Chromosome 3 (human)

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Chromosome 3 (human)
File:Human male karyotpe high resolution - Chromosome 3 cropped.png
Human chromosome 3 pair after G-banding. One is from mother, one is from father.
File:Human male karyotpe high resolution - Chromosome 3.png
Chromosome 3 pair
in human male karyogram.
Features
Length (bp)198,295,559 bp
(GRCh38)[1]
No. of genes1,024 (CCDS)[2]
TypeAutosome
Centromere positionMetacentric[3]
(90.9 Mbp[4])
Complete gene lists
CCDS?
HGNC?
UniProt?
NCBI?
External map viewers
EnsemblChromosome 3
EntrezChromosome 3
NCBIChromosome 3
UCSCChromosome 3
Full DNA sequences
RefSeqNC_000003 (FASTA)
GenBankCM000665 (FASTA)

Chromosome 3 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 3 spans almost 200 million base pairs (the building material of DNA) and represents about 6.5 percent of the total DNA in cells.

Genes

See also: Category:Genes on human chromosome 3.

Number of genes

The following are some of the gene count estimates of human chromosome 3. 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 1,024 – - [2] 2016-09-08
HGNC 1,036 483 761 [6] 2017-05-12
Ensembl 1,073 1,158 761 [7] 2017-03-29
NCBI 1,085 1,108 902 [8][9][10] 2017-05-19

Some genes requiring arm identification:

p-arm

The following are some of the genes located on p-arm (short arm) of human chromosome 3:

  • ALAS1: aminolevulinate, delta-, synthase 1
  • APEH: encoding enzyme Acylamino-acid-releasing enzyme
  • ARPP-21: Cyclic AMP-regulated phosphoprotein, 21 kDa
  • AZI2: encoding protein 5-azacytidine-induced protein 2
  • BRK1: SCAR/WAVE actin nucleating complex subunit
  • BRPF1: bromodomain and PHD finger containing 1
  • BTD: biotinidase
  • C3orf14-Chromosome 3 open reading frame 14: predicted DNA binding protein.
  • C3orf23: encoding protein Uncharacterized protein C3orf23
  • C3orf60/NDUFAF3: encoding enzyme NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 3
  • C3orf62: chromosome 3 open reading frame 62
  • CACNA2D3: calcium channel, voltage-dependent, alpha 2/delta subunit 3
  • CCR5: chemokine (C-C motif) receptor 5
  • CGGBP1: CGG triplet repeat binding protein 1
  • CMTM7: CKLF like MARVEL transmembrane domain containing 7
  • CNTN4: Contactin 4
  • COL7A1: Collagen, type VII, alpha 1 (epidermolysis bullosa, dystrophic, dominant and recessive)
  • CRBN: Cereblon protein[11]
  • DCLK3: Doublecortin like kinase 3
  • EAF1: ELL associated factor 1
  • ENTPD3: ectonucleoside triphosphate diphosphohydrolase 3
  • FAM107A: Family with sequence similarity 107 member A
  • FAM19A1: Family with sequence similarity 19 member A1, C-C motif chemokine like
  • FBXL2: F-box and leucine rich repeat protein 2
  • FOXP1: Forkhead Box Protein P1
  • GMPPB: GDP-mannose pyrophosphorylase B
  • HEMK1: encoding protein HemK methyltransferase family member 1
  • HIGD1A: HIG1 domain family member 1A
  • LARS2: leucyl-tRNA synthetase, mitochondrial
  • LIMD1: LIM domain-containing protein 1
  • LINC00312: Long intergenic non-protein-coding RNA 312
  • MITF: microphthalmia-associated transcription factor
  • MLH1: mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)
  • MYRIP: Myosin VIIA and Rab interacting protein
  • NBEAL2: Neurobeachin-like 2
  • NKTR: NK-tumor recognition protein
  • NPRL2: Nitrogen permease regulator 2-like protein
  • OXTR: oxytocin receptor
  • PTHR1: parathyroid hormone receptor 1
  • QRICH1: encoding protein QRICH1, also known as Glutamine-rich protein 1,
  • RBM6: RNA-binding protein 6
  • RPP14: Ribonuclease P protein subunit p14
  • SCN5A: sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)
  • SETD5: SET domain containing 5
  • SFMBT1: Scm-like with four mbt domains 1
  • SLC25A20: solute carrier family 25 (carnitine/acylcarnitine translocase), member 20
  • STT3B: catalytic subunit of the oligosaccharyltransferase complex
  • SYNPR: synaptoporin
  • TDGF1: Teratocarcinoma-derived growth factor 1
  • TMEM158: Transmembrane protein 158
  • TMIE: transmembrane inner ear
  • TRAK1: trafficking kinesin-binding protein 1
  • TRANK1: encoding protein Tetratricopeptide repeat and ankyrin repeat containing 1
  • TUSC2: tumor suppressor candidate 2
  • UCN2: Urocortin-2
  • VGLL3: vestigial-like family member 3
  • VHL: von Hippel-Lindau tumor suppressor
  • ZMYND10: zinc finger MYND-type containing 10
  • ZNF502: encoding protein Zinc finger protein 502
  • ZNF621: encoding protein Zinc finger protein 621

q-arm

The following are some of the genes located on q-arm (long arm) of human chromosome 3:

  • ADIPOQ: adiponectin
  • AMOTL2: encoding protein Angiomotin-like protein 2
  • ARHGAP31: Rho GRPase activating protein 31
  • C3orf1: chromosome 3 open reading frame 1
  • C3orf70 chromosome 3 open reading frame 70
  • CAMPD1: Camptodactyly
  • CCDC80: Coiled-coil domain containing protein 80
  • CD200R1: Cell surface glycoprotein CD200 receptor 1
  • CLDND1: Claudin domain containing 1
  • CPN2: Carboxypeptidase N subunit 2
  • CPOX: coproporphyrinogen oxidase (coproporphyria, harderoporphyria)
  • DPPA2: Developmental pluripotency associated 2
  • EAF2: ELL associated factor 2
  • EFCC1: EF-hand and coiled-coil domain containing 1
  • ETM1: Essential tremor 1
  • ETV5: ETS variant 5
  • FAM43A: family with sequence similarity 43 member A
  • FAM162A: family with sequence similarity 162 member A
  • GYG1: Glycogenin-1
  • HGD: homogentisate 1,2-dioxygenase (homogentisate oxidase)
  • IFT122: intraflagellar transport gene 122
  • KIAA1257: KIAA1257
  • LMLN: encoding protein Leishmanolysin-like (metallopeptidase M8 family)
  • LRRC15: leucine rich repeat containing 15
  • LSG1: large subunit GTPase 1 homolog
  • MB21D2: encoding protein Mab-21 domain containing 2
  • MCCC1: methylcrotonoyl-Coenzyme A carboxylase 1 (alpha)
  • MYLK: Telokin
  • NFKBIZ: NF-kappa-B inhibitor zeta
  • PCCB: propionyl Coenzyme A carboxylase, beta polypeptide
  • PDCD10: programmed cell death 10
  • PIK3CA: phosphoinositide-3-kinase, catalytic, alpha polypeptide
  • PROSER1: Proline and serine rich protein 1
  • RAB7: RAB7, member RAS oncogene family
  • RETNLB: resistin-like beta
  • RHO: rhodopsin visual pigment
  • RIOX2: Ribosomal oxygenase 2
  • SELT: Selenoprotein T
  • SENP7: Sentrin-specific protease 7
  • SERP1: Stress-associated endoplasmic reticulum protein 1
  • SOX2: transcription factor
  • SOX2OT: SOX2 overlapping transcript
  • SRPRB: Signal recognition particle receptor subunit beta
  • TM4SF1: Transmembrane 4 L6 family member 1
  • TRAT1: T-cell receptor-associated transmembrane adapter 1
  • USH3A: Usher syndrome 3A
  • ZBED2: encoding protein Zinc finger BED-type containing 2
  • ZNF9: zinc finger protein 9 (a cellular retroviral nucleic acid binding protein)

Diseases and disorders

This list is incomplete; you can help by expanding it.

The following diseases and disorders are some of those related to genes on chromosome 3:

Cytogenetic band

G-banding ideograms of human chromosome 3
File:Human chromosome 3 ideogram vertical.svg
G-banding ideogram of human chromosome 3 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).
File:Human chromosome 03 - 400 550 850 bphs.png
G-banding patterns of human chromosome 3 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 3 in resolution 850 bphs[4]
Chr. Arm[16] Band[17] ISCN
start[18] 		ISCN
stop[18] 		Basepair
start 		Basepair
stop 		Stain[19] Density
3 p 26.3 0 175 1 2,800,000 gpos 50
3 p 26.2 175 263 2,800,001 4,000,000 gneg
3 p 26.1 263 408 4,000,001 8,100,000 gpos 50
3 p 25.3 408 642 8,100,001 11,600,000 gneg
3 p 25.2 642 759 11,600,001 13,200,000 gpos 25
3 p 25.1 759 963 13,200,001 16,300,000 gneg
3 p 24.3 963 1269 16,300,001 23,800,000 gpos 100
3 p 24.2 1269 1357 23,800,001 26,300,000 gneg
3 p 24.1 1357 1561 26,300,001 30,800,000 gpos 75
3 p 23 1561 1751 30,800,001 32,000,000 gneg
3 p 22.3 1751 1926 32,000,001 36,400,000 gpos 50
3 p 22.2 1926 2013 36,400,001 39,300,000 gneg
3 p 22.1 2013 2188 39,300,001 43,600,000 gpos 75
3 p 21.33 2188 2451 43,600,001 44,100,000 gneg
3 p 21.32 2451 2626 44,100,001 44,200,000 gpos 50
3 p 21.31 2626 3239 44,200,001 50,600,000 gneg
3 p 21.2 3239 3385 50,600,001 52,300,000 gpos 25
3 p 21.1 3385 3676 52,300,001 54,400,000 gneg
3 p 14.3 3676 3910 54,400,001 58,600,000 gpos 50
3 p 14.2 3910 4143 58,600,001 63,800,000 gneg
3 p 14.1 4143 4362 63,800,001 69,700,000 gpos 50
3 p 13 4362 4566 69,700,001 74,100,000 gneg
3 p 12.3 4566 4814 74,100,001 79,800,000 gpos 75
3 p 12.2 4814 4946 79,800,001 83,500,000 gneg
3 p 12.1 4946 5077 83,500,001 87,100,000 gpos 75
3 p 11.2 5077 5135 87,100,001 87,800,000 gneg
3 p 11.1 5135 5266 87,800,001 90,900,000 acen
3 q 11.1 5266 5427 90,900,001 94,000,000 acen
3 q 11.2 5427 5602 94,000,001 98,600,000 gvar
3 q 12.1 5602 5762 98,600,001 100,300,000 gneg
3 q 12.2 5762 5850 100,300,001 101,200,000 gpos 25
3 q 12.3 5850 5996 101,200,001 103,100,000 gneg
3 q 13.11 5996 6229 103,100,001 106,500,000 gpos 75
3 q 13.12 6229 6361 106,500,001 108,200,000 gneg
3 q 13.13 6361 6594 108,200,001 111,600,000 gpos 50
3 q 13.2 6594 6682 111,600,001 113,700,000 gneg
3 q 13.31 6682 6871 113,700,001 117,600,000 gpos 75
3 q 13.32 6871 6973 117,600,001 119,300,000 gneg
3 q 13.33 6973 7148 119,300,001 122,200,000 gpos 75
3 q 21.1 7148 7294 122,200,001 124,100,000 gneg
3 q 21.2 7294 7440 124,100,001 126,100,000 gpos 25
3 q 21.3 7440 7674 126,100,001 129,500,000 gneg
3 q 22.1 7674 7936 129,500,001 134,000,000 gpos 25
3 q 22.2 7936 8053 134,000,001 136,000,000 gneg
3 q 22.3 8053 8228 136,000,001 139,000,000 gpos 25
3 q 23 8228 8461 139,000,001 143,100,000 gneg
3 q 24 8461 8811 143,100,001 149,200,000 gpos 100
3 q 25.1 8811 9001 149,200,001 152,300,000 gneg
3 q 25.2 9001 9162 152,300,001 155,300,000 gpos 50
3 q 25.31 9162 9264 155,300,001 157,300,000 gneg
3 q 25.32 9264 9366 157,300,001 159,300,000 gpos 50
3 q 25.33 9366 9453 159,300,001 161,000,000 gneg
3 q 26.1 9453 9803 161,000,001 167,900,000 gpos 100
3 q 26.2 9803 9949 167,900,001 171,200,000 gneg
3 q 26.31 9949 10183 171,200,001 176,000,000 gpos 75
3 q 26.32 10183 10329 176,000,001 179,300,000 gneg
3 q 26.33 10329 10489 179,300,001 183,000,000 gpos 75
3 q 27.1 10489 10620 183,000,001 184,800,000 gneg
3 q 27.2 10620 10737 184,800,001 186,300,000 gpos 25
3 q 27.3 10737 10883 186,300,001 188,200,000 gneg
3 q 28 10883 11175 188,200,001 192,600,000 gpos 75
3 q 29 11175 11700 192,600,001 198,295,559 gneg

References

  1. ↑ "Human Genome Assembly GRCh38 – Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04.
  2. ↑ 2.0 2.1 "Search results – 3[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. ↑ 4.0 4.1 4.2 Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  5. ↑ 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.
  6. ↑ "Statistics & Downloads for chromosome 3". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.
  7. ↑ "Chromosome 3: Chromosome summary – Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
  8. ↑ "Search results – 3[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 – 3[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 – 3[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) – Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  11. ↑ CRBN cereblon [Homo sapiens (human)] - Gene - NCBI
  12. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  13. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). 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:10.1109/JCSSE.2012.6261965.
  16. ↑ "p": Short arm; "q": Long arm.
  17. ↑ For cytogenetic banding nomenclature, see article locus.
  18. ↑ 18.0 18.1 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.

External links

  • National Institutes of Health. "Chromosome 3". Genetics Home Reference. Retrieved 2017-05-06.
  • "Chromosome 3". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.
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