Chromosome 9
From Wikipedia - Reading time: 11 min
| Chromosome 9 | |
|---|---|
 Human chromosome 9 pair after G-banding: One is from the mother, one is from the father. | |
 Chromosome 9 pair in human male karyogram | |
| Features | |
| Length (bp) | 150,617,247 bp (CHM13) |
| No. of genes | 739 (CCDS)[1] |
| Type | Autosome |
| Centromere position | Submetacentric[2] (43.0 Mbp[3]) |
| Complete gene lists | |
| CCDS | Gene list |
| HGNC | Gene list |
| UniProt | Gene list |
| NCBI | Gene list |
| External map viewers | |
| Ensembl | Chromosome 9 |
| Entrez | Chromosome 9 |
| NCBI | Chromosome 9 |
| UCSC | Chromosome 9 |
| Full DNA sequences | |
| RefSeq | NC_000009 (FASTA) |
| GenBank | CM000671 (FASTA) |
Chromosome 9 is one of the 23 pairs of chromosomes in humans. Humans normally have two copies of this chromosome, as they normally do with all chromosomes. Chromosome 9 spans about 138 million base pairs of nucleic acids (the building blocks of DNA) and represents between 4.0 and 4.5% of the total DNA in cells.
Genes
[edit]Number of genes
[edit]These are some of the gene count estimates of human chromosome 9. 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 | Noncoding RNA genes | Pseudogenes | Source | Release date |
|---|---|---|---|---|---|
| CCDS | 739 | — | — | [1] | 2016-09-08 |
| HGNC | 749 | 246 | 590 | [5] | 2017-05-12 |
| Ensembl | 775 | 788 | 663 | [6] | 2017-03-29 |
| UniProt | 812 | — | — | [7] | 2018-02-28 |
| NCBI | 822 | 830 | 738 | [8][9][10] | 2017-05-19 |
Gene list
[edit]The following is a partial list of genes on human chromosome 9. For a complete list, see the link in the infobox on the right.
- ABO: ABO histo-blood group glycosyltransferases
- ACTL7A: encoding protein Actin-like protein 7A
- ADAMTS13: ADAM metallopeptidase with thrombospondin type 1 motif, 13
- AIF1L: allograft inflammatory factor 1-like
- ALAD: aminolevulinate, delta-, dehydratase
- ALS4: amyotrophic lateral sclerosis 4
- ANGPTL2: angiopoietin-related protein 2
- ASS: argininosuccinate synthetase
- BANCR: encoding protein BRAF-activated non-protein coding RNA
- BNC2: zinc finger protein basonuclin-2
- C9orf64: chromosome 9 open reading frame 64
- C9orf78: encoding protein Uncharacterized protein C9orf78
- SHOC1: Shortage In Chiasmata 1
- C9orf25: encoding protein Chromosome 9 open reading frame 25
- C9orf43: encoding protein Chromosome 9 open reading frame 43
- C9orf135: encoding protein Chromosome 9 open reading frame 135
- C9orf152: chromosome 9 open reading frame 152
- C9orf156: encoding protein Chromosome 9 open reading frame 156
- CAAP1: caspase activity and apoptosis inhibitor 1
- CARD19: caspase recruitment domain family member 19
- CBWD1: COBW domain-containing protein 1
- CCDC180: Coiled coil domain-containing protein 180
- CCL21: chemokine (C-C motif) ligand 21, SCYA21
- CCL27: chemokine (C-C motif) ligand 27, SCYA27
- CFAP157: Cilia and flagella associated protein 157
- CHMP5: Charged multivesicular body protein 5
- CNTLN: centlein
- CDKN2BAS: CDKN2B antisense RNA 1 or antisense non-coding RNA in the INK4 locus (ANRIL)
- COL5A1: collagen, type V, alpha 1
- DDX31: DEAD box polypeptide 31
- DENND1A: DENN domain-containing protein 1A
- ENG: endoglin (Osler-Rendu-Weber syndrome 1)
- ENTPD2: encoding enzyme ectonucleoside triphosphate diphosphohydrolase 2
- EQTN: equatorin
- FAM73B: family with sequence similarity 73 member B
- FAM120A: Family with sequence similarity 120 member A
- FAM122a: encoding protein Family with sequence similarity 122A
- FBP1 Fructose-1,6-bisphosphatase 1
- FIBCD1: encoding protein Fibrinogen C domain containing 1
- FOCAD: focadhesin
- FXN: frataxin
- GALT: galactose-1-phosphate uridylyltransferase
- GAS1: growth arrest-specific protein 1
- GCNT1: glucosaminyl (N-acetyl) transferase 1
- GLE1L: Nucleoporin GLE1
- GPR107: G protein-coupled receptor 107
- GRHPR: glyoxylate redasductase/hydroxypyruvate reductase
- GSN: cytoplasmic and plasma gelsolin
- HAUS6: HAUS augmin-like complex subunit 6
- HEMGN: encoding protein hemogen
- IFN1@: Interferon, type 1, cluster
- IKBKAP: inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein
- INSL6: insulin like 6
- ISCA1: iron-sulfur cluster assembly 1 homolog, mitochondrial
- KIAA1958: protein KIAA1958
- KYAT1: Kynurenine aminotransferase 1
- LINGO2: leucine rich repeat and Ig domain containing 2
- LOC101928193: encoding protein LOC101928193
- MGC50722: Protein MGC50722, Uncharacterized Protein LOC399693
- MIR181A2HG encoding protein MIR181A2 host gene
- MIR7-1: microRNA 7-1
- MSMP: encoding protein Microseminoprotein, prostate associated
- MTAP: S-methyl-5'-thioadenosine phosphorylase
- NAA35: encoding protein N(alpha)-acetyltransferase 35, NatC auxiliary subunit
- NANS: N-acetylneuraminate synthase
- NINJ1: ninjurin-1
- NOL6: nucleolar protein 6
- NUDT2: nudix hydrolase 2
- OBP2B: encoding protein Odorant-binding protein 2B
- OLFM1: olfactomedin 1
- PHF2: PHD finger protein 2
- PHPT1: phosphohistidine phosphatase 1
- PIP5K1B: phosphatidylinositol-4-phosphate 5-kinase type-1 beta
- PLAA: phospholipase A-2-activating protein
- PMPCA: mitochondrial processing alpha subunit
- PRUNE2: protein prune homolog 2
- PTCH1: protein patched 1 transmembrane receptor protein
- RABGAP1: RAB GTPase activating protein 1
- REXO4: RNA exonuclease 4
- RNF183: encoding protein Ring finger protein 183
- SARDH: sarcosine dehydrogenase, mitochondrial
- SIT1: signaling threshold regulating transmembrane adapter 1
- SLC25A25-AS1: encoding protein SLC25A25 antisense RNA 1
- SNORD24: encoding protein small nucleolar RNA, C/D box 24
- SPAG8 sperm-associated antigen 8
- SPIN1: spindlin-1
- ST6GALNAC4 encoding enzyme ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 4, also known as sialyltransferase 3C (SIAT3-C) or sialyltransferase 7D (SIAT7-D)
- ST6GALNAC6: ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 6
- STOML2: stomatin-like protein 2
- STRBP: spermatid perinuclear RNA-binding protein
- TEX10: testis expressed 10
- TGFBR1: transforming growth factor beta, receptor type I
- TMC1: transmembrane channel-like 1
- TMEM215: encoding protein Transmembrane protein 215
- TMEM268: Transmembrane protein 268
- TOR2A encoding protein Torsin-2A
- TSC1: tuberous sclerosis complex 1
- TTC39B: tetratricopeptide repeat protein 39B
- UBAC1: ubiquitin-associated domain containing protein 1
- UBAP1: ubiquitin-associated protein 1
- UBAP2: ubiquitin-associated protein 2
- ZBTB43: zinc finger and BTB domain containing 43
- ZCCHC6: zinc finger, CCHC domain containing 6
- ZDHHC21: zinc finger DHHC-type containing 21
- ZNF79: zinc finger protein 79
- ZNF367: encoding protein Zinc finger protein 367
- ZNF510: zinc finger protein 510
Diseases and disorders
[edit]The following diseases are some of those related to genes on chromosome 9:
- Coronary artery disease
- chronic myelogenous leukemia (t9;22 - the Philadelphia chromosome)
- Diaphyseal Medullary Stenosis with Malignant Fibrous Histiosytoma (DMS-MFH, Hardcastle syndrome)
- Ehlers-Danlos syndrome
- familial dysautonomia
- Friedreich ataxia
- Frontotemporal dementia
- galactosemia
- Gorlin syndrome or nevoid basal cell carcinoma syndrome
- hereditary hemorrhagic telangiectasia
- lethal congenital contracture syndrome
- nail-patella syndrome (NPS)
- nonsyndromic deafness
- OCD
- polycythemia vera
- porphyria
- primary hyperoxaluria
- Tangier disease
- tetrasomy 9p
- thrombotic thrombocytopenic purpura
- trisomy 9
- tuberous sclerosis
- VLDLR-associated cerebellar hypoplasia
Cytogenetic band
[edit]G-banding ideograms of human chromosome 9
G-banding ideogram of human chromosome 9 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 9 in three different resolutions (400,[11] 550[12] and 850[3]). 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 |
|---|---|---|---|---|---|---|---|---|
| 9 | p | 24.3 | 0 | 127 | 1 | 2,200,000 | gneg | |
| 9 | p | 24.2 | 127 | 268 | 2,200,001 | 4,600,000 | gpos | 25 |
| 9 | p | 24.1 | 268 | 451 | 4,600,001 | 9,000,000 | gneg | |
| 9 | p | 23 | 451 | 677 | 9,000,001 | 14,200,000 | gpos | 75 |
| 9 | p | 22.3 | 677 | 846 | 14,200,001 | 16,600,000 | gneg | |
| 9 | p | 22.2 | 846 | 987 | 16,600,001 | 18,500,000 | gpos | 25 |
| 9 | p | 22.1 | 987 | 1085 | 18,500,001 | 19,900,000 | gneg | |
| 9 | p | 21.3 | 1085 | 1297 | 19,900,001 | 25,600,000 | gpos | 100 |
| 9 | p | 21.2 | 1297 | 1395 | 25,600,001 | 28,000,000 | gneg | |
| 9 | p | 21.1 | 1395 | 1621 | 28,000,001 | 33,200,000 | gpos | 100 |
| 9 | p | 13.3 | 1621 | 1917 | 33,200,001 | 36,300,000 | gneg | |
| 9 | p | 13.2 | 1917 | 2030 | 36,300,001 | 37,900,000 | gpos | 25 |
| 9 | p | 13.1 | 2030 | 2171 | 37,900,001 | 39,000,000 | gneg | |
| 9 | p | 12 | 2171 | 2312 | 39,000,001 | 40,000,000 | gpos | 50 |
| 9 | p | 11.2 | 2312 | 2523 | 40,000,001 | 42,200,000 | gneg | |
| 9 | p | 11.1 | 2523 | 2650 | 42,200,001 | 43,000,000 | acen | |
| 9 | q | 11 | 2650 | 2876 | 43,000,001 | 45,500,000 | acen | |
| 9 | q | 12 | 2876 | 3468 | 45,500,001 | 61,500,000 | gvar | |
| 9 | q | 13 | 3468 | 3609 | 61,500,001 | 65,000,000 | gneg | |
| 9 | q | 21.11 | 3609 | 3792 | 65,000,001 | 69,300,000 | gpos | 25 |
| 9 | q | 21.12 | 3792 | 3876 | 69,300,001 | 71,300,000 | gneg | |
| 9 | q | 21.13 | 3876 | 4060 | 71,300,001 | 76,600,000 | gpos | 50 |
| 9 | q | 21.2 | 4060 | 4229 | 76,600,001 | 78,500,000 | gneg | |
| 9 | q | 21.31 | 4229 | 4440 | 78,500,001 | 81,500,000 | gpos | 50 |
| 9 | q | 21.32 | 4440 | 4638 | 81,500,001 | 84,300,000 | gneg | |
| 9 | q | 21.33 | 4638 | 4835 | 84,300,001 | 87,800,000 | gpos | 50 |
| 9 | q | 22.1 | 4835 | 5074 | 87,800,001 | 89,200,000 | gneg | |
| 9 | q | 22.2 | 5074 | 5173 | 89,200,001 | 91,200,000 | gpos | 25 |
| 9 | q | 22.31 | 5173 | 5314 | 91,200,001 | 93,900,000 | gneg | |
| 9 | q | 22.32 | 5314 | 5455 | 93,900,001 | 96,500,000 | gpos | 25 |
| 9 | q | 22.33 | 5455 | 5638 | 96,500,001 | 99,800,000 | gneg | |
| 9 | q | 31.1 | 5638 | 5892 | 99,800,001 | 105,400,000 | gpos | 100 |
| 9 | q | 31.2 | 5892 | 6005 | 105,400,001 | 108,500,000 | gneg | |
| 9 | q | 31.3 | 6005 | 6146 | 108,500,001 | 112,100,000 | gpos | 25 |
| 9 | q | 32 | 6146 | 6456 | 112,100,001 | 114,900,000 | gneg | |
| 9 | q | 33.1 | 6456 | 6681 | 114,900,001 | 119,800,000 | gpos | 75 |
| 9 | q | 33.2 | 6681 | 6822 | 119,800,001 | 123,100,000 | gneg | |
| 9 | q | 33.3 | 6822 | 6949 | 123,100,001 | 127,500,000 | gpos | 25 |
| 9 | q | 34.11 | 6949 | 7217 | 127,500,001 | 130,600,000 | gneg | |
| 9 | q | 34.12 | 7217 | 7302 | 130,600,001 | 131,100,000 | gpos | 25 |
| 9 | q | 34.13 | 7302 | 7443 | 131,100,001 | 133,100,000 | gneg | |
| 9 | q | 34.2 | 7443 | 7555 | 133,100,001 | 134,500,000 | gpos | 25 |
| 9 | q | 34.3 | 7555 | 7950 | 134,500,001 | 138,394,717 | gneg |
References
[edit]- ^ a b "Search results - 1[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.
- ^ 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.
- ^ 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.
- ^ "Statistics & Downloads for chromosome 9". HUGO Gene Nomenclature Committee. 2017-05-12. Archived from the original on 2021-03-20. Retrieved 2017-05-19.
- ^ "Chromosome 9: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
- ^ "Human chromosome 9: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.
- ^ "Search results - 9[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
- ^ "Search results - 9[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 - 9[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". 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.
- ^ 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.
- ^ 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.
- ^ 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 (2001). "Disease genes and chromosomes: disease maps of the human genome. Chromosome 9". Genet Test. 5 (2): 157–74. doi:10.1089/109065701753145664. PMID 11551106.
- Humphray SJ, Oliver K, Hunt AR, et al. (2004). "DNA sequence and analysis of human chromosome 9". Nature. 429 (6990): 369–74. Bibcode:2004Natur.429..369H. doi:10.1038/nature02465. PMC 2734081. PMID 15164053.
- Wicking C, Berkman J, Wainwright B (1994). "Fine genetic mapping of the gene for nevoid basal cell carcinoma syndrome. Chromosome 9". Genomics. 22 (3): 505–11. doi:10.1006/geno.1994.1423. PMID 8001963.
- Mäkelä-Bengs P, Järvinen N, Vuopala K, Suomalainen A, Palotie A, Peltonen L (1997). "The assignment the lethal congenital contracture syndrome (LCCS) locus to chromosome 9q33-34". Am. J. Hum. Genet. 61 (suppl): A30.
External links
[edit]
Wikimedia Commons has media related to Human chromosome 9.
- National Institutes of Health. "Chromosome 9". Genetics Home Reference. Archived from the original on 2007-06-30. Retrieved 2017-05-06.
- "Chromosome 9". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.
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