Human chromosome
Chromosome 6 is one of the 23 pairs ofchromosomes inhumans . People normally have two copies of this chromosome. Chromosome 6 spans nearly 171 millionbase pairs (the building material ofDNA ) and represents between 5.5 and 6% of the total DNA incells . It contains themajor histocompatibility complex , which contains over 100 genes related to theimmune response , and plays a vital role inorgan transplantation .
The evolution of human centromere 6 [ edit ] Thecentromere of chromosome 6 illustrates an interesting example of centromere evolution. It was known[further explanation needed that in aCatarrhini ancestor the chromosome 6 centromere was situated near position 26 Mb of the modern human chromosome. InMacaca mulatta , this old centromere went defunct and repositioned to a different chromosomal location[relevant? . In the case of humans, the old centromere went defunct and a more recent form emerged near the modern position of human cen6 (size of 60 Mb). Such cases are known as Evolutionary New Centromeres (ENC). This assembly phenomenon of the human chromosome 6 gives researchers an opportunity to investigate the origin of the ENC on chromosome 6.[ 4]
Thehuman leukocyte antigen lies on chromosome 6, with the exception of the gene forβ2-microglobulin (which is located onchromosome 15 ), and encodes cell-surfaceantigen -presenting proteins among other functions.
In 2003, the entirety of chromosome 6 was manually annotated for proteins, resulting in the identification of 1,557 genes, and 633 pseudogenes.[ 5]
The following are some of the newer gene count estimates. Because researchers use different approaches togenome annotation their predictions of thenumber of genes on each chromosome varies (for technical details, seegene 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.[ 6]
The following is a partial list of genes on human chromosome 6.
The following are some of the genes located on p-arm (short arm) of human chromosome 6:
ADTRP : encodingprotein Androgen-dependent TFPI-regulating proteinAPOM : encodingprotein Apolipoprotein M (6p21.33)ARMC12 : encoding protein Armadillo repeat containing 12ATXN1 : encodingprotein Ataxin 1 (6p16.3-p16.76)TSBP1 : encodingprotein TSBP1 (6p21.32)C6orf62 : chromosome 6 open reading frame 62 (6p22.3)C6orf89 : chromosome 6 open reading frame 89 (6p21.2)CDKAL1 : CDK5 regulatory subunit associated protein 1 like 1 (6p22.3)COL11A2 : collagen, type XI, alpha 2(6p21.3)CRIP3 : encoding protein Cysteine rich protein 3CYP21A2 : cytochrome P450, family 21, subfamily A, polypeptide 2 (6p21.33)DHX16 : DEAH-box helicase 16 (6p21.33)DOM3Z : Decapping exoribonuclease (6p21.33)DSP : Desmoplakin gene linked to cardiomyopathy (6p24.3)ELOVL5 : ELOVL fatty acid elongase 5 (6p12.1)FBXO9 : F-box protein 9 (6p12.1)FOXP4-AS1 : encoding protein FOXP4 antisense RNA 1FTH1P5 : encoding protein Ferritin, heavy polypeptide 1 pseudogene 5G6B : Protein G6b (6p21.33)GCNT2 : N-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase (6p24.3)GGNBP1 : encoding protein Gametogenetin binding protein 1 (pseudogene)GMDS : GDP-mannose 4,6-dehydratase (6p25.3)GTPBP2 : encoding protein Gtp binding protein 2HCG4P11 : HLA complex group 4 pseudogene 11HFE : hemochromatosis (6p22.2)HIST1H2AH : histone cluster 1 H2A family member h (6p22.1)HLA-A ,HLA-B ,HLA-C : major histocompatibility complex (MHC), class I, A, B, and C loci. (6p21.3)HLA-DQA1 andHLA-DQB1 formHLA-DQ heterodimer MHC class II, DQ: Celiac1, IDDM (6p21.3)HLA-DRA ,HLA-DRB1 ,HLA-DRB3 ,HLA-DRB4 ,HLA-DRB5 formsHLA-DR , heterodimer MHC class II, DR (6p21.3) Mold / Biotoxin SusceptibilityHLA-DPA1 andHLA-DPB1 formsHLA-DP , MHC class II, DP (6p21.3)HLA-Cw*06:02 : gene variation related to psoriasis (6p21.3)KAAG1 : encoding protein Kidney associated antigen 1LOC100533655 : encoding protein Aryl hydrocarbon receptor pseudogeneLST1 : leukocyte specific transcript 1 (6p21.33)LY6G6E encodingprotein Lymphocyte antigen 6 complex, locus G6E (pseudogene) (6p21.33)MIR4640 : microRNA 4640 (6p21.33)MLIP : muscular LMNA interaction protein (6p12.1)MRPS18B : mitochondrial ribosomal protein S18B (6p21.33)MUT : methylmalonyl Coenzyme A mutase (6p12.3)NHLRC1 : NHL repeat containing E3 ubiquitin protein ligase 1 (6p22.3)NOL7 : nucleolar protein 7 (6p23)NQO2 : N-ribosyldihydronicotinamide:quinone reductase 2 (6p25.2)NRSN1 : neurensin 1 (6p22.3)NUDT3 : nudix hydrolase 3 (6p21.31)PFDN6 : prefoldin subunit 6 (6p21.32)PHACTR1 : phosphatase and actin regulator 1 (6p24.1)PKHD1 : polycystic kidney and hepatic disease 1 (autosomal recessive) (6p21.2-p12)PRICKLE4 : prickle planar cell polarity protein 4 (6p21.1)PRSS16 : protease, serine 16 (6p22.1)PSMB8-AS1 : PSMB8 antisense RNA 1 (head to head) (6p21.32)RAB44 : encoding protein Rab44, member ras oncogene familyRIPOR2 : RHO family interacting cell polarization regulator 2 (6p22.3)RPL10A : encodingprotein 60S ribosomal protein L10a (6p21.31)SKIV2L : Ski2 like RNA helicase (6p21.33)SSR1 : signal sequence receptor subunit 1 (6p24.3)TCF19 : transcription factor 19 (6p21.33)TCP11 : t-complex 11 (6p21.31)TJAP1 : tight junction associated protein 1 (6p21.1)TP53COR1 encodingprotein Tumor protein p53 pathway corepressor 1 (non-protein coding)TMEM151B : encodingprotein Transmembrane protein 151BTNXB : tenascin XB (6p21.3)TRAM2 : translocation associated membrane protein 2 (6p12.2)TRIM38 : encoding protein Tripartite motif containing 38TTBK1 : encoding protein Tau tubulin kinase 1UBR2 : ubiquitin protein ligase E3 component n-recognin 2 (6p21.2)UNC5CL : encodingprotein Unc-5 homolog C (C. elegans)-likeUSP8P1 : encoding protein Ubiquitin specific peptidase 8 pseudogene 1VEGF : vascular endothelial growth factor A (angiogenic growth factor) (6p21.1)VPS52 : GARP complex subunitVWA7 : encoding protein Von willebrand factor a domain containing 7ZKSCAN4 : encoding protein zinc finger with KRAB and SCAN domains 4ZNF76 : zinc finger protein 76 (6p21.31)ZNF193 : zinc finger protein 193 (6p22.1)ZNRD1 : zinc ribbon domain containing 1 (6p22.1)The following are some of the genes located onq-arm (long arm) of human chromosome 6:
AIM1 : encodingprotein Absent in melanoma 1 protein (6q21)AIG1 : encodingprotein Androgen-induced protein 1 (6q24.2)AKIRIN2 : akirin 2 (6q15)ARG1 : arginase 1 (6q23.2)BCKDHB : branched-chain keto acid dehydrogenase E1, beta polypeptide (maple syrup urine disease) (6q14.1)BMIQ3 : body mass index QTL 3TMEM242 encoding transmembrane protein TMEM242C6orf203 : encoding protein Chromosome 6 open reading frame 203C6orf58 : chromosome 6 open reading frame 58 (6q22.33)CFAP206 : encodingprotein Cilia And Flagella Associated Protein 206CMD1F : cardiomyopathy, dilated 1FCMD1K : cardiomyopathy, dilated 1KCNR1 : cannabinoid 1 receptor (6q14-q15)[ 13] DACT2 : encoding protein Dishevelled binding antagonist of beta catenin 2DFNB38 : deafness, autosomal recessive 38DYX4 : dyslexia susceptibility 4ECT2L : encodingprotein Epithelial cell transforming sequence 2 oncogene-likeESR1 : Estrogen receptor 1 (6q25)EYA4 : eyes absent homolog 4 (Drosophila)(6q23.2)FBXL4 : F-box and leucine rich repeat protein 4 (6q16.1-q16.2)FEB5 : febrile convulsions 5HACE1 :HECT domain andAnkyrin repeat containing, E3 ubiquitin protein ligase 1 (6q21)HEBP2 : heme binding protein 2 (6q24.1)IDDM8 : insulin dependent diabetes mellitus 8IDDM15 : insulin dependent diabetes mellitus 15IFNGR : interferon-γ receptor gene (6q23-q24)IGF2R : insulin-like growth factor 2 receptor (6q25.3)IMPG1 : interphotoreceptor matrix proteoglylcan 1 (6q14.1)KIAA0408 LGSN : encoding protein lengsinLIN28B : lin-28 homolog B (6q16.3-q21)MAN1A1 : mannosidase alpha class 1A member 1 (6q22.31)MB21D1 : encodingprotein Mab-21 domain containing 1MCDR1 : macular dystrophy, retinal, 1MDN1 : midasin AAA ATPase 1 (6q15)MOXD1 : monooxygenase DBH like 1 (6q23.2)MTO1 : mitochondrial tRNA translation optimization 1 (6q13)MRT18 : mental retardation, non-syndromic, autosomal recessiveMRT28 : mental retardation, non-syndromic, autosomal recessiveMTRF1L : mitochondrial translational release factor 1 like (6q25.2)MYO6 : myosin VI (6q14.1)NHEG1 : encoding protein Neuroblastoma highly expressed 1OA3 : ocular albinism 3OPRM1 : μ-opioid receptors (6q24-q25)OTSC7 : otosclerosis 7PLG : plasminogen (6q26)PBCRA1 PARK2 : Parkinson disease (autosomal recessive, juvenile) 2, parkin (6q26)PCMT1 : protein-L-isoaspartate (D-aspartate) O-methyltransferase (6q25.1)PERP : p53 apoptosis effector related to PMP-22 (6q23.3)PKIB : cAMP-dependent protein kinase inhibitor beta (6p22.31)PLAGL1 : (6q24.2)QRSL1 : encoding protein Glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1RCD1 : retinal cone dystrophy 1RFPL4B : Ret finger protein like 4BRP63 : retinitis pigmentosa 63SASH1 : SAM and SH3 domain containing 1 (6q24.3-q25.1)SCZD5 : schizophrenia disorder 5SEN6 : senescence (cellular)-related 6SENP6 : SUMO1/sentrin specific peptidase 6 (6q14.1)SERAC1 : serine active site containing 1 (6q25.3)SERINC1 : serine incorporator 1 (6q22.31)SF3B5 : splicing factor 3b subunit 5 (6q24.2)SMAP1 : small ArfGAP 1 (6q13)SOBP : sine oculis binding protein homolog (6q21)SPG25 : spastic paraplegia 25SYNJ2 : synaptojanin 2 (6q25.3)T : Tbrachyury transcription factor (more commonly known as the T gene) linked toHepatocellular carcinoma andChordoma (6q27)[ 14] TAAR1 : trace amine associated receptor 1 (6q23.1)TAAR2 : trace amine associated receptor 2 (6q24)TMEM200A : encodingprotein Transmembrane protein 200ATSPYL1 : TSPY like 1 (6q22.1)UNC93A : encodingprotein Unc-93 homolog A (C. elegans)VNN1 : vanin 1 (6q23.2)VNN2 : vanin 2 (6q23.2)VTA1 : Vesicle trafficking 1 (6q24.1-2)ZC2HC1 : encodingprotein Zinc finger C2HC-type containing 1BZDHHC14 : encodingprotein Zinc finger, DHHC-type containing 14Diseases and disorders [ edit ] The following diseases are some of those related to genes on chromosome 6:
ankylosing spondylitis , HLA-Bcollagenopathy, types II and XI Coeliac disease HLA-DQA1 & DQB1Ehlers-Danlos syndrome , classical, hypermobility, and Tenascin-X typesHashimoto's thyroiditis hemochromatosis Hemochromatosis type 1 21-hydroxylase deficiency maple syrup urine disease methylmalonic acidemia Autosomalnonsyndromic deafness Narcolepsy North Carolina macular dystrophy otospondylomegaepiphyseal dysplasia Parkinson disease polycystic kidney disease porphyria porphyria cutanea tarda Rheumatoid arthritis , HLA-DRCIRS (Chronic Inflammatory Response Syndrome ), Sick Building Syndrome, Mold Toxin Susceptibility / Poisoning, HLA-DR/DQ Spinocerebellar ataxia type 1 , ATXN1Stickler syndrome , COL11A2Systemic lupus erythematosus Diabetes mellitus type 1 , HLA-DR, DQA1 & DQB1X-linked sideroblastic anemia Epilepsy Guillain Barre Syndrome Chordoma Hepatocellular carcinoma Schizophrenia G-banding ideograms of human chromosome 6
G-banding ideogram of human chromosome 6 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 6 in three different resolutions (400,
[ 15] 550
[ 16] and 850
[ 3] ). Band length in this diagram is based on the ideograms from ISCN (2013).
[ 17] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the
mitotic process .
[ 18] G-bands of human chromosome 6 in resolution 850 bphs[ 19] Chr. Arm[ 20] Band[ 21] ISCN[ 22] ISCN[ 22] Basepair Basepair Stain[ 23] Density 6 p 25.3 0 118 gneg 6 p 25.2 118 207 gpos 25 6 p 25.1 207 355 gneg 6 p 24.3 355 548 gpos 50 6 p 24.2 548 592 gneg 6 p 24.1 592 740 gpos 25 6 p 23 740 844 gneg 6 p 22.3 844 1185 gpos 75 6 p 22.2 1185 1348 gneg 6 p 22.1 1348 1585 gpos 50 6 p 21.33 1585 1718 gneg 6 p 21.32 1718 1836 gpos 25 6 p 21.31 1836 2162 gneg 6 p 21.2 2162 2310 gpos 25 6 p 21.1 2310 2755 gneg 6 p 12.3 2755 3080 gpos 100 6 p 12.2 3080 3140 gneg 6 p 12.1 3140 3377 gpos 100 6 p 11.2 3377 3421 gneg 6 p 11.1 3421 3554 acen 6 q 11.1 3554 3658 acen 6 q 11.2 3658 3732 gneg 6 q 12 3732 4147 gpos 100 6 q 13 4147 4324 gneg 6 q 14.1 4324 4621 gpos 50 6 q 14.2 4621 4709 gneg 6 q 14.3 4709 4917 gpos 50 6 q 15 4917 5228 gneg 6 q 16.1 5228 5613 gpos 100 6 q 16.2 5613 5687 gneg 6 q 16.3 5687 5983 gpos 100 6 q 21 5983 6531 gneg 6 q 22.1 6531 6753 gpos 75 6 q 22.2 6753 6872 gneg 6 q 22.31 6872 7168 gpos 100 6 q 22.32 7168 7345 gneg 6 q 22.33 7345 7642 gpos 75 6 q 23.1 7642 7923 gneg 6 q 23.2 7923 8145 gpos 50 6 q 23.3 8145 8352 gneg 6 q 24.1 8352 8560 gpos 75 6 q 24.2 8560 8708 gneg 6 q 24.3 8708 8886 gpos 75 6 q 25.1 8886 9078 gneg 6 q 25.2 9078 9241 gpos 50 6 q 25.3 9241 9596 gneg 6 q 26 9596 9774 gpos 50 6 q 27 9774 10100 gneg
^a b "Search results - 6[CHR] AND "Homo sapiens"[Organism] AND ("has ccds"[Properties] AND alive[prop]) - Gene" .NCBI . CCDS Release 20 forHomo sapiens . 2016-09-08. Retrieved2017-05-28 .^ Tom Strachan; Andrew Read (2 April 2010).Human Molecular Genetics ISBN 978-1-136-84407-2 ^a b Genome Decoration Page, NCBI.Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3) . Last update 2014-06-03. Retrieved 2017-04-26. ^ Altemose, Nicolas; Logsdon, Glennis A.; Bzikadze, Andrey V.; Sidhwani, Pragya; Langley, Sasha A.; Caldas, Gina V.; Hoyt, Savannah J.; Uralsky, Lev; Ryabov, Fedor D.; Shew, Colin J.; Sauria, Michael E. G.; Borchers, Matthew; Gershman, Ariel; Mikheenko, Alla; Shepelev, Valery A. (April 2022)."Complete genomic and epigenetic maps of human centromeres" .Science .376 (6588) eabl4178.doi :10.1126/science.abl4178 .ISSN 0036-8075 .PMC 9233505 PMID 35357911 . ^ Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, et al. (October 2003)."The DNA sequence and analysis of human chromosome 6" .Nature .425 (6960):805– 11.Bibcode :2003Natur.425..805M .doi :10.1038/nature02055 PMID 14574404 . ^ 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 . ^ "Statistics & Downloads for chromosome 6" .HUGO Gene Nomenclature Committee . 2017-05-12. Archived fromthe original on 2017-08-18. Retrieved2017-05-19 .^ "Chromosome 6: Chromosome summary - Homo sapiens" .Ensembl Release 88 . 2017-03-29. Retrieved2017-05-19 .^ "Human chromosome 6: entries, gene names and cross-references to MIM" .UniProt . 2018-02-28. Retrieved2018-03-16 .^ "Search results - 6[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene" .NCBI . 2017-05-19. Retrieved2017-05-20 .^ "Search results - 6[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. Retrieved2017-05-20 .^ "Search results - 6[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene" .NCBI . 2017-05-19. Retrieved2017-05-20 .^ Matsuda LA, Lolait SJ, Brownstein MJ, Young AC, Bonner TI (August 1990). "Structure of a cannabinoid receptor and functional expression of the cloned cDNA".Nature .346 (6284):561– 4.Bibcode :1990Natur.346..561M .doi :10.1038/346561a0 .PMID 2165569 .S2CID 4356509 . ^ "T brachyury transcription factor" .T - T brachyury transcription factor - Genetics Home Reference . Archived fromthe original on March 3, 2012.^ Genome Decoration Page, NCBI.Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3) . Last update 2014-03-04. Retrieved 2017-04-26. ^ Genome Decoration Page, NCBI.Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3) . Last update 2015-08-11. Retrieved 2017-04-26. ^ International Standing Committee on Human Cytogenetic Nomenclature (2013).ISCN 2013: An International System for Human Cytogenetic Nomenclature (2013) ISBN 978-3-318-02253-7 ^ 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) 276– 282.doi :10.1109/JCSSE.2012.6261965 .ISBN 978-1-4673-1921-8 S2CID 16666470 . ^ Genome Decoration Page, NCBI.Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3) . Last update 2014-06-03. Retrieved 2017-04-26. ^ "p ": Short arm; "q ": Long arm. ^ For cytogenetic banding nomenclature, see articlelocus . ^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 . ^ gpos : Region which is positively stained byG banding , generallyAT-rich and gene poor;gneg : Region which is negatively stained by G banding, generallyCG-rich and gene rich;acen Centromere .var : Variable region;stalk : Stalk.Notes National Institutes of Health."Chromosome 6" .Genetics Home Reference . Archived fromthe original on 2007-08-12. Retrieved2017-05-06 . "Chromosome 6" .Human Genome Project Information Archive 1990–2003 . Retrieved2017-05-06 ."Chromosome 6 Research Project" .Parent-driven research for genotype-phenotype studies on chromosome 6 disorders. Retrieved 2017-06-17
Basic Types Processes Structures
See also
