Chromosome 9

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 and 4.5 percent of the total DNA in cells.

Chromosome 9
Human chromosome 9 pair after G-banding. One is from mother, one is from father.
Chromosome 9 pair in human male karyogram.
Features
Length (bp)	138,394,717 bp (GRCh38)[1]
No. of genes	739 (CCDS)[2]
Type	Autosome
Centromere position	Submetacentric[3] (43.0 Mbp[4])
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)

Genes

Number of genes

The following 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.[5]

Estimated by	Protein-coding genes	Non-coding RNA genes	Pseudogenes	Source	Release date
CCDS	739	—	—	[2]	2016-09-08
HGNC	749	246	590	[6]	2017-05-12
Ensembl	775	788	663	[7]	2017-03-29
UniProt	812	—	—	[8]	2018-02-28
NCBI	822	830	738	[9][10][11]	2017-05-19

Gene list

The following is a partial list of genes on human chromosome 9. For complete list, see the link in the infobox on the right.

ABO gene which determines ABO blood type, is located on the long arm of this chromosome. (Location: 9q34.2)

• 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
• BNC2: zinc finger protein basonuclin-2
• C9orf64: chromosome 9 open reading frame 64
• C9orf78: encoding protein Uncharacterized protein C9orf78
• SHOC1: Shortage In Chiasmata 1
• C9orf135: encoding protein Chromosome 9 open reading frame 135
• C9orf152: chromosome 9 open reading frame 152
• 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
• 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
• 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
• 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
• 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
• 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
• 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
• ZNF510: zinc finger protein 510

Diseases and disorders

The following diseases are some of those related to genes on chromosome 9:

• acytosiosis
• ALA-D deficiency porphyria
• Amyotrophic lateral sclerosis
• citrullinemia
• 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
• 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's disease
• tetrasomy 9p
• thrombotic thrombocytopenic purpura
• trisomy 9
• tuberous sclerosis
• VLDLR-associated cerebellar hypoplasia

Cytogenetic band

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,[12] 550[13] and 850[4]). 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 9 in resolution 850 bphs[16]

Chr.	Arm[17]	Band[18]	ISCN start[19]	ISCN stop[19]	Basepair start	Basepair stop	Stain[20]	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

1. "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04.
2. "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.
3. Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2.
4. 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 9". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.
7. "Chromosome 9: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
8. "Human chromosome 9: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.
9. "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.
10. "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.
11. "Search results - 9[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
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. In Computer Science and Software Engineering (JCSSE), 2012 International Joint Conference on. pp. 276–282. doi:10.1109/JCSSE.2012.6261965. ISBN 978-1-4673-1921-8.
16. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
17. "p": Short arm; "q": Long arm.
18. For cytogenetic banding nomenclature, see article locus.
19. 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.
20. 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. 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

• National Institutes of Health. "Chromosome 9". Genetics Home Reference. Retrieved 2017-05-06.
• "Chromosome 9". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.