | 25 |
| 13 | q | 32.3 | 5636 | 5834 | 98,700,001 | 101,100,000 | gneg | |
| 13 | q | 33.1 | 5834 | 5989 | 101,100,001 | 104,200,000 | gpos | 100 |
| 13 | q | 33.2 | 5989 | 6087 | 104,200,001 | 106,400,000 | gneg | |
| 13 | q | 33.3 | 6087 | 6256 | 106,400,001 | 109,600,000 | gpos | 100 |
| 13 | q | 34 | 6256 | 6510 | 109,600,001 | 114,364,328 | gneg |
References
- ↑ "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04.
- 1 2 "Search results - 13[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.
- 1 2 Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
- ↑ Pertea M, Salzberg SL (2010). "Between a chicken and a grape: estimating the number of human genes.". Genome Biol. 11 (5): 206. PMC 2898077
. PMID 20441615. doi:10.1186/gb-2010-11-5-206. - ↑ "Statistics & Downloads for chromosome 13". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.
- ↑ "Chromosome 13: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
- ↑ "Search results - 13[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
- ↑ "Search results - 13[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 - 13[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
- ↑ 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" (PDF). In Computer Science and Software Engineering (JCSSE), 2012 International Joint Conference on: 276–282. doi:10.1109/JCSSE.2012.6261965.
- ↑ 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.
- 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.
- ↑ 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.
- Baud O, Cormier-Daire V, Lyonnet S, Desjardins L, Turleau C, Doz F (1999). "Dysmorphic phenotype and neurological impairment in 22 retinoblastoma patients with constitutional cytogenetic 13q deletion". Clin Genet. 55 (6): 478–82. PMID 10450867. doi:10.1034/j.1399-0004.1999.550614.x.
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- Gilbert F (2000). "Chromosome 13". Genet Test. 4 (1): 85–94. PMID 10794368. doi:10.1089/109065700316543.
- Kivela T, Tuppurainen K, Riikonen P, Vapalahti M (2003). "Retinoblastoma associated with chromosomal 13q14 deletion mosaicism". Ophthalmology. 110 (10): 1983–8. PMID 14522775. doi:10.1016/S0161-6420(03)00484-6.
External links
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Wikimedia Commons has media related to Human chromosome 13. |
- National Institutes of Health. "Chromosome 13". Genetics Home Reference. Retrieved 2017-05-06.
- "Chromosome 13". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.
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