Chromosome 3

Chromosome 3
Human chromosome 3 pair after G-banding. One is from mother, one is from father.
Chromosome 3 pair in human male karyogram.
Features
Length (bp)	198,295,559 bp (GRCh38)[1]
No. of genes	1,024 (CCDS)[2]
Type	Autosome
Centromere position	Metacentric[3] (90.9 Mbp[4])
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 almost 200 million base pairs (the building material of DNA) and represents about 6.5 percent of the total DNA in cells.

Contents

• 
  1 Genes
  
  
  
  • 
    1.1 Number of genes
    
  
  
  • 
    1.2 List of genes
    
    
    
    • 
      1.2.1 p-arm
      
    
    
    • 
      1.2.2 q-arm
      
    
    
    
    
  
  
  
  


• 
  2 Diseases and disorders
  


• 
  3 Cytogenetic band
  


• 
  4 References
  


• 
  5 External links
  

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.^[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
UniProt	1,081	—	—	[8]	2018-02-28
NCBI	1,085	1,108	902	[9][10][11]	2017-05-19

List of genes

See also: Category:Genes on human chromosome 3.

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.


• 
  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^[12]
  


• 
  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


• 
  FRA3A encoding protein Fragile site, aphidicolin type, common, fra(3)(p24.2)


• 
  FRMD4B encoding protein FERM domain containing 4B


• 
  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


• 
  PHF7 encoding protein PHD finger protein 7


• 
  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


• 
  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


• 
  ZNF502: encoding protein Zinc finger protein 502


• 
  ZNF621: encoding protein Zinc finger protein 621

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


• 
  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


• 
  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


• 
  FAM43A: family with sequence similarity 43 member A


• 
  FAM162A: family with sequence similarity 162 member A


• 
  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


• 
  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


• 
  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


• 
  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


• 
  SPG14 encoding protein Spastic paraplegia 14 (autosomal recessive)


• 
  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:

• 3-methylcrotonyl-CoA carboxylase deficiency


• 3q29 microdeletion syndrome


• 
  Acute Myeloid Leukemia (AML)


• Alkaptonuria


• Arrhythmogenic right ventricular dysplasia


• Atransferrinemia


• Autism


• Autosomal Dominant Optic Atrophy


• ADOA Plus Syndrome


• Biotinidase deficiency


• Blepharophimosis, epicanthus inversus and ptosis type 1


• Breast/colon/lung/pancreatic cancer


• Brugada syndrome


• Castillo fever


• Carnitine-acylcarnitine translocase deficiency


• Cataracts


• Cerebral cavernous malformation


• Charcot-Marie-Tooth disease, type 2


• Charcot-Marie-Tooth disease


• Chromosome 3q duplication syndrome


• Coproporphyria


• Dandy-Walker syndrome


• Deafness


• Diabetes


• Dystrophic epidermolysis bullosa


• Endplate acetylcholinesterase deficiency


• Essential tremors


• Ectrodactyly, Case 4


• 
  Glaucoma, primary open angle


• Glycogen storage disease


• Hailey-Hailey disease


• Harderoporphyrinuria


• Heart block, progressive/nonprogressive


• Hereditary coproporphyria


• Hereditary nonpolyposis colorectal cancer


• 
  HIV infection, susceptibility/resistance to


• Hypobetalipoproteinemia, familial


• Hypothermia


• Leukoencephalopathy with vanishing white matter


• Long QT syndrome


• Lymphomas


• Malignant hyperthermia susceptibility


• Metaphyseal chondrodysplasia, Murk Jansen type


• Microcoria


• Moebius syndrome


• Moyamoya disease


• Mucopolysaccharidosis


• Muir-Torre family cancer syndrome


• Myotonic dystrophy


• Neuropathy, hereditary motor and sensory, Okinawa type


• Night blindness


• Nonsyndromic deafness


• Ovarian cancer


• Porphyria


• Propionic acidemia


• Protein S deficiency


• Pseudo-Zellweger syndrome


• Retinitis pigmentosa


• Romano-Ward syndrome


• Seckel Syndrome


• Sensenbrenner syndrome


• Septo-optic dysplasia


• Short stature


• Spinocerebellar ataxia


• Sucrose intolerance


• T-cell leukemia translocation altered gene


• Usher syndrome


• von Hippel-Lindau syndrome


• Waardenburg syndrome


• Xeroderma pigmentosum, complementation group c

Cytogenetic band

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G-banding ideograms of human chromosome 3

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).

G-banding patterns of human chromosome 3 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 3 in resolution 850 bphs^[4]

Chr.	Arm[17]	Band[18]	ISCN start[19]	ISCN stop[19]	Basepair start	Basepair stop	Stain[20]	Density
3	p	26.3	0	175	7000100000000000000♠1	7006280000000000000♠2,800,000	gpos	50
3	p	26.2	175	263	7006280000100000000♠2,800,001	7006400000000000000♠4,000,000	gneg
3	p	26.1	263	408	7006400000100000000♠4,000,001	7006810000000000000♠8,100,000	gpos	50
3	p	25.3	408	642	7006810000100000000♠8,100,001	7007116000000000000♠11,600,000	gneg
3	p	25.2	642	759	7007116000010000000♠11,600,001	7007132000000000000♠13,200,000	gpos	25
3	p	25.1	759	963	7007132000010000000♠13,200,001	7007163000000000000♠16,300,000	gneg
3	p	24.3	963	1269	7007163000010000000♠16,300,001	7007238000000000000♠23,800,000	gpos	100
3	p	24.2	1269	1357	7007238000010000000♠23,800,001	7007263000000000000♠26,300,000	gneg
3	p	24.1	1357	1561	7007263000010000000♠26,300,001	7007308000000000000♠30,800,000	gpos	75
3	p	23	1561	1751	7007308000010000000♠30,800,001	7007320000000000000♠32,000,000	gneg
3	p	22.3	1751	1926	7007320000010000000♠32,000,001	7007364000000000000♠36,400,000	gpos	50
3	p	22.2	1926	2013	7007364000010000000♠36,400,001	7007393000000000000♠39,300,000	gneg
3	p	22.1	2013	2188	7007393000010000000♠39,300,001	7007436000000000000♠43,600,000	gpos	75
3	p	21.33	2188	2451	7007436000010000000♠43,600,001	7007441000000000000♠44,100,000	gneg
3	p	21.32	2451	2626	7007441000010000000♠44,100,001	7007442000000000000♠44,200,000	gpos	50
3	p	21.31	2626	3239	7007442000010000000♠44,200,001	7007506000000000000♠50,600,000	gneg
3	p	21.2	3239	3385	7007506000010000000♠50,600,001	7007523000000000000♠52,300,000	gpos	25
3	p	21.1	3385	3676	7007523000010000000♠52,300,001	7007544000000000000♠54,400,000	gneg
3	p	14.3	3676	3910	7007544000010000000♠54,400,001	7007586000000000000♠58,600,000	gpos	50
3	p	14.2	3910	4143	7007586000010000000♠58,600,001	7007638000000000000♠63,800,000	gneg
3	p	14.1	4143	4362	7007638000010000000♠63,800,001	7007697000000000000♠69,700,000	gpos	50
3	p	13	4362	4566	7007697000010000000♠69,700,001	7007741000000000000♠74,100,000	gneg
3	p	12.3	4566	4814	7007741000010000000♠74,100,001	7007798000000000000♠79,800,000	gpos	75
3	p	12.2	4814	4946	7007798000010000000♠79,800,001	7007835000000000000♠83,500,000	gneg
3	p	12.1	4946	5077	7007835000010000000♠83,500,001	7007871000000000000♠87,100,000	gpos	75
3	p	11.2	5077	5135	7007871000010000000♠87,100,001	7007878000000000000♠87,800,000	gneg
3	p	11.1	5135	5266	7007878000010000000♠87,800,001	7007909000000000000♠90,900,000	acen
3	q	11.1	5266	5427	7007909000010000000♠90,900,001	7007940000000000000♠94,000,000	acen
3	q	11.2	5427	5602	7007940000010000000♠94,000,001	7007986000000000000♠98,600,000	gvar
3	q	12.1	5602	5762	7007986000010000000♠98,600,001	7008100300000000000♠100,300,000	gneg
3	q	12.2	5762	5850	7008100300001000000♠100,300,001	7008101200000000000♠101,200,000	gpos	25
3	q	12.3	5850	5996	7008101200001000000♠101,200,001	7008103100000000000♠103,100,000	gneg
3	q	13.11	5996	6229	7008103100001000000♠103,100,001	7008106500000000000♠106,500,000	gpos	75
3	q	13.12	6229	6361	7008106500001000000♠106,500,001	7008108200000000000♠108,200,000	gneg
3	q	13.13	6361	6594	7008108200001000000♠108,200,001	7008111600000000000♠111,600,000	gpos	50
3	q	13.2	6594	6682	7008111600001000000♠111,600,001	7008113700000000000♠113,700,000	gneg
3	q	13.31	6682	6871	7008113700001000000♠113,700,001	7008117600000000000♠117,600,000	gpos	75
3	q	13.32	6871	6973	7008117600001000000♠117,600,001	7008119300000000000♠119,300,000	gneg
3	q	13.33	6973	7148	7008119300001000000♠119,300,001	7008122200000000000♠122,200,000	gpos	75
3	q	21.1	7148	7294	7008122200001000000♠122,200,001	7008124100000000000♠124,100,000	gneg
3	q	21.2	7294	7440	7008124100001000000♠124,100,001	7008126100000000000♠126,100,000	gpos	25
3	q	21.3	7440	7674	7008126100001000000♠126,100,001	7008129500000000000♠129,500,000	gneg
3	q	22.1	7674	7936	7008129500001000000♠129,500,001	7008134000000000000♠134,000,000	gpos	25
3	q	22.2	7936	8053	7008134000001000000♠134,000,001	7008136000000000000♠136,000,000	gneg
3	q	22.3	8053	8228	7008136000001000000♠136,000,001	7008139000000000000♠139,000,000	gpos	25
3	q	23	8228	8461	7008139000001000000♠139,000,001	7008143100000000000♠143,100,000	gneg
3	q	24	8461	8811	7008143100001000000♠143,100,001	7008149200000000000♠149,200,000	gpos	100
3	q	25.1	8811	9001	7008149200001000000♠149,200,001	7008152300000000000♠152,300,000	gneg
3	q	25.2	9001	9162	7008152300001000000♠152,300,001	7008155300000000000♠155,300,000	gpos	50
3	q	25.31	9162	9264	7008155300001000000♠155,300,001	7008157300000000000♠157,300,000	gneg
3	q	25.32	9264	9366	7008157300001000000♠157,300,001	7008159300000000000♠159,300,000	gpos	50
3	q	25.33	9366	9453	7008159300001000000♠159,300,001	7008161000000000000♠161,000,000	gneg
3	q	26.1	9453	9803	7008161000001000000♠161,000,001	7008167900000000000♠167,900,000	gpos	100
3	q	26.2	9803	9949	7008167900001000000♠167,900,001	7008171200000000000♠171,200,000	gneg
3	q	26.31	9949	10183	7008171200001000000♠171,200,001	7008176000000000000♠176,000,000	gpos	75
3	q	26.32	10183	10329	7008176000001000000♠176,000,001	7008179300000000000♠179,300,000	gneg
3	q	26.33	10329	10489	7008179300001000000♠179,300,001	7008183000000000000♠183,000,000	gpos	75
3	q	27.1	10489	10620	7008183000001000000♠183,000,001	7008184800000000000♠184,800,000	gneg
3	q	27.2	10620	10737	7008184800001000000♠184,800,001	7008186300000000000♠186,300,000	gpos	25
3	q	27.3	10737	10883	7008186300001000000♠186,300,001	7008188200000000000♠188,200,000	gneg
3	q	28	10883	11175	7008188200001000000♠188,200,001	7008192600000000000♠192,600,000	gpos	75
3	q	29	11175	11700	7008192600001000000♠192,600,001	7008198295559000000♠198,295,559	gneg

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   ^ "Human chromosome 3: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.
   


9. 
   ^ "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.
   


10. 
    ^ "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.
    


11. 
    ^ "Search results – 3[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) – Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
    


12. 
    ^ CRBN cereblon [Homo sapiens (human)] - Gene - NCBI
    


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. 
    ^ "p": Short arm; "q": Long arm.
    


18. 
    ^ For cytogenetic banding nomenclature, see article locus.
    


19. 
    ^ ^ab 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.
    


20. 
    ^ 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

Wikimedia Commons has media related to Human chromosome 3.

• 
  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.
  

v t e Human genome
Nuclear genome	Autosome 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 Sex chromosome X Y
Mitochondrial genome	Human mitochondrial DNA

v t e Cytogenetics: chromosomes
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See also	Extrachromosomal DNA Plasmid List of organisms by chromosome count List of chromosome lengths for various organisms List of sequenced genomes International System for Human Cytogenetic Nomenclature
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