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Chromosome 13

From Wikipedia, the free encyclopedia
Chromosome 13
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)113,566,686 bp
(CHM13)
No. of genes308 (CCDS)[1]
TypeAutosome
Centromere positionAcrocentric[2]
(17.7 Mbp[3])
Complete gene lists
CCDSGene list
HGNCGene list
UniProtGene list
NCBIGene list
External map viewers
EnsemblChromosome 13
EntrezChromosome 13
NCBIChromosome 13
UCSCChromosome 13
Full DNA sequences
RefSeqNC_000013 (FASTA)
GenBankCM000675 (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 113 million base pairs (the building material of DNA) and represents between 3.5 and 4% of the total DNA in cells.

Genes

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Number of genes

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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.[4]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS 308 — — [1] 2016-09-08
HGNC 309 323 469 [5] 2017-05-12
Ensembl 324 586 373 [6] 2017-03-29
UniProt 329 — — [7] 2018-02-28
NCBI 343 622 481 [8][9][10] 2017-05-19

Gene list

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See also: Category:Genes on human chromosome 13

The following is a partial list of genes on human chromosome 13. For complete list, see the link in the infobox on the right.

  • ARGLU1: encoding protein Arginine and glutamate-rich protein 1
  • ATP7B: ATPase, Cu transporting, beta polypeptide (Wilson disease)
  • BRCA2: breast cancer 2, early onset
  • BRCA3 encoding protein Breast cancer 3
  • C13orf42: encoding protein C13orf42
  • 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
  • CLYBL: Citrate lyase beta like
  • CPB2-AS1: encoding protein Cpb2 antisense rna 1
  • CRYL1: encoding protein Crystallin, lambda 1
  • 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)
  • EPSTI1: encoding protein Epithelial stromal interaction 1
  • 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
  • ITGBL1: encoding protein Integrin subunit beta like 1
  • GPALPP1: encoding protein KIAA1704
  • L1TD1P1: encoding protein LINE-1 type transposase domain containing 1 pseudogene 1
  • LACC1: encoding protein Laccase (multicopper oxidoreductase) domain containing 1
  • LHFP: encoding protein Lipoma HMGIC fusion partner
  • LINC00327: encoding protein Long intergenic non-protein coding RNA 327
  • LINC00346: encoding protein Long intergenic non-protein coding RNA 346
  • LINC00598: encoding protein Long intergenic non-protein coding rna 598
  • LOC107984557 encoding protein Methylcytosine dioxygenase TET1-like
  • MBNL2: encoding protein Muscleblind-like protein 2
  • MIPEP: encoding enzyme Mitochondrial intermediate peptidase
  • MIRH1: encoding protein Putative microRNA host gene 1 protein
  • MTRF1:
  • MTUS2: encoding protein Microtubule associated scaffold protein 2
  • NDFIP2: encoding protein NEDD4 family-interacting protein 2
  • NUPL1: encoding protein Nucleoporin p58/p45
  • OLFM4: encoding protein Olfactomedin 4
  • POMP: encoding proteasome maturation protein
  • 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
  • RNA28S1: encoding protein RNA, 28S ribosomal 1
  • RNR1: encoding RNA, ribosomal 45S cluster 1
  • 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

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The following diseases and disorders are some of those related to genes on chromosome 13:

Chromosomal conditions

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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.[11] Children with these chromosomal deletions may also have intellectual disability, 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. Intellectual disability 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

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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,[12] 550[13] and 850[3]). Band length in this diagram is based on the ideograms from ISCN (2013).[14] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[15]
G-bands of human chromosome 13 in resolution 850 bphs[3]
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

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  1. ^ a b "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.
  2. ^ Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2.
  3. ^ a b c Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  4. ^ 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.
  5. ^ "Statistics & Downloads for chromosome 13". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.
  6. ^ "Chromosome 13: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
  7. ^ "Human chromosome 13: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.
  8. ^ "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.
  9. ^ "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.
  10. ^ "Search results - 13[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  11. ^ Dunham A, Matthews LH, Burton J, Ashurst JL, Howe KL, Ashcroft KJ, et al. (2004). "The DNA sequence and analysis of human chromosome 13". Nature. 428 (6982): 522–8. Bibcode:2004Natur.428..522D. doi:10.1038/nature02379. PMC 2665288. PMID 15057823.
  12. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  13. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  14. ^ 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.
  15. ^ 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. S2CID 16666470.
  16. ^ "p": Short arm; "q": Long arm.
  17. ^ For cytogenetic banding nomenclature, see article locus.
  18. ^ 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.
  19. ^ 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.
[edit]
Wikimedia Commons has media related to Human chromosome 13.
  • National Institutes of Health. "Chromosome 13". Genetics Home Reference. Archived from the original on October 9, 2004. Retrieved 2017-05-06.
  • "Chromosome 13". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.
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