Chromosome 1 (human)

Chromosome 1 (human)

Human chromosome 1 pair after G-banding. One is from mother, one is from father.

Chromosome 1 pair
in human male karyogram.
Features
Length (bp) 248,956,422 bp
(GRCh38)[1]
No. of genes 1,961 (CCDS)[2]
Type Autosome
Centromere position Metacentric[3]
(123.4 Mbp[4])
External map viewers
Ensembl Chromosome 1
Entrez Chromosome 1
NCBI Chromosome 1
UCSC Chromosome 1
Full DNA sequences
RefSeq NC_000001 (FASTA)
GenBank CM000663 (FASTA)

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.[5] It represents about 8% of the total DNA in human cells.[6]

It was the last completed chromosome, sequenced two decades after the beginning of the Human Genome Project.

Genes

Number of genes

The following are some of the gene count estimates of human chromosome 1. 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.[7]

When simply saying "number of genes", in most cases, it refers only to "number of protein-coding genes".

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS 1,961 - - [2] 2016-09-08
HGNC 1,993 707 1,113 [8] 2017-05-12
Ensembl 2,044 1,924 1,223 [9] 2017-03-29
NCBI 2,093 1,790 1,426 [10][11][12] 2017-05-19

Some genes needing arm identification:

p-arm

The following are some of the genes located on p-arm (short arm) of human chromosome 1:

  • AADACL3: Arylacetamide deacetylase-like 3
  • AADACL4: Arylacetamide deacetylase-like 4
  • ACADM: acyl-Coenzyme A dehydrogenase, C-4 to C-12 straight chain
  • ACTL8: Actin-like 8
  • ADPRHL2: Poly(ADP-ribose) glycohydrolase ARH3
  • AMPD2: encoding enzyme AMP deaminase 2
  • ATXN7L2: Ataxin 7-like 2
  • AZIN2: encoding enzyme Antizyme inhibitor 2 (AzI2) also known as arginine decarboxylase (ADC)
  • BCAS2: Breast carcinoma amplified sequence 2
  • C1orf103: encoding protein Ligand-dependent nuclear receptor-interacting factor 1 (LRIF1)
  • C1orf109: chromosome 1 open reading frame 109
  • C1orf123: chromosome 1 open reading frame 123
  • CASZ1: Castor zinc finger 1
  • CMPK: UMP-CMP kinase
  • COL11A1: collagen, type XI, alpha 1
  • CPT2: carnitine palmitoyltransferase II
  • CRYZ: Crystallin zeta
  • CSDE1: Cold shock domain containing E1
  • DBT: dihydrolipoamide branched chain transacylase E2
  • DCLRE1B: DNA cross-link repair 1B
  • DEPDC1 encoding protein DEP domain containing 1
  • DIRAS3: DIRAS family, GTP-binding RAS-like 3
  • DPH5: Diphthine synthase
  • ESPN: espin (autosomal recessive deafness 36)
  • EVI5: ecotropic viral integration site 5
  • EXTL1: exostosin like glycosyltransferase 1
  • EXTL2: exostosin like glycosyltransferase 2
  • FAM46B: family with sequence similarity 46, member B
  • FAM46C: family with sequence similarity 46, member C
  • FAM76A: family with sequence similarity 76, member A
  • FBXO2: F-box protein 2
  • FPGT: Fucose-1-phosphate guanylyltransferase
  • GALE: UDP-galactose-4-epimerase
  • GBP2: guanylate binding protein 2
  • GJB3: gap junction protein, beta 3, 31kDa (connexin 31)
  • GNL2: G protein nucleolar 2
  • HES2: Hes family bHLH transcription factor 2
  • HES3: Hes family bHLH transcription factor 3
  • HMGCL: 3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase (hydroxymethylglutaricaciduria)
  • HAO2 encoding protein Hydroxyacid oxidase 2
  • HMGCS2: 3-hydroxy-3-methylglutaryl-CoA synthase 2
  • HP1BP3: Heterochromatin protein 1, binding protein 3
  • IFI6: Interferon alpha-inducible protein 6
  • INTS11: Integrator complex subunit 11
  • KCNQ4: potassium voltage-gated channel, KQT-like subfamily, member 4
  • KIF1B: kinesin family member 1B
  • L1TD1: LINE-1 type transposase domain containing 1
  • LRRC39: Leucine-rich repeat-containing protein 39
  • LRRC40: Leucine-rich repeat-containing protein 40
  • LRRC41: Leucine-rich repeat-containing protein 41
  • LRRC8D: Leucine-rich repeat-containing protein 8D
  • MAN1A2: Mannosyl-oligosaccharide 1,2-alpha-mannosidase IB
  • MEAF6: MYST/ESA1 associated factor 6
  • MECR: Trans-2-enoyl-CoA reductase, mitochondrial
  • MFAP2: Microfibrillar-associated protein 2
  • MFN2: mitofusin 2
  • MFSD2: Major facilitator superfamily domain containing 2A
  • MIR6079: microRNA 6079
  • MMEL1: Membrane metallo-endopeptidase-like 1
  • MTFR1L: mitochondrial fission regulator 1 like
  • MTHFR: 5,10-methylenetetrahydrofolate reductase (NADPH)
  • MUL1: Mitochondrial E3 ubiquitin protein ligase 1
  • MUTYH: mutY homolog (E. coli)
  • NBPF3: Neuroblastoma breakpoint family member 3
  • NGF: Nerve Growth Factor
  • NOL9: Nucleolar protein 9
  • OLFML3: Olfactomedin-like 3
  • OMA1: Metalloendopeptidase OMA1, mitochondrial
  • OVGP1: Oviductal glycoprotein 1
  • PARK7: Parkinson disease (autosomal recessive, early onset) 7
  • PINK1: PTEN induced putative kinase 1
  • PLOD1: procollagen-lysine 1, 2-oxoglutarate 5-dioxygenase 1
  • PRMT6: Protein arginine methyltransferase 6
  • PSRC1: Proline/serine-rich coiled-coil protein 1
  • RAD54L: RAD54-like
  • RCC2: Regulator of chromosome condensation 2
  • RHBDL2: Rhomboid like 2
  • RLF: rearranged L-myc fusion
  • RNF220: RING finger protein 220
  • SDC3: Syndecan-3
  • SGIP1: SH3 domain GRB2-like protein 3-interaction protein 1
  • SH3BGRL3: SH3 domain-binding glutamic acid-rich-like protein 3
  • SPSB1: SPRY domain-containing SOCS box protein 1
  • SYCP1: Synaptonemal complex protein 1
  • SZT2: Seizure threshold 2 homolog
  • TACSTD2: tumour-associated calcium signal transducer 2
  • TCEB3: Transcription elongation factor B polypeptide 3
  • TMCO4: encoding protein transmembrane and coiled-coil domains 4
  • TMEM48: encoding protein nucleoporin NDC1
  • TMEM50A: Transmembrane protein 50A
  • TMEM59: Transmembrane protein 59
  • TMEM69: Transmembrane protein 69
  • TMEM222: Transmembrane protein 222
  • TOE1: Target of EGR1 protein 1
  • TRAPPC3: Trafficking protein particle complex subunit 3
  • TRIT1: tRNA isopentenyltransferase, mitochondrial
  • TSHB: thyroid stimulating hormone, beta
  • TTC39A: Tetratricopeptide repeat 39A
  • UBR4: E3 ubiquitin-protein ligase component n-recognin 4
  • UROD: uroporphyrinogen decarboxylase (the gene for porphyria cutanea tarda)
  • USP48: Ubiquitin carboxyl-terminal hydrolase 48
  • VPS13D: Vacuolar protein sorting-associated protein 13D
  • WARS2: Tryptophanyl-tRNA synthetase, mitochondrial
  • ZCCHC17: zinc finger CCHC-type containing 17
  • ZMYM1 encoding protein Zinc finger MYM-type containing 1
  • ZNF436: Zinc finger protein 436
  • ZYG11B encoding protein Zyg-11 family member B, cell cycle regulator
  • ZZZ3: ZZ-type zinc finger-containing protein 3

q-arm

The following are some of the genes located on q-arm (long arm) of human chromosome 1:

  • AHCTF1: encoding protein ELYS
  • ANGPTL1: Angiopoietin-related protein 1
  • ARID4B: encoding protein AT-rich interactive domain-containing protein 4B
  • ASPM: a brain size determinant
  • C1orf21: chromosome 1 open reading frame 21
  • C1orf35 encoding protein Chromosome 1 open reading frame 35
  • C1orf49: chromosome 1 open reading frame 49
  • C1orf74: chromosome 1 open reading frame 74
  • C1orf106: chromosome 1 open reading frame 106
  • CD5L: CD5 molecule like
  • CENPL: Centromere protein L
  • CHTOP: Chromatin target of prmt1
  • CNIH4: cornichon homolog 4
  • CNST: Consortin
  • CREG1: Cellular repressor of E1A stimulated genes 1
  • CRP: C-reactive protein
  • CSRP1: Cysteine and glycine rich protein 1
  • DDX59: DEAD-box helicase 59
  • DPT: Dermatopontin
  • DNAH14 encoding protein Dynein, axonemal, heavy chain 14
  • EDEM3: ER degradation enhancing alpha-mannosidase like protein 3
  • F5: coagulation factor V (proaccelerin, labile factor)
  • FAM20B: FAM20B, glycosaminoglycan xylosylkinase
  • FAM63A: Family with sequence similarity 63, member A
  • FAM78B: family with sequence similarity 78, member B
  • FAM129A: family with sequence similarity 129, member A
  • FBXO28: F-box protein 28
  • FCMR: Fc fragment of IgM receptor
  • FMO3: flavin containing monooxygenase 3
  • GBA: glucosidase, beta; acid (includes glucosylceramidase) (gene for Gaucher disease)
  • GBAP1: glucosylceramidase beta pseudogene 1
  • GLC1A: gene for glaucoma
  • GON4L: gon-4 like
  • GPR37L1 G protein-coupled receptor 37 like 1
  • HEATR1: HEAT repeat-containing protein 1
  • HFE2: hemochromatosis type 2 (juvenile)
  • HIST2H2AB: Histone 2A type 2-B
  • HIST2H2BF: Histone H2B type 2-F
  • HIST3H2A: Histone H2A type 3
  • HIST3H2BB: Histone H2B type 3-B
  • HPC1: gene for prostate cancer
  • INTS3: Integrator complex subunit 3
  • IRF6: gene for connective tissue formation
  • LEFTY1: Left-right determination factor 1
  • LMNA: lamin A/C
  • LYPLAL1: Lysophospholipase-like 1
  • MIR194-1: microRNA 194-1
  • MIR5008: microRNA 5008
  • MPC2: Mitochondrial pyruvate carrier 2
  • MOSC1: MOCO sulphurase C-terminal domain containing 1
  • MOSC2: MOSC domain-containing protein 2, mitochondrial
  • MPZ: myelin protein zero (Charcot–Marie–Tooth neuropathy 1B)
  • MSTO1: misato 1
  • MTR: 5-methyltetrahydrofolate-homocysteine methyltransferase
  • NAV1: Neuron navigator 1
  • NBPF16: Neuroblastoma breakpoint family, member 16
  • NOC2L: Nucleolar complex protein 2 homolog
  • NUCKS1: Nuclear ubiquitous casein and cyclin-dependent kinases substrate
  • NVL: Nuclear valosin-containing protein-like
  • OLFML2B: Olfactomedin-like 2B
  • OPTC: Opticin
  • OTUD7B: OTU domain-containing protein 7B
  • PGDB5: PiggyBac transposable element derived 5
  • PI4KB: Phosphatidylinositol 4-kinase beta
  • PIP5K1A: Phosphatidylinositol-4-phosphate 5-kinase type-1 alpha
  • PPOX: protoporphyrinogen oxidase
  • PRR9 encoding protein Proline rich 9
  • PSEN2: presenilin 2 (Alzheimer disease 4)
  • RABIF: RAB interacting factor
  • SCAMP3: Secretory carrier-associated membrane protein 3
  • SDHB: succinate dehydrogenase complex subunit B
  • SLC50A1: Solute carrier family 50 member 1
  • SMCP: Sperm mitochondrial-associated cysteine-rich protein
  • SMG7: nonsense mediated mRNA decay factor
  • SPRR1A: Cornifin-A
  • SPRR1B: Cornifin-B
  • SPRR2A: Small proline rich protein 2A
  • SPRTN: Spartan
  • TARBP1: TAR (HIV-1) RNA-binding protein 1
  • TBCE: Tubulin-specific chaperone E
  • THBS3: Thrombospondin 3
  • TMCO1: Transmembrane and coiled-coil domain-containing protein 1
  • TMEM9: Transmembrane protein 9
  • TMEM63A: Transmembrane protein 63A
  • TNNT2: cardiac troponin T2
  • TOR1AIP1: Torsin-1A-interacting protein 1
  • UAP1: UDP-N-acetylhexosamine pyrophosphorylase
  • USH2A: Usher syndrome 2A (autosomal recessive, mild)
  • VPS45: Vacuolar protein sorting-associated protein 45
  • VPS72: Vacuolar protein sorting-associated protein 72
  • YY1AP1: YY1-associated protein 1
  • ZBED6: Zinc finger, BED-type containing 6
  • ZC3H11A: Zing finger CCCH domain-containing protein 11A
  • ZNF687: zing finger protein 687
  • ZNF648 encoding protein Zinc finger protein 648
  • ZNF695: Zinc finger protein 695

Diseases and disorders

There are 890 known diseases related to this chromosome. Some of these diseases are hearing loss, Alzheimer disease, glaucoma and breast cancer. Rearrangements and mutations of chromosome 1 are prevalent in cancer and many other diseases. Patterns of sequence variation reveal signals of recent selection in specific genes that may contribute to human fitness, and also in regions where no function is evident. The following diseases are some of those related to genes on chromosome 1 (which contains the most known genetic diseases of any human chromosome):

Cytogenetic band

G-banding ideograms of human chromosome 1
G-banding ideogram of human chromosome 1 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 1 in three different resolutions (400,[13] 550[14] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[15] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[16]
G-bands of human chromosome 1 in resolution 850 bphs[17]
Chr. Arm[18] Band[19] ISCN
start[20] 		ISCN
stop[20]		 Basepair
start 		Basepair
stop 		Stain[21] Density
1 p 36.33 0 100 1 2,300,000 gneg
1 p 36.32 100 244 2,300,001 5,300,000 gpos 25
1 p 36.31 244 344 5,300,001 7,100,000 gneg
1 p 36.23 344 459 7,100,001 9,100,000 gpos 25
1 p 36.22 459 660 9,100,001 12,500,000 gneg
1 p 36.21 660 861 12,500,001 15,900,000 gpos 50
1 p 36.13 861 1206 15,900,001 20,100,000 gneg
1 p 36.12 1206 1321 20,100,001 23,600,000 gpos 25
1 p 36.11 1321 1521 23,600,001 27,600,000 gneg
1 p 35.3 1521 1651 27,600,001 29,900,000 gpos 25
1 p 35.2 1651 1780 29,900,001 32,300,000 gneg
1 p 35.1 1780 1895 32,300,001 34,300,000 gpos 25
1 p 34.3 1895 2210 34,300,001 39,600,000 gneg
1 p 34.2 2210 2411 39,600,001 43,700,000 gpos 25
1 p 34.1 2411 2770 43,700,001 46,300,000 gneg
1 p 33 2770 2986 46,300,001 50,200,000 gpos 75
1 p 32.3 2986 3273 50,200,001 55,600,000 gneg
1 p 32.2 3273 3416 55,600,001 58,500,000 gpos 50
1 p 32.1 3416 3732 58,500,001 60,800,000 gneg
1 p 31.3 3732 3976 60,800,001 68,500,000 gpos 50
1 p 31.2 3976 4206 68,500,001 69,300,000 gneg
1 p 31.1 4206 4852 69,300,001 84,400,000 gpos 100
1 p 22.3 4852 5210 84,400,001 87,900,000 gneg
1 p 22.2 5210 5440 87,900,001 91,500,000 gpos 75
1 p 22.1 5440 5741 91,500,001 94,300,000 gneg
1 p 21.3 5741 5957 94,300,001 99,300,000 gpos 75
1 p 21.2 5957 6029 99,300,001 101,800,000 gneg
1 p 21.1 6029 6244 101,800,001 106,700,000 gpos 100
1 p 13.3 6244 6459 106,700,001 111,200,000 gneg
1 p 13.2 6459 6660 111,200,001 115,500,000 gpos 50
1 p 13.1 6660 6861 115,500,001 117,200,000 gneg
1 p 12 6861 7048 117,200,001 120,400,000 gpos 50
1 p 11.2 7048 7119 120,400,001 121,700,000 gneg
1 p 11.1 7119 7335 121,700,001 123,400,000 acen
1 q 11 7335 7579 123,400,001 125,100,000 acen
1 q 12 7579 8483 125,100,001 143,200,000 gvar
1 q 21.1 8483 8756 143,200,001 147,500,000 gneg
1 q 21.2 8756 8957 147,500,001 150,600,000 gpos 50
1 q 21.3 8957 9244 150,600,001 155,100,000 gneg
1 q 22 9244 9459 155,100,001 156,600,000 gpos 50
1 q 23.1 9459 9832 156,600,001 159,100,000 gneg
1 q 23.2 9832 10048 159,100,001 160,500,000 gpos 50
1 q 23.3 10048 10349 160,500,001 165,500,000 gneg
1 q 24.1 10349 10507 165,500,001 167,200,000 gpos 50
1 q 24.2 10507 10679 167,200,001 170,900,000 gneg
1 q 24.3 10679 10894 170,900,001 173,000,000 gpos 75
1 q 25.1 10894 11009 173,000,001 176,100,000 gneg
1 q 25.2 11009 11196 176,100,001 180,300,000 gpos 50
1 q 25.3 11196 11598 180,300,001 185,800,000 gneg
1 q 31.1 11598 11827 185,800,001 190,800,000 gpos 100
1 q 31.2 11827 11942 190,800,001 193,800,000 gneg
1 q 31.3 11942 12172 193,800,001 198,700,000 gpos 100
1 q 32.1 12172 12617 198,700,001 207,100,000 gneg
1 q 32.2 12617 12803 207,100,001 211,300,000 gpos 25
1 q 32.3 12803 13033 211,300,001 214,400,000 gneg
1 q 41 13033 13320 214,400,001 223,900,000 gpos 100
1 q 42.11 13320 13406 223,900,001 224,400,000 gneg
1 q 42.12 13406 13607 224,400,001 226,800,000 gpos 25
1 q 42.13 13607 13966 226,800,001 230,500,000 gneg
1 q 42.2 13966 14153 230,500,001 234,600,000 gpos 50
1 q 42.3 14153 14397 234,600,001 236,400,000 gneg
1 q 43 14397 14756 236,400,001 243,500,000 gpos 75
1 q 44 14756 15100 243,500,001 248,956,422 gneg

References

  1. ↑ "Human Genome Assembly GRCh38 - Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04.
  2. 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.
  3. ↑ Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2.
  4. 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.
  5. ↑ http://vega.sanger.ac.uk/Homo_sapiens/mapview?chr=1 Chromosome size and number of genes derived from this database, retrieved 2012-03-11.
  6. ↑ Gregory SG, Barlow KF, McLay KE; et al. (May 2006). "The DNA sequence and biological annotation of human chromosome 1". Nature. 441 (7091): 315–21. Bibcode:2006Natur.441..315G. PMID 16710414. doi:10.1038/nature04727.
  7. ↑ Pertea M, Salzberg SL (2010). "Between a chicken and a grape: estimating the number of human genes.". Genome Biol. 11 (5): 206. PMC 2898077 Freely accessible. PMID 20441615. doi:10.1186/gb-2010-11-5-206.
  8. ↑ "Statistics & Downloads for chromosome 1". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.
  9. ↑ "Chromosome 1: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
  10. ↑ "Search results - 1[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  11. ↑ "Search results - 1[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.
  12. ↑ "Search results - 1[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  13. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  14. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  15. ↑ 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.
  16. ↑ 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.
  17. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  18. ↑ "p": Short arm; "q": Long arm.
  19. ↑ For cytogenetic banding nomenclature, see article locus.
  20. 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.
  21. ↑ 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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