Chromosome 9 (human)

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Chromosome 9 (human)
Human male karyotpe high resolution - Chromosome 9 cropped.png
Human chromosome 9 pair after G-banding.
One is from mother, one is from father.
Human male karyotpe high resolution - Chromosome 9.png
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])
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. People 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[edit]

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
NCBI 822 830 738 [8][9][10] 2017-05-19

The following are some of the genes located on chromosome 9:

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
  • 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
  • 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[edit]

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

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[4]). 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]
G-bands of human chromosome 9 in resolution 850 bphs[15]
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]

  1. ^ "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04. 
  2. ^ 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. 
  3. ^ Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2. 
  4. ^ 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.
  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 2898077Freely accessible. 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. ^ "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. 
  9. ^ "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. 
  10. ^ "Search results - 9[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20. 
  11. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  12. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  13. ^ 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. 
  14. ^ 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. 
  15. ^ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  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.

External links[edit]

  • 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.