Chromosome 9

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)

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.

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 byProtein-coding genesNon-coding RNA genesPseudogenesSourceRelease date
CCDS739-- [2] 2016-09-08
HGNC749246590 [6] 2017-05-12
Ensembl775788663 [7] 2017-03-29
UniProt812-- [8] 2018-02-28
NCBI822830738 [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
  • C9orf84: chromosome 9 open reading frame 84
  • 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
  • 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:

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
9p 24.3012712,200,000 gneg
9p 24.21272682,200,0014,600,000 gpos25
9p 24.12684514,600,0019,000,000 gneg
9p 234516779,000,00114,200,000 gpos75
9p 22.367784614,200,00116,600,000 gneg
9p 22.284698716,600,00118,500,000 gpos25
9p 22.1987108518,500,00119,900,000 gneg
9p 21.31085129719,900,00125,600,000 gpos100
9p 21.21297139525,600,00128,000,000 gneg
9p 21.11395162128,000,00133,200,000 gpos100
9p 13.31621191733,200,00136,300,000 gneg
9p 13.21917203036,300,00137,900,000 gpos25
9p 13.12030217137,900,00139,000,000 gneg
9p 122171231239,000,00140,000,000 gpos50
9p 11.22312252340,000,00142,200,000 gneg
9p 11.12523265042,200,00143,000,000 acen
9q 112650287643,000,00145,500,000 acen
9q 122876346845,500,00161,500,000 gvar
9q 133468360961,500,00165,000,000 gneg
9q 21.113609379265,000,00169,300,000 gpos25
9q 21.123792387669,300,00171,300,000 gneg
9q 21.133876406071,300,00176,600,000 gpos50
9q 21.24060422976,600,00178,500,000 gneg
9q 21.314229444078,500,00181,500,000 gpos50
9q 21.324440463881,500,00184,300,000 gneg
9q 21.334638483584,300,00187,800,000 gpos50
9q 22.14835507487,800,00189,200,000 gneg
9q 22.25074517389,200,00191,200,000 gpos25
9q 22.315173531491,200,00193,900,000 gneg
9q 22.325314545593,900,00196,500,000 gpos25
9q 22.335455563896,500,00199,800,000 gneg
9q 31.15638589299,800,001105,400,000 gpos100
9q 31.258926005105,400,001108,500,000 gneg
9q 31.360056146108,500,001112,100,000 gpos25
9q 3261466456112,100,001114,900,000 gneg
9q 33.164566681114,900,001119,800,000 gpos75
9q 33.266816822119,800,001123,100,000 gneg
9q 33.368226949123,100,001127,500,000 gpos25
9q 34.1169497217127,500,001130,600,000 gneg
9q 34.1272177302130,600,001131,100,000 gpos25
9q 34.1373027443131,100,001133,100,000 gneg
9q 34.274437555133,100,001134,500,000 gpos25
9q 34.375557950134,500,001138,394,717 gneg

References

  1. ↑ "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04.
  2. 1 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. 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.
  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" (PDF). In Computer Science and Software Engineering (JCSSE), 2012 International Joint Conference on: 276–282. doi:10.1109/JCSSE.2012.6261965.
  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. 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.
  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.

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