Chromosome 9

Last updated
Chromosome 9
Human male karyotpe high resolution - Chromosome 9 cropped.png
Human chromosome 9 pair after G-banding:
One is from the mother, one is from the father.
Human male karyotpe high resolution - Chromosome 9.png
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.

Contents

Genes

Number of genes

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 SourceRelease date
CCDS 739 [1] 2016-09-08
HGNC 749246590 [5] 2017-05-12
Ensembl 775788663 [6] 2017-03-29
UniProt 812 [7] 2018-02-28
NCBI 822830738 [8] [9] [10] 2017-05-19

Gene list

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.

The ABO gene, which determines ABO blood type, is located on the long arm of this chromosome. (Location: 9q34.2) Ics-codablock-blood-bag sample.jpg
The 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
  • 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

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

Cytogenetic band

G-banding ideograms of human chromosome 9
Human chromosome 9 ideogram vertical.svg
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).
Human chromosome 09 - 400 550 850 bphs.png
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]
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
9p24.3012712,200,000gneg
9p24.21272682,200,0014,600,000gpos25
9p24.12684514,600,0019,000,000gneg
9p234516779,000,00114,200,000gpos75
9p22.367784614,200,00116,600,000gneg
9p22.284698716,600,00118,500,000gpos25
9p22.1987108518,500,00119,900,000gneg
9p21.31085129719,900,00125,600,000gpos100
9p21.21297139525,600,00128,000,000gneg
9p21.11395162128,000,00133,200,000gpos100
9p13.31621191733,200,00136,300,000gneg
9p13.21917203036,300,00137,900,000gpos25
9p13.12030217137,900,00139,000,000gneg
9p122171231239,000,00140,000,000gpos50
9p11.22312252340,000,00142,200,000gneg
9p11.12523265042,200,00143,000,000acen
9q112650287643,000,00145,500,000acen
9q122876346845,500,00161,500,000gvar
9q133468360961,500,00165,000,000gneg
9q21.113609379265,000,00169,300,000gpos25
9q21.123792387669,300,00171,300,000gneg
9q21.133876406071,300,00176,600,000gpos50
9q21.24060422976,600,00178,500,000gneg
9q21.314229444078,500,00181,500,000gpos50
9q21.324440463881,500,00184,300,000gneg
9q21.334638483584,300,00187,800,000gpos50
9q22.14835507487,800,00189,200,000gneg
9q22.25074517389,200,00191,200,000gpos25
9q22.315173531491,200,00193,900,000gneg
9q22.325314545593,900,00196,500,000gpos25
9q22.335455563896,500,00199,800,000gneg
9q31.15638589299,800,001105,400,000gpos100
9q31.258926005105,400,001108,500,000gneg
9q31.360056146108,500,001112,100,000gpos25
9q3261466456112,100,001114,900,000gneg
9q33.164566681114,900,001119,800,000gpos75
9q33.266816822119,800,001123,100,000gneg
9q33.368226949123,100,001127,500,000gpos25
9q34.1169497217127,500,001130,600,000gneg
9q34.1272177302130,600,001131,100,000gpos25
9q34.1373027443131,100,001133,100,000gneg
9q34.274437555133,100,001134,500,000gpos25
9q34.375557950134,500,001138,394,717gneg

Related Research Articles

<span class="mw-page-title-main">Chromosome 21</span> Human chromosome

Chromosome 21 is one of the 23 pairs of chromosomes in humans. Chromosome 21 is both the smallest human autosome and chromosome, with 46.7 million base pairs representing about 1.5 percent of the total DNA in cells. Most people have two copies of chromosome 21, while those with three copies of chromosome 21 have Down syndrome.

<span class="mw-page-title-main">Chromosome 1</span> Human chromosome

Chromosome 1 is the designation for the largest human chromosome. Humans have two copies of chromosome 1, as they do with all of the autosomes, which are the non-sex chromosomes. Chromosome 1 spans about 249 million nucleotide base pairs, which are the basic units of information for DNA. It represents about 8% of the total DNA in human cells.

<span class="mw-page-title-main">Chromosome 6</span> Human chromosome

Chromosome 6 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 6 spans nearly 171 million base pairs and represents between 5.5 and 6% of the total DNA in cells. It contains the major histocompatibility complex, which contains over 100 genes related to the immune response, and plays a vital role in organ transplantation.

<span class="mw-page-title-main">Chromosome 13</span> Human chromosome

Chromosome 13 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 13 spans about 113 million base pairs and represents between 3.5 and 4% of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 2</span> Human chromosome

Chromosome 2 is one of the twenty-three pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 2 is the second-largest human chromosome, spanning more than 242 million base pairs and representing almost eight percent of the total DNA in human cells.

<span class="mw-page-title-main">Chromosome 3</span> Human chromosome

Chromosome 3 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 3 spans more than 198 million base pairs and represents about 6.5 percent of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 4</span> Human chromosome

Chromosome 4 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 4 spans more than 190 million base pairs and represents between 6 and 6.5 percent of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 5</span> Human chromosome

Chromosome 5 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 5 spans about 182 million base pairs and represents almost 6% of the total DNA in cells. Chromosome 5 is the 5th largest human chromosome, yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of non-coding and syntenic conservation with non-mammalian vertebrates, suggesting they are functionally constrained.

<span class="mw-page-title-main">Chromosome 7</span> Human chromosome

Chromosome 7 is one of the 23 pairs of chromosomes in humans, who normally have two copies of this chromosome. Chromosome 7 spans about 160 million base pairs and represents between 5 and 5.5 percent of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 8</span> Human chromosome

Chromosome 8 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 8 spans about 146 million base pairs and represents between 4.5 and 5.0% of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 10</span> Human chromosome

Chromosome 10 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 10 spans about 134 million base pairs and represents between 4 and 4.5 percent of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 11</span> Human chromosome

Chromosome 11 is one of the 23 pairs of chromosomes in humans. Humans normally have two copies of this chromosome. Chromosome 11 spans about 135 million base pairs and represents between 4 and 4.5 percent of the total DNA in cells. The shorter arm is termed 11p while the longer arm is 11q. At about 21.5 genes per megabase, chromosome 11 is one of the most gene-rich, and disease-rich, chromosomes in the human genome.

<span class="mw-page-title-main">Chromosome 12</span> Human chromosome

Chromosome 12 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 12 spans about 133 million base pairs and represents between 4 and 4.5 percent of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 14</span> Human chromosome

Chromosome 14 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 14 spans about 107 million base pairs and represents between 3 and 3.5% of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 15</span> Human chromosome

Chromosome 15 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 15 spans about 99.7 million base pairs and represents between 3% and 3.5% of the total DNA in cells. Chromosome 15 is an acrocentric chromosome, with a very small short arm, which contains few protein coding genes among its 19 million base pairs. It has a larger long arm that is gene rich, spanning about 83 million base pairs.

<span class="mw-page-title-main">Chromosome 16</span> Human chromosome

Chromosome 16 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 16 spans about 90 million base pairs and represents just under 3% of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 17</span> Human chromosome

Chromosome 17 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 17 spans more than 84 million base pairs and represents between 2.5 and 3% of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 18</span> Human chromosome

Chromosome 18 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 18 spans about 80 million base pairs and represents about 2.5 percent of the total DNA in cells.

<span class="mw-page-title-main">Chromosome 19</span> Human chromosome

Chromosome 19 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 19 spans more than 61.7 million base pairs, the building material of DNA. It is considered the most gene-rich chromosome containing roughly 1,500 genes, despite accounting for only 2 percent of the human genome.

<span class="mw-page-title-main">Chromosome 20</span> Human chromosome

Chromosome 20 is one of the 23 pairs of chromosomes in humans. Chromosome 20 spans around 66 million base pairs and represents between 2 and 2.5 percent of the total DNA in cells. Chromosome 20 was fully sequenced in 2001 and was reported to contain over 59 million base pairs. Since then, due to sequencing improvements and fixes, the length of chromosome 20 has been updated to just over 66 million base pairs.

References

  1. 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.
  2. Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN   978-1-136-84407-2.
  3. 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.
  4. 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.
  5. "Statistics & Downloads for chromosome 9". HUGO Gene Nomenclature Committee. 2017-05-12. Archived from the original on 2021-03-20. Retrieved 2017-05-19.
  6. "Chromosome 9: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
  7. "Human chromosome 9: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.
  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". 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.
  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. 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.
  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.