Chromosome 12

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Chromosome 12
File:Human male karyotpe high resolution - Chromosome 12 cropped.png
Human chromosome 12 pair after G-banding.
One is from mother, one is from father.
File:Human male karyotpe high resolution - Chromosome 12.png
Chromosome 12 pair
in human male karyogram.
Features
Length (bp)133,275,309 bp
(GRCh38)[1]
No. of genes988 (CCDS)[2]
TypeAutosome
Centromere positionSubmetacentric[3]
(35.5 Mbp[4])
Complete gene lists
CCDSGene list
HGNCGene list
UniProtGene list
NCBIGene list
External map viewers
EnsemblChromosome 12
EntrezChromosome 12
NCBIChromosome 12
UCSCChromosome 12
Full DNA sequences
RefSeqNC_000012 (FASTA)
GenBankCM000674 (FASTA)

Chromosome 12 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 12 spans about 133 million base pairs (the building material of DNA) and represents between 4 and 4.5 percent of the total DNA in cells.

Chromosome 12 contains the Homeobox C gene cluster.

Genes

Number of genes

The following are some of the gene count estimates of human chromosome 12. 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]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS 988 — — [2] 2016-09-08
HGNC 995 318 545 [6] 2017-05-12
Ensembl 1,033 1,202 617 [7] 2017-03-29
UniProt 1,032 — — [8] 2018-02-28
NCBI 1,036 853 693 [9][10][11] 2017-05-19

Gene list

See also: Category:Genes on human chromosome 12.

The following is a partial list of genes on human chromosome 12. For complete list, see the link in the infobox on the right.

  • ACAD10: encoding protein Acyl-CoA dehydrogenase family, member 10
  • ACSS3: encoding protein Acyl-CoA synthetase short-chain family member 3
  • ACVRL1: activin A receptor type II-like 1f
  • APOF: encoding protein Apolipoprotein F
  • APOLD1: apolipoprotein L domain containing 1
  • ARL6IP4: encoding protein ADP-ribosylation-like factor 6 interacting protein 4
  • ARPC3: encoding protein Actin-related protein 2/3 complex subunit 3
  • Asun: encoding protein Protein asunder homolog (Asun)
  • ATG101: Autophagy-related protein 101
  • BCAT1: encoding protein Branched chain amino acid transaminase 1
  • C12orf42: encoding protein uncharacterised chromosome 12 open reading frame 42
  • C12orf43: encoding protein. Uncharacterized.
  • C12orf60: encoding protein Uncharacterized protein C12orf60
  • CALCOCO1: Calcium-binding and coiled-coil domain-containing protein 1
  • CBX5: chromobox homolog 5
  • CCDC53: Coiled-coil domain-containing protein 53
  • CKAP4: Cytoskeleton associated protein 4
  • CNOT2: encoding protein CCR4-NOT transcription complex subunit 2
  • CNPY2: encoding protein Canopy FGF signaling regulator 2
  • CCDC42B: encoding protein Coiled Coil Domain Containing protein 42B
  • COL2A1: collagen, type II, alpha 1 (primary osteoarthritis, spondyloepiphyseal dysplasia, congenital)
  • CRACR2A: encoding protein Calcium release activated channel regulator 2A
  • CSRP2: Cysteine and glycine-rich protein 2
  • DDX23: DEAD-box helicase 23
  • DDX47: DEAD-box helicase 47
  • DHH: Desert hedgehog protein
  • DPPA3: Developmental pluripotency-associated protein 3
  • DPY19L2: encoding protein Dpy-19-like 2 (C. elegans)
  • E2F7: E2F transcription factor 7
  • EMP1: Epithelial membrane protein 1
  • ERGIC2: encoding protein a protein of 377 amino acid residues
  • FAM60A: encoding protein FAM60A
  • FAM186B: encoding protein Protein FAM186B
  • GPD1: encoding protein Glycerol-3-phosphate dehydrogenase 1
  • GOLT1B: Golgi transport 1B
  • GPN3: encoding enzyme GPN-loop GTPase 3
  • HNF1A-AS1: encoding protein HNF1A antisense RNA 1
  • HPD: 4-hydroxyphenylpyruvate dioxygenase
  • IFFO1: encoding protein Intermediate filament family orphan 1
  • KANSL2: encoding protein KAT8 regulatory NSL complex subunit 2 (KANSL2)
  • KCNA1: potassium voltage-gated channel subfamily A member 1 at 12p13.32
  • KDM2B: encoding protein Lysine (K)-specific demethylase 2B
  • KERA: keratocan
  • KRAS: V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog
  • LARP4: encoding protein La-related protein 4
  • LEPREL2: encoding enzyme Prolyl 3-hydroxylase 3
  • LMBR1L: encoding protein Protein LMBR1L
  • LRRC23: encoding protein Leucine-rich repeat-containing protein 23
  • LRRIQ1: encoding protein Leucine-rich repeats and IQ motif containing 1
  • LRRK2: leucine-rich repeat kinase 2
  • MBOAT5: encoding enzyme Lysophospholipid acyltransferase 5
  • METTL1: encoding enzyme tRNA (guanine-N(7)-)-methyltransferase
  • MFAP5: encoding protein Microfibrillar-associated protein 5
  • MIR196A2: encoding microRNA MicroRNA 196a-2
  • MMAB: methylmalonic aciduria (cobalamin deficiency) cblB type
  • MON2: encoding protein Protein MON2 homolog
  • MUCL1: encoding protein Mucin-like protein 1
  • MYO1A: myosin IA
  • NANOG: NK-2 type homeodomain gene
  • NAP1L1: encoding protein Nucleosome assembly protein 1-like 1
  • NRIP2: encoding protein Nuclear receptor-interacting protein 2
  • NUDT4: encoding enzyme Diphosphoinositol polyphosphate phosphohydrolase 2
  • PAH: phenylalanine hydroxylase
  • PIP4K2C: encoding protein Phosphatidylinositol-5-phosphate 4-kinase, type II, gamma
  • PIWIL1: encoding protein Piwi-like protein 1
  • POP5: encoding enzyme Ribonuclease P/MRP protein subunit POP5
  • PPHLN1: encoding protein Periphilin-1
  • PPP1R12A: protein phosphatase 1, regulatory (inhibitor) subungfdit 12A
  • PRB1: encoding protein Basic salivary proline-rich protein 1
  • PRB3: encoding protein Basic salivary proline-rich protein 3
  • PRB4: encoding protein Basic salivary proline-rich protein 4
  • PZP: encoding protein Pregnancy zone protein
  • PRH1: encoding protein Salivary acidic proline-rich phosphoprotein 1/2
  • PRH2: encoding protein Proline-rich protein HaeIII subfamily 2
  • PRR4: encoding protein Proline-rich protein 4
  • PTMS: encoding protein Parathymosin
  • PTPN11: protein tyrosine phosphatase, non-receptor type 11 (Noonan syndrome 1)
  • PUS1: encoding enzyme tRNA pseudouridine synthase A
  • PUS7L: encoding enzyme Pseudouridylate synthase 7 homolog-like protein
  • RAB3IP: encoding protein RAB3A-interacting protein
  • RASSF8: encoding protein Ras association domain-containing protein 8
  • RASSF9: encoding protein Ras association domain-containing protein 9
  • RERG: encoding protein RAS-like, estrogen-regulated, growth inhibitor
  • RNF34: encoding enzyme E3 ubiquitin-protein ligase RNF34
  • SARNP: SAP domain-containing ribonucleoprotein
  • Serpina3f: encoding protein Serine (or cysteine) peptidase inhibitor, clade A, member 3F
  • SLC8B1: solute carrier family 8 member B1
  • TBC1D15: encoding protein TBC1 domain family member 15
  • TBX3: encoding protein T-box transcription factor 3
  • TCHP: encoding protein Trichoplein keratin filament-binding protein
  • TESPA1: encoding protein Thymocyte expressed, positive selection associated 1
  • THAP2: encoding protein THAP domain-containing protein 2
  • TMTC1: encoding protein Transmembrane and tetratricopeptide repeat containing 1
  • TMEM117: encoding protein Transmembrane protein 117
  • TRAFD1: encoding protein TRAF-type zinc finger domain-containing protein 1
  • TSFM: encoding protein Elongation factor Ts, mitochondrial
  • TWF1: twinfilin-1
  • UNQ1887:
  • USP52: encoding enzyme PAB-dependent poly(A)-specific ribonuclease subunit 2
  • UTP20: encoding protein Small subunit processome component 20 homolog
  • VEZT: encoding protein Vezatin
  • YAF2: encoding protein YY1-associated factor 2
  • ZCCHC8: encoding protein Zinc finger CCHC domain-containing protein 8
  • ZFC3H1: encoding protein Zinc finger C3H1-type containing
  • ZNF26: encoding protein Zinc finger protein 26
  • ZNF84: encoding protein Zinc finger protein 84
  • ZNF268: encoding protein Zinc finger protein 268
  • ZNF664: encoding protein Zinc finger protein 664

Diseases and disorders

The following diseases are some of those related to genes on chromosome 12:

Cytogenetic band

G-banding ideograms of human chromosome 12
File:Human chromosome 12 ideogram vertical.svg
G-banding ideogram of human chromosome 12 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).
File:Human chromosome 12 - 400 550 850 bphs.png
G-banding patterns of human chromosome 12 in three different resolutions (400,[13] 550[14] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[15] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[16]
G-bands of human chromosome 12 in resolution 850 bphs[17]
Chr. Arm[18] Band[19] ISCN
start[20] 		ISCN
stop[20] 		Basepair
start 		Basepair
stop 		Stain[21] Density
12 p 13.33 0 216 1 3,200,000 gneg
12 p 13.32 216 345 3,200,001 5,300,000 gpos 25
12 p 13.31 345 633 5,300,001 10,000,000 gneg
12 p 13.2 633 806 10,000,001 12,600,000 gpos 75
12 p 13.1 806 921 12,600,001 14,600,000 gneg
12 p 12.3 921 1195 14,600,001 19,800,000 gpos 100
12 p 12.2 1195 1252 19,800,001 21,100,000 gneg
12 p 12.1 1252 1526 21,100,001 26,300,000 gpos 100
12 p 11.23 1526 1655 26,300,001 27,600,000 gneg
12 p 11.22 1655 1785 27,600,001 30,500,000 gpos 50
12 p 11.21 1785 1900 30,500,001 33,200,000 gneg
12 p 11.1 1900 2015 33,200,001 35,500,000 acen
12 q 11 2015 2116 35,500,001 37,800,000 acen
12 q 12 2116 2562 37,800,001 46,000,000 gpos 100
12 q 13.11 2562 2706 46,000,001 48,700,000 gneg
12 q 13.12 2706 2850 48,700,001 51,100,000 gpos 25
12 q 13.13 2850 3210 51,100,001 54,500,000 gneg
12 q 13.2 3210 3383 54,500,001 56,200,000 gpos 25
12 q 13.3 3383 3498 56,200,001 57,700,000 gneg
12 q 14.1 3498 3700 57,700,001 62,700,000 gpos 75
12 q 14.2 3700 3786 62,700,001 64,700,000 gneg
12 q 14.3 3786 3959 64,700,001 67,300,000 gpos 50
12 q 15 3959 4203 67,300,001 71,100,000 gneg
12 q 21.1 4203 4362 71,100,001 75,300,000 gpos 75
12 q 21.2 4362 4549 75,300,001 79,900,000 gneg
12 q 21.31 4549 4837 79,900,001 86,300,000 gpos 100
12 q 21.32 4837 4894 86,300,001 88,600,000 gneg
12 q 21.33 4894 5125 88,600,001 92,200,000 gpos 100
12 q 22 5125 5355 92,200,001 95,800,000 gneg
12 q 23.1 5355 5571 95,800,001 101,200,000 gpos 75
12 q 23.2 5571 5643 101,200,001 103,500,000 gneg
12 q 23.3 5643 5873 103,500,001 108,600,000 gpos 50
12 q 24.11 5873 6104 108,600,001 111,300,000 gneg
12 q 24.12 6104 6219 111,300,001 111,900,000 gpos 25
12 q 24.13 6219 6334 111,900,001 113,900,000 gneg
12 q 24.21 6334 6478 113,900,001 116,400,000 gpos 50
12 q 24.22 6478 6579 116,400,001 117,700,000 gneg
12 q 24.23 6579 6737 117,700,001 120,300,000 gpos 50
12 q 24.31 6737 7083 120,300,001 125,400,000 gneg
12 q 24.32 7083 7255 125,400,001 128,700,000 gpos 50
12 q 24.33 7255 7500 128,700,001 133,275,309 gneg

References

  1. ↑ "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04.
  2. ↑ 2.0 2.1 "Search results - 12[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. ↑ 4.0 4.1 Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  5. ↑ 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.
  6. ↑ "Statistics & Downloads for chromosome 12". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.
  7. ↑ "Chromosome 12: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
  8. ↑ "Human chromosome 12: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.
  9. ↑ "Search results - 12[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  10. ↑ "Search results - 12[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.
  11. ↑ "Search results - 12[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  12. ↑ Riaz N; Steinberg S; Ahmad J; et al. (April 2005). "Genomewide significant linkage to stuttering on chromosome 12". Am. J. Hum. Genet. 76 (4): 647–51. doi:10.1086/429226. PMC 1199301. PMID 15714404.
  13. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  14. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  15. ↑ 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.
  16. ↑ 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.
  17. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  18. ↑ "p": Short arm; "q": Long arm.
  19. ↑ For cytogenetic banding nomenclature, see article locus.
  20. ↑ 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.
  21. ↑ 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.
  • Gilbert F, Kauff N (2000). "Disease genes and chromosomes: disease maps of the human genome.Chromosome 12". Genet Test. 4 (3): 319–33. doi:10.1089/10906570050501588. PMID 11142767.
  • Montgomery KT, Lee E, Miller A, Lau S, Shim C, Decker J, Chiu D, Emerling S, Sekhon M, Kim R, Lenz J, Han J, Ioshikhes I, Renault B, Marondel I, Yoon SJ, Song K, Murty VV, Scherer S, Yonescu R, Kirsch IR, Ried T, McPherson J, Gibbs R, Kucherlapati R (2001). "A high-resolution map of human chromosome 12". Nature. 409 (6822): 945–6. doi:10.1038/35057174. PMID 11237017.

External links

  • National Institutes of Health. "Chromosome 12". Genetics Home Reference. Retrieved 2017-05-06.
  • "Chromosome 12". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.
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