Chromosome 2

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

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)242,193,529 bp
(GRCh38)[1]
No. of genes1,194 (CCDS)[2]
TypeAutosome
Centromere positionSubmetacentric[3]
(93.9 Mbp[4])
Complete gene lists
CCDSGene list
HGNCGene list
UniProtGene list
NCBIGene list
External map viewers
EnsemblChromosome 2
EntrezChromosome 2
NCBIChromosome 2
UCSCChromosome 2
Full DNA sequences
RefSeqNC_000002 (FASTA)
GenBankCM000664 (FASTA)
Fusion of ancestral chromosomes left distinctive remnants of telomeres, and a vestigial centromere

Chromosome 2 contains the HOXD homeobox gene cluster.[6]

Evolution
Further information: Chimpanzee genome project

Humans have only twenty-three pairs of chromosomes, while all other extant members of Hominidae have twenty-four pairs.[7] (It is believed that Neanderthals and Denisovans had twenty-three pairs.)[7] Human chromosome 2 is a result of an end-to-end fusion of two ancestral chromosomes.[8][9][10]

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.[11][12]
  • 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.[13]
  • 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.[14]

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[14]

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.[15]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS1,194—— [2] 2016-09-08
HGNC1,196450931 [16] 2017-05-12
Ensembl1,2921,5981,029 [17] 2017-03-29
UniProt1,274—— [18] 2018-02-28
NCBI1,2811,4461,207 [19][20][21] 2017-05-19

List of genes

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
  • ABCG5 and ABCG8: ATP-binding cassette, subfamily A, members 5 and 8
  • SLC35F6: encoding protein Transmembrane protein SLC35F6
  • ATRAID: encoding protein Apoptosis-related protein 3
  • CAPG: capping acting protein
  • CCDC142: Coiled-Coil Domain Containing 142
  • CTLA4: cytotoxic T-Lymphocyte Antigen 4
  • DHX57: DExH-box helicase 57
  • DPYSL5: Dihydropyrimidinase like 5
  • ERLEC1: Endoplasmic reticulum lectin 1
  • EVA1A: encoding protein Eva-1 homolog A (C. elegans)
  • 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
  • GEN1 encoding protein GEN1, Holliday junction 5' flap endonuclease
  • 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
  • LEPQTL1: Leptin, serum levels of
  • 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
  • NRBP1: Nuclear receptor-binding protein 1
  • ODC1: Ornithine decarboxylase
  • OTOF: otoferlin
  • PARK3 encoding protein Parkinson disease 3 (autosomal dominant, Lewy body)
  • 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
  • SH3YL1: SH3 and SYLF domain-containing 1
  • 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
  • WDR35 (IFT121: TULP4): intraflagellar transport 121
  • C2orf16: unknown protein C2orf16

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
  • BMPR2: bone morphogenetic protein receptor, type II (serine/threonine kinase)
  • CCDC88A: Coiled-coil domain-containing protein 88A
  • CCDC93: Coiled-coil domain-containing protein 93
  • CCDC138: Coiled-coil domain-containing protein 138
  • CDCA7: Cell division cycle associated protein 1
  • CHPF: Chondroitin sulfate synthase 2
  • 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
  • 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
  • MALL: MAL-like protein
  • MGAT5: mannosyl (alpha-1,6-)-glycoprotein beta-1,6-N-acetyl-glucosaminyltransferase
  • 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
  • POLR1B: DNA-directed RNA polymerase I subunit RPA2
  • PRR21: Proline-rich protein 21
  • PRSS56: Putative serine protease 56
  • RIF1: replication timing regulatory factor 1
  • RNU4ATAC: RNA, U4atac small nuclear (U12-dependent splicing)
  • RPL37A: encoding protein 60S ribosomal protein L37a
  • SATB2: Homeobox 2
  • 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
  • SPATS2L: spermatogenesis associated, serine-rich 2-like protein
  • SSB: Sjogren syndrome antigen B
  • SSFA2: Sperm-specific antigen 2
  • TBR1: T-box, brain, 1
  • THAP4: THAP domain-containing protein 4
  • TMBIM1: Transmembrane BAX inhibitor motif-containing protein 1
  • TNRC15: PERQ amino acid-rich with GYF domain-containing protein 2
  • TSGA10 encoding protein Testis specific 10
  • TTN: titin
  • UBXD2: UBX domain-containing protein 4
  • UXS1: UDP-glucuronic acid decarboxylase 1
  • XIRP2: Xin actin-binding repeat-containing protein 2
  • ZNF142: zinc finger protein 142

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

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,[23] 550[24] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[25] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[26]
G-bands of human chromosome 2 in resolution 850 bphs[4]
Chr. Arm[27] Band[28] ISCN
start[29]		 ISCN
stop[29]		 Basepair
start		 Basepair
stop		 Stain[30] Density
2p 25.3038814,400,000 gneg
2p 25.23885664,400,0016,900,000 gpos50
2p 25.15669546,900,00112,000,000 gneg
2p 24.3954119312,000,00116,500,000 gpos75
2p 24.21193131216,500,00119,000,000 gneg
2p 24.11312156519,000,00123,800,000 gpos75
2p 23.31565178923,800,00127,700,000 gneg
2p 23.21789190827,700,00129,800,000 gpos25
2p 23.11908202729,800,00131,800,000 gneg
2p 22.32027229631,800,00136,300,000 gpos75
2p 22.22296241536,300,00138,300,000 gneg
2p 22.12415260938,300,00141,500,000 gpos50
2p 212609296641,500,00147,500,000 gneg
2p 16.32966322047,500,00152,600,000 gpos100
2p 16.23220329452,600,00154,700,000 gneg
2p 16.13294354854,700,00161,000,000 gpos100
2p 153548375761,000,00163,900,000 gneg
2p 143757393563,900,00168,400,000 gpos50
2p 13.33935411468,400,00171,300,000 gneg
2p 13.24114424871,300,00173,300,000 gpos50
2p 13.14248435373,300,00174,800,000 gneg
2p 124353486074,800,00183,100,000 gpos100
2p 11.24860530783,100,00191,800,000 gneg
2p 11.15307554591,800,00193,900,000 acen
2q 11.15545572493,900,00196,000,000 acen
2q 11.25724602296,000,001102,100,000 gneg
2q 12.160226261102,100,001105,300,000 gpos50
2q 12.262616395105,300,001106,700,000 gneg
2q 12.363956559106,700,001108,700,000 gpos25
2q 1365596812108,700,001112,200,000 gneg
2q 14.168127036112,200,001118,100,000 gpos50
2q 14.270367334118,100,001121,600,000 gneg
2q 14.373347602121,600,001129,100,000 gpos50
2q 21.176027826129,100,001131,700,000 gneg
2q 21.278268050131,700,001134,300,000 gpos25
2q 21.380508169134,300,001136,100,000 gneg
2q 22.181698437136,100,001141,500,000 gpos100
2q 22.284378497141,500,001143,400,000 gneg
2q 22.384978646143,400,001147,900,000 gpos100
2q 23.186468735147,900,001149,000,000 gneg
2q 23.287358795149,000,001149,600,000 gpos25
2q 23.387959078149,600,001154,000,000 gneg
2q 24.190789361154,000,001158,900,000 gpos75
2q 24.293619585158,900,001162,900,000 gneg
2q 24.395859928162,900,001168,900,000 gpos75
2q 31.1992810435168,900,001177,100,000 gneg
2q 31.21043510599177,100,001179,700,000 gpos50
2q 31.31059910733179,700,001182,100,000 gneg
2q 32.11073311091182,100,001188,500,000 gpos75
2q 32.21109111225188,500,001191,100,000 gneg
2q 32.31122511538191,100,001196,600,000 gpos75
2q 33.11153811925196,600,001202,500,000 gneg
2q 33.21192512060202,500,001204,100,000 gpos50
2q 33.31206012283204,100,001208,200,000 gneg
2q 341228312641208,200,001214,500,000 gpos100
2q 351264113014214,500,001220,700,000 gneg
2q 36.11301413237220,700,001224,300,000 gpos75
2q 36.21323713297224,300,001225,200,000 gneg
2q 36.31329713595225,200,001230,100,000 gpos100
2q 37.11359513893230,100,001234,700,000 gneg
2q 37.21389313998234,700,001236,400,000 gpos50
2q 37.31399814400236,400,001242,193,529 gneg

References
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  27. "p": Short arm; "q": Long arm.
  28. For cytogenetic banding nomenclature, see article locus.
  29. 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.
  30. 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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