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Chromosome 3

chromosome 3, chromosome 3 deletion
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 65 percent of the total DNA in cells

Contents

  • 1 Genes
    • 11 Number of genes
    • 12 List of genes
      • 121 p-arm
      • 122 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 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, fra3p242
  • 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 PolyADP-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

G-banding ideograms of human chromosome 3G-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 eg Ensembl, UCSC Genome BrowserG-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 263 0 175 7000100000000000000♠1 7006280000000000000♠2,800,000 gpos 50
3 p 262 175 263 7006280000100000000♠2,800,001 7006400000000000000♠4,000,000 gneg
3 p 261 263 408 7006400000100000000♠4,000,001 7006810000000000000♠8,100,000 gpos 50
3 p 253 408 642 7006810000100000000♠8,100,001 7007116000000000000♠11,600,000 gneg
3 p 252 642 759 7007116000010000000♠11,600,001 7007132000000000000♠13,200,000 gpos 25
3 p 251 759 963 7007132000010000000♠13,200,001 7007163000000000000♠16,300,000 gneg
3 p 243 963 1269 7007163000010000000♠16,300,001 7007238000000000000♠23,800,000 gpos 100
3 p 242 1269 1357 7007238000010000000♠23,800,001 7007263000000000000♠26,300,000 gneg
3 p 241 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 223 1751 1926 7007320000010000000♠32,000,001 7007364000000000000♠36,400,000 gpos 50
3 p 222 1926 2013 7007364000010000000♠36,400,001 7007393000000000000♠39,300,000 gneg
3 p 221 2013 2188 7007393000010000000♠39,300,001 7007436000000000000♠43,600,000 gpos 75
3 p 2133 2188 2451 7007436000010000000♠43,600,001 7007441000000000000♠44,100,000 gneg
3 p 2132 2451 2626 7007441000010000000♠44,100,001 7007442000000000000♠44,200,000 gpos 50
3 p 2131 2626 3239 7007442000010000000♠44,200,001 7007506000000000000♠50,600,000 gneg
3 p 212 3239 3385 7007506000010000000♠50,600,001 7007523000000000000♠52,300,000 gpos 25
3 p 211 3385 3676 7007523000010000000♠52,300,001 7007544000000000000♠54,400,000 gneg
3 p 143 3676 3910 7007544000010000000♠54,400,001 7007586000000000000♠58,600,000 gpos 50
3 p 142 3910 4143 7007586000010000000♠58,600,001 7007638000000000000♠63,800,000 gneg
3 p 141 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 123 4566 4814 7007741000010000000♠74,100,001 7007798000000000000♠79,800,000 gpos 75
3 p 122 4814 4946 7007798000010000000♠79,800,001 7007835000000000000♠83,500,000 gneg
3 p 121 4946 5077 7007835000010000000♠83,500,001 7007871000000000000♠87,100,000 gpos 75
3 p 112 5077 5135 7007871000010000000♠87,100,001 7007878000000000000♠87,800,000 gneg
3 p 111 5135 5266 7007878000010000000♠87,800,001 7007909000000000000♠90,900,000 acen
3 q 111 5266 5427 7007909000010000000♠90,900,001 7007940000000000000♠94,000,000 acen
3 q 112 5427 5602 7007940000010000000♠94,000,001 7007986000000000000♠98,600,000 gvar
3 q 121 5602 5762 7007986000010000000♠98,600,001 7008100300000000000♠100,300,000 gneg
3 q 122 5762 5850 7008100300001000000♠100,300,001 7008101200000000000♠101,200,000 gpos 25
3 q 123 5850 5996 7008101200001000000♠101,200,001 7008103100000000000♠103,100,000 gneg
3 q 1311 5996 6229 7008103100001000000♠103,100,001 7008106500000000000♠106,500,000 gpos 75
3 q 1312 6229 6361 7008106500001000000♠106,500,001 7008108200000000000♠108,200,000 gneg
3 q 1313 6361 6594 7008108200001000000♠108,200,001 7008111600000000000♠111,600,000 gpos 50
3 q 132 6594 6682 7008111600001000000♠111,600,001 7008113700000000000♠113,700,000 gneg
3 q 1331 6682 6871 7008113700001000000♠113,700,001 7008117600000000000♠117,600,000 gpos 75
3 q 1332 6871 6973 7008117600001000000♠117,600,001 7008119300000000000♠119,300,000 gneg
3 q 1333 6973 7148 7008119300001000000♠119,300,001 7008122200000000000♠122,200,000 gpos 75
3 q 211 7148 7294 7008122200001000000♠122,200,001 7008124100000000000♠124,100,000 gneg
3 q 212 7294 7440 7008124100001000000♠124,100,001 7008126100000000000♠126,100,000 gpos 25
3 q 213 7440 7674 7008126100001000000♠126,100,001 7008129500000000000♠129,500,000 gneg
3 q 221 7674 7936 7008129500001000000♠129,500,001 7008134000000000000♠134,000,000 gpos 25
3 q 222 7936 8053 7008134000001000000♠134,000,001 7008136000000000000♠136,000,000 gneg
3 q 223 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 251 8811 9001 7008149200001000000♠149,200,001 7008152300000000000♠152,300,000 gneg
3 q 252 9001 9162 7008152300001000000♠152,300,001 7008155300000000000♠155,300,000 gpos 50
3 q 2531 9162 9264 7008155300001000000♠155,300,001 7008157300000000000♠157,300,000 gneg
3 q 2532 9264 9366 7008157300001000000♠157,300,001 7008159300000000000♠159,300,000 gpos 50
3 q 2533 9366 9453 7008159300001000000♠159,300,001 7008161000000000000♠161,000,000 gneg
3 q 261 9453 9803 7008161000001000000♠161,000,001 7008167900000000000♠167,900,000 gpos 100
3 q 262 9803 9949 7008167900001000000♠167,900,001 7008171200000000000♠171,200,000 gneg
3 q 2631 9949 10183 7008171200001000000♠171,200,001 7008176000000000000♠176,000,000 gpos 75
3 q 2632 10183 10329 7008176000001000000♠176,000,001 7008179300000000000♠179,300,000 gneg
3 q 2633 10329 10489 7008179300001000000♠179,300,001 7008183000000000000♠183,000,000 gpos 75
3 q 271 10489 10620 7008183000001000000♠183,000,001 7008184800000000000♠184,800,000 gneg
3 q 272 10620 10737 7008184800001000000♠184,800,001 7008186300000000000♠186,300,000 gpos 25
3 q 273 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

References

  1. ^ "Human Genome Assembly GRCh38 – Genome Reference Consortium" National Center for Biotechnology Information 2013-12-24 Retrieved 2017-03-04 
  2. ^ a b "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. ^ a b c Genome Decoration Page, NCBI Ideogram data for Homo sapience 850 bphs, Assembly GRCh38p3 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:101186/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. ^ "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 GRCh38p3 Last update 2014-03-04 Retrieved 2017-04-26
  14. ^ Genome Decoration Page, NCBI Ideogram data for Homo sapience 550 bphs, Assembly GRCh38p3 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:101109/JCSSE20126261965 
  17. ^ "p": Short arm; "q": Long arm
  18. ^ For cytogenetic banding nomenclature, see article locus
  19. ^ a b 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

  • 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 

chromosome 3, chromosome 3 deletion, chromosome 3 disorder, chromosome 3 duplication, chromosome 3 film, chromosome 3 genes, chromosome 3 trisomy, chromosome 3d model, chromosome 3p25 deletion, chromosome 3p25-26


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