Chromosome 3

Last updated
Chromosome 3
Human male karyotpe high resolution - Chromosome 3 cropped.png
Human chromosome 3 pair after G-banding. One is from mother, one is from father.
Human male karyotpe high resolution - Chromosome 3.png
Chromosome 3 pair
in human male karyogram.
Features
Length (bp)201,105,948 bp
(CHM13)
No. of genes 1,024 (CCDS) [1]
Type Autosome
Centromere position Metacentric [2]
(90.9 Mbp [3] )
Complete gene lists
CCDS Gene list
HGNC Gene list
UniProt Gene list
NCBI Gene list
External map viewers
Ensembl Chromosome 3
Entrez Chromosome 3
NCBI Chromosome 3
UCSC Chromosome 3
Full DNA sequences
RefSeq NC_000003 (FASTA)
GenBank CM000665 (FASTA)

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 201 million base pairs (the building material of DNA) and represents about 6.5 percent of the total DNA in cells.

Contents

Genes

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. [4]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes SourceRelease date
CCDS 1,024—— [1] 2016-09-08
HGNC 1,036483761 [5] 2017-05-12
Ensembl 1,0731,158761 [6] 2017-03-29
UniProt 1,081—— [7] 2018-02-28
NCBI 1,0851,108902 [8] [9] [10] 2017-05-19

List of genes

The following is a partial list of genes on human chromosome 3. 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 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.
  • CFAP20DC: encoding protein Chromosome 3 open reading frame 67
  • 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
  • DLEC1: encoding protein Deleted in lung and esophageal cancer 1
  • 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
  • FRA3A encoding protein Fragile site, aphidicolin type, common, fra(3)(p24.2)
  • FRMD4B encoding protein FERM domain containing 4B
  • GHRLOS: non-coding RNA ghrelin opposite strand (non-protein coding)
  • GMPPB: GDP-mannose pyrophosphorylase B
  • HACL1: encoding protein 2-hydroxyacyl-CoA lyase 1
  • HEMK1: encoding protein HemK methyltransferase family member 1
  • HIGD1A: HIG1 domain family member 1A
  • HSN1B: Hereditary sensory neuropathy, type ib
  • HTD2: encoding protein Hydroxyacyl-thioester dehydratase type 2
  • LARS2: leucyl-tRNA synthetase, mitochondrial
  • LIMD1: LIM domain-containing protein 1
  • LOC105377021: encoding protein LOC105377021
  • LINC00312: Long intergenic non-protein-coding RNA 312
  • LZTFL1: Leucine zipper transcription factor like 1
  • MIR138-1: encoding protein MicroRNA 138-1
  • MIR425: MicroRNA 425
  • MIR885: encoding protein MicroRNA 885
  • 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
  • NDUFAF3: encoding enzyme NADH dehydrogenase [ubiquinone] 1 alpha subcomplex assembly factor 3
  • NKTR: NK-tumor recognition protein
  • NPRL2: Nitrogen permease regulator 2-like protein
  • OXTR: oxytocin receptor
  • PCAF: acetyltransferase activity
  • PHF7 encoding protein PHD finger protein 7
  • PRICKLE2: encoding protein Prickle planar cell polarity protein 2
  • 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
  • TAFA4: encoding protein Family with sequence similarity 19 member A4, C-C motif chemokine like
  • TCAIM: encoding protein T-cell activation inhibitor, mitochondrial
  • 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
  • TTLL3: encoding protein Tubulin tyrosine ligase-like family, member 3
  • TUSC2: tumor suppressor candidate 2
  • UCN2: Urocortin-2
  • ULK4: UNC-51 like kinase 4
  • VGLL3: vestigial-like family member 3
  • VHL: von Hippel-Lindau tumor suppressor
  • ZMYND10: zinc finger MYND-type containing 10
  • ZNF197: encoding protein Zinc finger protein 197
  • ZNF502: encoding protein Zinc finger protein 502
  • ZNF620: encoding protein Zinc finger protein 620
  • ZNF621: encoding protein Zinc finger protein 621
  • ZNF717: encoding protein Zinc finger protein 717

q-arm

Partial list 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
  • BCHE: butyrylcholinesterase
  • C3orf70 chromosome 3 open reading frame 70
  • CAMPD1: Camptodactyly
  • CCDC80: Coiled-coil domain containing protein 80
  • CD200R1: Cell surface glycoprotein CD200 receptor 1
  • CHST13: encoding protein Carbohydrate (chondroitin 4) sulfotransferase 13
  • CLDND1: Claudin domain containing 1
  • CPN2: Carboxypeptidase N subunit 2
  • CPOX: coproporphyrinogen oxidase (coproporphyria, harderoporphyria)
  • DPPA2: Developmental pluripotency associated 2
  • DTX3L: encoding protein Deltex e3 ubiquitin ligase 3l
  • DZIP3: encoding protein DAZ interacting zinc finger protein 3
  • EAF2: ELL associated factor 2
  • EFCC1: EF-hand and coiled-coil domain containing 1
  • ETM1: Essential tremor 1
  • ETV5: ETS variant 5
  • FAM3D: family with sequence similarity 3, member D
  • FAM43A: family with sequence similarity 43 member A
  • FAM162A: family with sequence similarity 162 member A
  • FBXO40: encoding protein F-box protein 40
  • FILIP1L: encoding protein Filamin A interacting protein 1 like
  • GYG1: Glycogenin-1
  • HACD2 encoding protein 3-hydroxyacyl-CoA dehydratase 2
  • HGD: homogentisate 1,2-dioxygenase (homogentisate oxidase)
  • IFT122: intraflagellar transport gene 122
  • KIAA1257: KIAA1257
  • LINC01279: encoding protein long intergenic non-protein coding RNA 1279
  • LNCR5: encoding protein lung cancer susceptibility 5
  • 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)
  • MORC1: encoding protein Morc family cw-type zinc finger 1
  • MYLK: Telokin
  • NEPRO: encoding protein Nucleolus and neural progenitor protein
  • NFKBIZ: NF-kappa-B inhibitor zeta
  • OTOL1: encoding glycoprotein Otolin
  • PARP14 encoding protein Poly(ADP-ribose) polymerase family member 14
  • PCCB: propionyl Coenzyme A carboxylase, beta polypeptide
  • PDCD10: programmed cell death 10
  • PIK3CA: phosphoinositide-3-kinase, catalytic, alpha polypeptide
  • PISRT1: long non-coding RNA
  • PROSER1: Proline and serine rich protein 1
  • RAB7: RAB7, member RAS oncogene family
  • RASA2: encoding protein Ras p21 protein activator 2
  • 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
  • SPG14 encoding protein Spastic paraplegia 14 (autosomal recessive)
  • SRPRB: Signal recognition particle receptor subunit beta
  • TEX55: encoding protein Testis expressed 55
  • TIMMDC1: TIMMDC1
  • TMEM44: encoding protein Transmembrane protein 44
  • TM4SF1: Transmembrane 4 L6 family member 1
  • TMPRSS7: encoding protein Transmembrane serine protease 7
  • TP63: Tumor protein p63
  • 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

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

Cytogenetic band

G-banding ideograms of human chromosome 3
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).
Human chromosome 03 - 400 550 850 bphs.png
G-banding patterns of human chromosome 3 in three different resolutions (400, [14] 550 [15] and 850 [3] ). Band length in this diagram is based on the ideograms from ISCN (2013). [16] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process. [17]
G-bands of human chromosome 3 in resolution 850 bphs [3]
Chr.Arm [18] Band [19] ISCN
start [20] 		ISCN
stop [20] 		Basepair
start		Basepair
stop		Stain [21] Density
3p26.3017512,800,000gpos50
3p26.21752632,800,0014,000,000gneg
3p26.12634084,000,0018,100,000gpos50
3p25.34086428,100,00111,600,000gneg
3p25.264275911,600,00113,200,000gpos25
3p25.175996313,200,00116,300,000gneg
3p24.3963126916,300,00123,800,000gpos100
3p24.21269135723,800,00126,300,000gneg
3p24.11357156126,300,00130,800,000gpos75
3p231561175130,800,00132,000,000gneg
3p22.31751192632,000,00136,400,000gpos50
3p22.21926201336,400,00139,300,000gneg
3p22.12013218839,300,00143,600,000gpos75
3p21.332188245143,600,00144,100,000gneg
3p21.322451262644,100,00144,200,000gpos50
3p21.312626323944,200,00150,600,000gneg
3p21.23239338550,600,00152,300,000gpos25
3p21.13385367652,300,00154,400,000gneg
3p14.33676391054,400,00158,600,000gpos50
3p14.23910414358,600,00163,800,000gneg
3p14.14143436263,800,00169,700,000gpos50
3p134362456669,700,00174,100,000gneg
3p12.34566481474,100,00179,800,000gpos75
3p12.24814494679,800,00183,500,000gneg
3p12.14946507783,500,00187,100,000gpos75
3p11.25077513587,100,00187,800,000gneg
3p11.15135526687,800,00190,900,000acen
3q11.15266542790,900,00194,000,000acen
3q11.25427560294,000,00198,600,000gvar
3q12.15602576298,600,001100,300,000gneg
3q12.257625850100,300,001101,200,000gpos25
3q12.358505996101,200,001103,100,000gneg
3q13.1159966229103,100,001106,500,000gpos75
3q13.1262296361106,500,001108,200,000gneg
3q13.1363616594108,200,001111,600,000gpos50
3q13.265946682111,600,001113,700,000gneg
3q13.3166826871113,700,001117,600,000gpos75
3q13.3268716973117,600,001119,300,000gneg
3q13.3369737148119,300,001122,200,000gpos75
3q21.171487294122,200,001124,100,000gneg
3q21.272947440124,100,001126,100,000gpos25
3q21.374407674126,100,001129,500,000gneg
3q22.176747936129,500,001134,000,000gpos25
3q22.279368053134,000,001136,000,000gneg
3q22.380538228136,000,001139,000,000gpos25
3q2382288461139,000,001143,100,000gneg
3q2484618811143,100,001149,200,000gpos100
3q25.188119001149,200,001152,300,000gneg
3q25.290019162152,300,001155,300,000gpos50
3q25.3191629264155,300,001157,300,000gneg
3q25.3292649366157,300,001159,300,000gpos50
3q25.3393669453159,300,001161,000,000gneg
3q26.194539803161,000,001167,900,000gpos100
3q26.298039949167,900,001171,200,000gneg
3q26.31994910183171,200,001176,000,000gpos75
3q26.321018310329176,000,001179,300,000gneg
3q26.331032910489179,300,001183,000,000gpos75
3q27.11048910620183,000,001184,800,000gneg
3q27.21062010737184,800,001186,300,000gpos25
3q27.31073710883186,300,001188,200,000gneg
3q281088311175188,200,001192,600,000gpos75
3q291117511700192,600,001198,295,559gneg

See also

References

  1. 1 2 "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.
  2. ↑ Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN   978-1-136-84407-2.
  3. 1 2 3 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 3". HUGO Gene Nomenclature Committee. 2017-05-12. Archived from the original on 2017-06-29. Retrieved 2017-05-19.
  6. ↑ "Chromosome 3: Chromosome summary – Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
  7. ↑ "Human chromosome 3: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.
  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. ↑ "Scientists pinpoint genes common among people with severe coronavirus infections". MSN .
  13. ↑ Severe Covid-19 GWAS Group; et al. (2020). "Genomewide Association Study of Severe Covid-19 with Respiratory Failure". New England Journal of Medicine. 383 (16): 1522–1534. doi:10.1056/NEJMoa2020283. PMC   7315890 . PMID   32558485.{{cite journal}}: CS1 maint: numeric names: authors list (link)
  14. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  15. ↑ Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  16. ↑ 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.
  17. ↑ 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.
  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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