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Chromosome 9

chromosome 9 abnormality, chromosome 9 deletion syndrome
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 45 percent of the total DNA in cells

Contents

  • 1 Genes
    • 11 Number of genes
    • 12 Gene list
  • 2 Diseases and disorders
  • 3 Cytogenetic band
  • 4 References
  • 5 External links

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

See also: Category:Genes on human chromosome 9

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: 9q342
  • 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 Nalpha-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
  • 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 9G-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 eg Ensembl, UCSC Genome BrowserG-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 243 0 127 7000100000000000000♠1 7006220000000000000♠2,200,000 gneg
9 p 242 127 268 7006220000100000000♠2,200,001 7006460000000000000♠4,600,000 gpos 25
9 p 241 268 451 7006460000100000000♠4,600,001 7006900000000000000♠9,000,000 gneg
9 p 23 451 677 7006900000100000000♠9,000,001 7007142000000000000♠14,200,000 gpos 75
9 p 223 677 846 7007142000010000000♠14,200,001 7007166000000000000♠16,600,000 gneg
9 p 222 846 987 7007166000010000000♠16,600,001 7007185000000000000♠18,500,000 gpos 25
9 p 221 987 1085 7007185000010000000♠18,500,001 7007199000000000000♠19,900,000 gneg
9 p 213 1085 1297 7007199000010000000♠19,900,001 7007256000000000000♠25,600,000 gpos 100
9 p 212 1297 1395 7007256000010000000♠25,600,001 7007280000000000000♠28,000,000 gneg
9 p 211 1395 1621 7007280000010000000♠28,000,001 7007332000000000000♠33,200,000 gpos 100
9 p 133 1621 1917 7007332000010000000♠33,200,001 7007363000000000000♠36,300,000 gneg
9 p 132 1917 2030 7007363000010000000♠36,300,001 7007379000000000000♠37,900,000 gpos 25
9 p 131 2030 2171 7007379000010000000♠37,900,001 7007390000000000000♠39,000,000 gneg
9 p 12 2171 2312 7007390000010000000♠39,000,001 7007400000000000000♠40,000,000 gpos 50
9 p 112 2312 2523 7007400000010000000♠40,000,001 7007422000000000000♠42,200,000 gneg
9 p 111 2523 2650 7007422000010000000♠42,200,001 7007430000000000000♠43,000,000 acen
9 q 11 2650 2876 7007430000010000000♠43,000,001 7007455000000000000♠45,500,000 acen
9 q 12 2876 3468 7007455000010000000♠45,500,001 7007615000000000000♠61,500,000 gvar
9 q 13 3468 3609 7007615000010000000♠61,500,001 7007650000000000000♠65,000,000 gneg
9 q 2111 3609 3792 7007650000010000000♠65,000,001 7007693000000000000♠69,300,000 gpos 25
9 q 2112 3792 3876 7007693000010000000♠69,300,001 7007713000000000000♠71,300,000 gneg
9 q 2113 3876 4060 7007713000010000000♠71,300,001 7007766000000000000♠76,600,000 gpos 50
9 q 212 4060 4229 7007766000010000000♠76,600,001 7007785000000000000♠78,500,000 gneg
9 q 2131 4229 4440 7007785000010000000♠78,500,001 7007815000000000000♠81,500,000 gpos 50
9 q 2132 4440 4638 7007815000010000000♠81,500,001 7007843000000000000♠84,300,000 gneg
9 q 2133 4638 4835 7007843000010000000♠84,300,001 7007878000000000000♠87,800,000 gpos 50
9 q 221 4835 5074 7007878000010000000♠87,800,001 7007892000000000000♠89,200,000 gneg
9 q 222 5074 5173 7007892000010000000♠89,200,001 7007912000000000000♠91,200,000 gpos 25
9 q 2231 5173 5314 7007912000010000000♠91,200,001 7007939000000000000♠93,900,000 gneg
9 q 2232 5314 5455 7007939000010000000♠93,900,001 7007965000000000000♠96,500,000 gpos 25
9 q 2233 5455 5638 7007965000010000000♠96,500,001 7007998000000000000♠99,800,000 gneg
9 q 311 5638 5892 7007998000010000000♠99,800,001 7008105400000000000♠105,400,000 gpos 100
9 q 312 5892 6005 7008105400001000000♠105,400,001 7008108500000000000♠108,500,000 gneg
9 q 313 6005 6146 7008108500001000000♠108,500,001 7008112100000000000♠112,100,000 gpos 25
9 q 32 6146 6456 7008112100001000000♠112,100,001 7008114900000000000♠114,900,000 gneg
9 q 331 6456 6681 7008114900001000000♠114,900,001 7008119800000000000♠119,800,000 gpos 75
9 q 332 6681 6822 7008119800001000000♠119,800,001 7008123100000000000♠123,100,000 gneg
9 q 333 6822 6949 7008123100001000000♠123,100,001 7008127500000000000♠127,500,000 gpos 25
9 q 3411 6949 7217 7008127500001000000♠127,500,001 7008130600000000000♠130,600,000 gneg
9 q 3412 7217 7302 7008130600001000000♠130,600,001 7008131100000000000♠131,100,000 gpos 25
9 q 3413 7302 7443 7008131100001000000♠131,100,001 7008133100000000000♠133,100,000 gneg
9 q 342 7443 7555 7008133100001000000♠133,100,001 7008134500000000000♠134,500,000 gpos 25
9 q 343 7555 7950 7008134500001000000♠134,500,001 7008138394717000000♠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. ^ 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 GRCh38p3 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:101186/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 GRCh38p3 Last update 2014-03-04 Retrieved 2017-04-26
  13. ^ Genome Decoration Page, NCBI Ideogram data for Homo sapience 550 bphs, Assembly GRCh38p3 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:101109/JCSSE20126261965 
  16. ^ Genome Decoration Page, NCBI Ideogram data for Homo sapience 850 bphs, Assembly GRCh38p3 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. ^ 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
  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:101089/109065701753145664 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:101038/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:101006/geno19941423 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 

chromosome 9, chromosome 9 abnormality, chromosome 9 deficiency, chromosome 9 deletion syndrome, chromosome 9 disorders, chromosome 9 duplication, chromosome 9 genes, chromosome 9 inversion, chromosome 9 syndrome, chromosome 9p


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