Chromosome 2

Chromosome 2
Human chromosome 2 pair after G banding. One is from mother, one is from father.
Chromosome 2 pair in human male karyogram.
Features
Length (bp)	242,696,752 bp (CHM13)
No. of genes	1,194 (CCDS) [1]
Type	Autosome
Centromere position	Submetacentric [2] (93.9 Mbp [3] )
Complete gene lists
CCDS	Gene list
HGNC	Gene list
UniProt	Gene list
NCBI	Gene list
External map viewers
Ensembl	Chromosome 2
Entrez	Chromosome 2
NCBI	Chromosome 2
UCSC	Chromosome 2
Full DNA sequences
RefSeq	NC_000002 (FASTA)
GenBank	CM000664 (FASTA)

Fusion of ancestral chromosomes left distinctive remnants of telomeres, and a vestigial centromere

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 ^[4] and representing almost eight percent of the total DNA in human cells.

Chromosome 2 contains the HOXD homeobox gene cluster. ^[5]

Chromosomes

Further information: Chimpanzee genome project

Humans have only twenty-three pairs of chromosomes, while all other extant members of Hominidae have twenty-four pairs. ^[6] It is believed that Neanderthals and Denisovans had twenty-three pairs. ^[6]

Human chromosome 2 is a result of an end-to-end fusion of two ancestral chromosomes. ^{[7] [8] [9]} The evidence for this includes:

• The correspondence of chromosome 2 to two ape chromosomes. The closest human relative, the chimpanzee, has nearly identical DNA sequences to human chromosome 2, but they are found in two separate chromosomes. The same is true of the more distant gorilla and orangutan. ^{[10] [11]}
• The presence of a vestigial centromere. Normally a chromosome has just one centromere, but in chromosome 2 there are remnants of a second centromere in the q21.3–q22.1 region. ^[12]
• The presence of vestigial telomeres. These are normally found only at the ends of a chromosome, but in chromosome 2 there are additional telomere sequences in the q13 band, far from either end of the chromosome. ^[13]

We conclude that the locus cloned in cosmids c8.1 and c29B is the relic of an ancient telomere-telomere fusion and marks the point at which two ancestral ape chromosomes fused to give rise to human chromosome 2.

— Jacob W. Ijdo ^[13]

Genes

Number of genes

The following are some of the gene count estimates of human chromosome 2. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome vary. 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. ^[14]

Estimated by	Protein-coding genes	Non-coding RNA genes	Pseudogenes	Source	Release date
CCDS	1,194	—	—	[1]	2016-09-08
HGNC	1,196	450	931	[15]	2017-05-12
Ensembl	1,292	1,598	1,029	[16]	2017-03-29
UniProt	1,274	—	—	[17]	2018-02-28
NCBI	1,281	1,446	1,207	[18] [19] [20]	2017-05-19

List of genes

See also: Category:Genes on human chromosome 2

The following is a partial list of genes on human chromosome 2. For complete list, see the link in the infobox on the right.

p-arm

Partial list of the genes located on p-arm (short arm) of human chromosome 2:

• ACTR2: encoding protein Actin-related protein 2
• ADI1: encoding enzyme 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase
• AFF3: encoding protein AF4/FMR2 family member 3
• AFTPH: encoding protein Aftiphilin
• ALMS1: Alstrom syndrome 1
• ABCG5 and ABCG8: ATP-binding cassette, subfamily A, members 5 and 8
• ASXL2: Additional sex combs like 2, transcriptional regulator
• ATOH8: encoding protein Atonal bHLH transcription factor 8
• ATRAID: encoding protein Apoptosis-related protein 3
• BCYRN1: BC200 lncRNA
• C2orf16: unknown protein C2orf16
• CAPG: capping acting protein
• CCDC104: Coiled-coil domain containing 104
• CCDC142: Coiled-coil domain containing 142
• CCDC142: Coiled-Coil Domain Containing 142
• CGREF1: encoding protein Cell growth regulator with EF-hand domain 1
• CLEC4F: encoding protein C-type lectin domain family 4 member F
• CTLA4: cytotoxic T-Lymphocyte Antigen 4
• CYTOR: Cytoskeleton regulator RNA
• DHX57: DExH-box helicase 57
• DPYSL5: Dihydropyrimidinase like 5
• ERLEC1: Endoplasmic reticulum lectin 1
• EVA1A: encoding protein Eva-1 homolog A (C. elegans)
• EXOC6B: encoding protein Exocyst complex component 6b
• FAM49A: Family with sequence similarity 49 member A
• FAM98A: Family with sequence similarity 98 member A
• FAM136A: Family with sequence similarity 136 member A
• FBXO11: F-box protein 11
• FTH1P3: encoding protein Ferritin heavy chain 1 pseudogene 3
• GEN1 encoding protein GEN1, Holliday junction 5' flap endonuclease
• GCKR: Glucokinase regulator
• GFPT1: glutamine—fructose-6-phosphate transaminase 1
• GKN1: gastrokine 1
• GPATCH11: G-patch domain containing protein 11
• GTF2A1L: General transcription factor IIA subunit 1 like
• HADHA: hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit
• HADHB: hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit
• HSPC159: Galectin-related protein
• ID2-AS1: encoding protein Id2 antisense rna 1 (head to head)
• LCLAT1: encoding protein Lysocardiolipin acyltransferase 1
• LEPQTL1: Leptin, serum levels of
• MBOAT2: encoding protein Membrane bound o-acyltransferase domain containing 2
• MEMO1: Mediator of cell motility 1
• MPHOSPH10: M-phase phosphoprotein 10
• MSH2: mutS homolog 2, colon cancer, nonpolyposis type 1 ( E. coli )
• MSH6: mutS homolog 6 ( E. coli )
• MTHFD2: Bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase, mitochondrial
• MTIF2: mitochondrial translational initiation factor 2
• NDUFAF7: Protein arginine methyltransferase NDUFAF7, mitochondrial
• NRBP1: Nuclear receptor-binding protein 1
• ODC1: Ornithine decarboxylase
• OTOF: otoferlin
• PAIP2B: Poly(a) binding protein interacting protein 2b
• PARK3 encoding protein Parkinson disease 3 (autosomal dominant, Lewy body)
• PCBP1-AS1: encoding protein PCBP1 antisense RNA 1
• PCYOX1: prenylcysteine oxidase 1
• PELI1: Ubiquitin ligase
• PLGLB2: Plasminogen-related protein B
• POLR1A: DNA-directed RNA polymerase I subunit RPA1
• PREPL: Prolyl endopeptidase-like
• PXDN: Peroxidasin homolog
• QPCT: Glutaminyl-peptide cyclotransferase
• RETSAT: All-trans-retinol 13,14-reductase
• RNF103: encoding protein Ring finger protein 103
• RNF103-CHMP3: encoding protein RNF103-CHMP3 readthrough
• SH3YL1: SH3 and SYLF domain-containing 1
• SLC35F6: encoding protein Transmembrane protein SLC35F6
• TGOLN2: Trans-Golgi network integral membrane protein 2
• THADA: encoding protein Thyroid adenoma associated
• TIA1: TIA1 cytotoxic granule-associated RNA binding protein
• TMEM150: Transmembrane protein 150A
• TP53I3: Putative quinone oxidoreducatse
• TPO: thyroid peroxidase
• TTC7A: familial multiple intestinal atresia
• WBP1: WW domain-binding protein 1
• WDCP: WD Repeat and Coiled Coil Containing Protein
• WDPCP: encoding protein Wd repeat containing planar cell polarity effector

q-arm

Partial list of the genes located on q-arm (long arm) of human chromosome 2:

• ABCA12: ATP-binding cassette, subfamily A (ABC1), member 12
• ACTR1B: encoding protein Beta-centractin
• AGXT: alanine-glyoxylate aminotransferase (oxalosis I; hyperoxaluria I; glycolicaciduria; serine-pyruvate aminotransferase)
• ALS2: amyotrophic lateral sclerosis 2 (juvenile)
• ALS2CR8: encoding protein Amyotrophic lateral sclerosis 2 chromosomal region candidate gene 8 protein also known as calcium-response factor (CaRF)
• ARMC9: encoding protein LisH domain-containing protein ARMC9
• B3GNT7: encoding protein UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 7
• BCS1L: GRACILE (Finnish heritage disease) related gene
• BMPR2: bone morphogenetic protein receptor, type II (serine/threonine kinase)
• C2orf40: encoding protein Augurin
• C2orf54: Chromosome 2 open reading frame 54
• CCDC115: encoding protein Coiled-coil domain containing 115
• CCDC138: Coiled-coil domain-containing protein 138
• CCDC74A: Coiled-coil domain containing 74a
• CCDC88A: Coiled-coil domain-containing protein 88A
• CCDC93: Coiled-coil domain-containing protein 93
• CDCA7: Cell division cycle associated protein 1
• CHPF: Chondroitin sulfate synthase 2
• CKAP2L: encoding protein Cytoskeleton associated protein 2 like
• COL3A1: collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant)
• COL4A3: collagen, type IV, alpha 3 (Goodpasture antigen)
• COL4A4: collagen, type IV, alpha 4
• COL5A2: collagen, type V, alpha 2
• DES: Desmin protein
• DIS3L2: DIS3 mitotic control homolog-like 2
• ECEL1: Endothelin converting enzyme like 1
• EPC2: Enhancer of polycomb homolog 2
• EPB41L5: encoding protein Erythrocyte membrane protein band 4.1 like 5
• ERICH2: encoding protein Glutamate rich protein 2
• FASTKD1: FAST kinase domain-containing protein 1
• IMP4: U3 small nucleolar ribonucleoprotein
• INPP1: Inositol polyphosphate 1-phosphatase
• INPP4A: inositol polyphosphate-4-phosphatase type A
• ITM2C: Integral membrane protein 2C
• KANSL3: KAT8 regulatory NSL complex subunit 3
• KIAA1211L: Uncharacterized Protein KIAA1211- Like
• LANCL1: LanC like 1
• LINC00607: Long intergenic non-protein coding RNA 607
• LOC100287387: LOC100287387
• MALL: MAL-like protein
• MBD5: encoding protein Methyl-cpg binding domain protein 5
• MFSD2B: encoding protein Major facilitator superfamily domain containing 2b
• MGAT5: mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase
• MIR375: encoding protein MicroRNA 375
• MIR561: encoding protein MicroRNA 561
• NABP1: Nucleic acid binding protein 1
• NEURL3: encoding protein Neuralized E3 ubiquitin protein ligase 3
• NCL: Nucleolin
• NR4A2: nuclear receptor subfamily 4, group A, member 2
• OLA1: Obg-like ATPase 1
• PARD3B encoding protein Partitioning defective 3 homolog B
• PAX3: paired box gene 3 (Waardenburg syndrome 1)
• PAX8: paired box gene 8
• PID1: Phosphotyrosine interaction domain containing 1
• POLR1B: DNA-directed RNA polymerase I subunit RPA2
• PRR21: Proline-rich protein 21
• PRSS56: Putative serine protease 56
• RBM44: Rna binding motif protein 44
• RFX8: Rfx family member 8, lacking rfx dna binding domain
• RIF1: replication timing regulatory factor 1
• RNU4ATAC: RNA, U4atac small nuclear (U12-dependent splicing)
• RPL37A: encoding protein 60S ribosomal protein L37a
• SATB2: Homeobox 2
• SCARNA5: Small Cajal body-specific RNA 5
• SDPR: Serum deprivation-response protein
• SGOL2: Shugoshin-like 2
• SH3BP4: SH3 domain-binding protein 4
• SLC9A4: solute carrier family 9 member A4
• SLC40A1: solute carrier family 40 (iron-regulated transporter), member 1
• SMPD4: Sphingomyelin phosphodiesterase 4
• SP140: encoding protein SP140 nuclear body protein
• SP140L: encoding protein Sp140 nuclear body protein like
• SPATS2L: spermatogenesis associated, serine-rich 2-like protein
• SSB: Sjögren syndrome antigen B
• SSFA2: Sperm-specific antigen 2
• STK11IP: encoding protein Serine/threonine kinase 11 interacting protein
• TBR1: T-box, brain, 1
• THAP4: THAP domain-containing protein 4
• TMBIM1: Transmembrane BAX inhibitor motif-containing protein 1
• TMEM182: encoding protein Transmembrane protein 182
• TNRC15: PERQ amino acid-rich with GYF domain-containing protein 2
• TSGA10 encoding protein Testis specific 10
• TTN: titin
• TUBA4B: encoding protein Tubulin alpha 4b
• UBE2F: encoding protein Ubiquitin conjugating enzyme E2 F (putative)
• UBXD2: UBX domain-containing protein 4
• UXS1: UDP-glucuronic acid decarboxylase 1
• VIL1: encoding protein Villin 1
• XIRP2: Xin actin-binding repeat-containing protein 2
• ZEB2-AS1: encoding protein ZEB2-AS1
• ZNF142: zinc finger protein 142
• ZNF2: encoding protein Zinc finger protein 2

Related disorders and traits

The following diseases and traits are related to genes located on chromosome 2:

• 2p15-16.1 microdeletion syndrome
• Autism ^[21]
• Alport syndrome
• Alström syndrome
• Amyotrophic lateral sclerosis
• Brachydactyly type D
• Cleft chin ^[22]
• Congenital hypothyroidism
• Crigler–Najjar syndrome types I/II
• Dementia with Lewy bodies
• Ehlers–Danlos syndrome
• Ehlers–Danlos syndrome, classical type
• Ehlers–Danlos syndrome, vascular type
• Fibrodysplasia ossificans progressiva
• Gilbert's syndrome
• Harlequin-type ichthyosis
• Hemochromatosis
• Hemochromatosis type 4
• Hereditary nonpolyposis colorectal cancer
• Infantile-onset ascending hereditary spastic paralysis
• Juvenile primary lateral sclerosis
• Lactose intolerance
• Long-chain 3-hydroxyacyl-coenzyme A dehydrogenase deficiency
• Lowry-Wood syndrome ^[23]
• Maturity-onset diabetes of the young type 6
• Mitochondrial trifunctional protein deficiency
• Nonsyndromic deafness
• Photic sneeze reflex ^[24]
• Primary hyperoxaluria
• Primary pulmonary hypertension
• Sitosterolemia (knockout of either ABCG5 or ABCG8)
• Sensenbrenner syndrome
• Synesthesia
• Waardenburg syndrome

Cytogenetic band

G-banding ideograms of human chromosome 2

G-banding ideogram of human chromosome 2 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 2 in three different resolutions (400, ^[25] 550 ^[26] and 850 ^[3] ). Band length in this diagram is based on the ideograms from ISCN (2013). ^[27] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process. ^[28]

G-bands of human chromosome 2 in resolution 850 bphs ^[3]

Chr.	Arm [29]	Band [30]	ISCN start [31]	ISCN stop [31]	Basepair start	Basepair stop	Stain [32]	Density
2	p	25.3	0	388	1	4,400,000	gneg
2	p	25.2	388	566	4,400,001	6,900,000	gpos	50
2	p	25.1	566	954	6,900,001	12,000,000	gneg
2	p	24.3	954	1193	12,000,001	16,500,000	gpos	75
2	p	24.2	1193	1312	16,500,001	19,000,000	gneg
2	p	24.1	1312	1565	19,000,001	23,800,000	gpos	75
2	p	23.3	1565	1789	23,800,001	27,700,000	gneg
2	p	23.2	1789	1908	27,700,001	29,800,000	gpos	25
2	p	23.1	1908	2027	29,800,001	31,800,000	gneg
2	p	22.3	2027	2296	31,800,001	36,300,000	gpos	75
2	p	22.2	2296	2415	36,300,001	38,300,000	gneg
2	p	22.1	2415	2609	38,300,001	41,500,000	gpos	50
2	p	21	2609	2966	41,500,001	47,500,000	gneg
2	p	16.3	2966	3220	47,500,001	52,600,000	gpos	100
2	p	16.2	3220	3294	52,600,001	54,700,000	gneg
2	p	16.1	3294	3548	54,700,001	61,000,000	gpos	100
2	p	15	3548	3757	61,000,001	63,900,000	gneg
2	p	14	3757	3935	63,900,001	68,400,000	gpos	50
2	p	13.3	3935	4114	68,400,001	71,300,000	gneg
2	p	13.2	4114	4248	71,300,001	73,300,000	gpos	50
2	p	13.1	4248	4353	73,300,001	74,800,000	gneg
2	p	12	4353	4860	74,800,001	83,100,000	gpos	100
2	p	11.2	4860	5307	83,100,001	91,800,000	gneg
2	p	11.1	5307	5545	91,800,001	93,900,000	acen
2	q	11.1	5545	5724	93,900,001	96,000,000	acen
2	q	11.2	5724	6022	96,000,001	102,100,000	gneg
2	q	12.1	6022	6261	102,100,001	105,300,000	gpos	50
2	q	12.2	6261	6395	105,300,001	106,700,000	gneg
2	q	12.3	6395	6559	106,700,001	108,700,000	gpos	25
2	q	13	6559	6812	108,700,001	112,200,000	gneg
2	q	14.1	6812	7036	112,200,001	118,100,000	gpos	50
2	q	14.2	7036	7334	118,100,001	121,600,000	gneg
2	q	14.3	7334	7602	121,600,001	129,100,000	gpos	50
2	q	21.1	7602	7826	129,100,001	131,700,000	gneg
2	q	21.2	7826	8050	131,700,001	134,300,000	gpos	25
2	q	21.3	8050	8169	134,300,001	136,100,000	gneg
2	q	22.1	8169	8437	136,100,001	141,500,000	gpos	100
2	q	22.2	8437	8497	141,500,001	143,400,000	gneg
2	q	22.3	8497	8646	143,400,001	147,900,000	gpos	100
2	q	23.1	8646	8735	147,900,001	149,000,000	gneg
2	q	23.2	8735	8795	149,000,001	149,600,000	gpos	25
2	q	23.3	8795	9078	149,600,001	154,000,000	gneg
2	q	24.1	9078	9361	154,000,001	158,900,000	gpos	75
2	q	24.2	9361	9585	158,900,001	162,900,000	gneg
2	q	24.3	9585	9928	162,900,001	168,900,000	gpos	75
2	q	31.1	9928	10435	168,900,001	177,100,000	gneg
2	q	31.2	10435	10599	177,100,001	179,700,000	gpos	50
2	q	31.3	10599	10733	179,700,001	182,100,000	gneg
2	q	32.1	10733	11091	182,100,001	188,500,000	gpos	75
2	q	32.2	11091	11225	188,500,001	191,100,000	gneg
2	q	32.3	11225	11538	191,100,001	196,600,000	gpos	75
2	q	33.1	11538	11925	196,600,001	202,500,000	gneg
2	q	33.2	11925	12060	202,500,001	204,100,000	gpos	50
2	q	33.3	12060	12283	204,100,001	208,200,000	gneg
2	q	34	12283	12641	208,200,001	214,500,000	gpos	100
2	q	35	12641	13014	214,500,001	220,700,000	gneg
2	q	36.1	13014	13237	220,700,001	224,300,000	gpos	75
2	q	36.2	13237	13297	224,300,001	225,200,000	gneg
2	q	36.3	13297	13595	225,200,001	230,100,000	gpos	100
2	q	37.1	13595	13893	230,100,001	234,700,000	gneg
2	q	37.2	13893	13998	234,700,001	236,400,000	gpos	50
2	q	37.3	13998	14400	236,400,001	242,193,529	gneg

References

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5. Vega Homo sapiens genome browser: HoxD cluster on Chromosome 2
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12. Avarello; et al. (1992). "Evidence for an ancestral alphoid domain on the long arm of human chromosome 2". Human Genetics. 89 (2): 247–9. doi:10.1007/BF00217134. PMID   1587535. S2CID   1441285.
13. Ijdo, Jacob W.; et al. (1991). "Origin of human chromosome 2: an ancestral telomere-telomere fusion". Proc. Natl. Acad. Sci. U.S.A. 88 (20): 9051–5. Bibcode:1991PNAS...88.9051I. doi: 10.1073/pnas.88.20.9051 . PMC   52649 . PMID   1924367.
14. 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.
15. "Statistics & Downloads for chromosome 2". HUGO Gene Nomenclature Committee. 12 May 2017. Archived from the original on 29 June 2017. Retrieved 19 May 2017.
16. "Chromosome 2: Chromosome summary – Homo sapiens". Ensembl Release 88. 29 March 2017. Retrieved 19 May 2017.
17. "Human chromosome 2: entries, gene names and cross-references to MIM". UniProt. 28 February 2018. Retrieved 16 March 2018.
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20. "Search results – 2[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) – Gene". NCBI. 19 May 2017. Retrieved 20 May 2017.
21. Swaminathan, Nikhil. "Largest Ever Autism Study Identifies Two Genetic Culprits". Scientific American. Retrieved 25 January 2018.
22. "Cleft Chin | AncestryDNA® Traits Learning Hub". ancestry.com. Retrieved 22 February 2022.
23. Shelihan, I.; Ehresmann, S.; Magnani, C.; Forzano, F.; Baldo, C.; Brunetti-Pierri, N.; Campeau, P. M. (2018). "Lowry-Wood syndrome: Further evidence of association with RNU4ATAC, and correlation between genotype and phenotype". Human Genetics. 137 (11–12): 905–909. doi:10.1007/s00439-018-1950-8. PMID   30368667. S2CID   53079178.
24. "Photic Sneeze Reflex | AncestryDNA® Traits Learning Hub". ancestry.com. Retrieved 22 February 2022.
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27. 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.
28. 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.
29. "p": Short arm; "q": Long arm.
30. For cytogenetic banding nomenclature, see article locus.
31. 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.
32. 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

• National Institutes of Health. "Chromosome 2". Genetics Home Reference. Archived from the original on 9 March 2016. Retrieved 6 May 2017.
• "Chromosome 2". Human Genome Project Information Archive 1990–2003. Retrieved 6 May 2017.