gene components

Summary

Summary: The parts of the gene sequence that carry out the different functions of the GENES.

Top Publications

  1. Cooper G, Stone E, Asimenos G, Green E, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005;15:901-13 pubmed
    ..We anticipate that GERP and the types of analyses it facilitates will provide further insights and improved annotation for the human genome as mammalian genome sequence data become richer. ..
  2. Ferrier D, Dewar K, Cook A, Chang J, Hill Force A, Amemiya C. The chordate ParaHox cluster. Curr Biol. 2005;15:R820-2 pubmed
  3. Benna C, Bonaccorsi S, Wülbeck C, Helfrich Forster C, Gatti M, Kyriacou C, et al. Drosophila timeless2 is required for chromosome stability and circadian photoreception. Curr Biol. 2010;20:346-52 pubmed publisher
    ..tim2's residual role in light entrainment thus provides an evolutionary link that may explain why its derived paralog, tim1, came to play such a major role in both circadian photosensitivity and core clock function. ..
  4. Shahin H, Walsh T, Sobe T, Abu Sa ed J, Abu Rayan A, Lynch E, et al. Mutations in a novel isoform of TRIOBP that encodes a filamentous-actin binding protein are responsible for DFNB28 recessive nonsyndromic hearing loss. Am J Hum Genet. 2006;78:144-52 pubmed
    ..Antibodies to TRIOBP reveal expression in sensory cells of the inner ear and colocalization with F-actin along the length of the stereocilia. ..
  5. Maekawa K, Fukushima Uesaka H, Tohkin M, Hasegawa R, Kajio H, Kuzuya N, et al. Four novel defective alleles and comprehensive haplotype analysis of CYP2C9 in Japanese. Pharmacogenet Genomics. 2006;16:497-514 pubmed
    ..Taken together, novel defective alleles and detailed haplotype structures would be useful for determining metabolic phenotypes of CYP2C9 substrate drugs in Japanese and probably Asians. ..
  6. Groenewald M, Groenewald J, Harrington T, Abeln E, Crous P. Mating type gene analysis in apparently asexual Cercospora species is suggestive of cryptic sex. Fungal Genet Biol. 2006;43:813-25 pubmed publisher
    ..beticola, C. zeae-maydis and C. zeina populations, in contrast to single mating types in C. apii (MAT1) and C. apiicola (MAT2), suggests that a sexual cycle may be active in some of these species...
  7. Castaman G, Mancuso M, Giacomelli S, Tosetto A, Santagostino E, Mannucci P, et al. Molecular and phenotypic determinants of the response to desmopressin in adult patients with mild hemophilia A. J Thromb Haemost. 2009;7:1824-31 pubmed publisher
    ..54 IU dL(-1); P < 0.001; fold 1.8 +/- 0.6 vs. 2.9 +/- 0.8; P = 0.002). In this cohort of patients with mild hemophilia A, a poor biologic response to desmopressin was frequently associated with the absence of detectable F8 mutations. ..
  8. Ingelman Sundberg M, Rodriguez Antona C. Pharmacogenetics of drug-metabolizing enzymes: implications for a safer and more effective drug therapy. Philos Trans R Soc Lond B Biol Sci. 2005;360:1563-70 pubmed
    ..However, it will take time before this will be a reality within the clinic. We describe some important aspects in the field with emphasis on cytochrome P450 and discuss also polymorphic aspects of foetal expression of CYP3A5 and CYP3A7. ..
  9. Slavec B, Bercic R, Cizelj I, Narat M, Zorman Rojs O, Dovc P, et al. Variation of vlhA gene in Mycoplasma synoviae clones isolated from chickens. Avian Pathol. 2011;40:481-9 pubmed publisher
    ..This is the first demonstration of temporal diversity of the vlhA gene in M. synoviae populations isolated from chicken tracheas...

More Information

Publications62

  1. Ali R, Mellenthin K, Fahmy K, Da Rocha S, Baumgartner S. Structural conservation of the salivary gland-specific slalom gene in the blowfly Lucilia sericata. Dev Genes Evol. 2005;215:537-43 pubmed
    ..Moreover, it suggests that the salivary gland-specific expression of slalom bears an important and conserved function for sulfation of specific macromolecules. ..
  2. Piotrowski A, Xie J, Liu Y, Poplawski A, Gomes A, Madanecki P, et al. Germline loss-of-function mutations in LZTR1 predispose to an inherited disorder of multiple schwannomas. Nat Genet. 2014;46:182-7 pubmed publisher
    ..Our findings identify LZTR1 as a gene predisposing to an autosomal dominant inherited disorder of multiple schwannomas in ?80% of 22q-related schwannomatosis cases lacking mutation in SMARCB1. ..
  3. Tomita M, Okutani A, Beiles A, Nevo E. Genomic, RNA, and ecological divergences of the Revolver transposon-like multi-gene family in Triticeae. BMC Evol Biol. 2011;11:269 pubmed publisher
  4. Francis V, Zorzano A, Teleman A. dDOR is an EcR coactivator that forms a feed-forward loop connecting insulin and ecdysone signaling. Curr Biol. 2010;20:1799-808 pubmed publisher
    ..Furthermore, because ecdysone signaling inhibits insulin signaling in the fat body, this also uncovers a feed-forward mechanism whereby ecdysone potentiates its own signaling via dDOR. ..
  5. Nakamura S, Horie M, Fujino K, Matsumoto Y, Honda T, Tomonaga K. Generation of human bronchial epithelial cell lines expressing inactive mutants of GALNT3. J Vet Med Sci. 2012;74:1493-6 pubmed
    ..These results suggested that the established cell lines express inactive forms of GALNT3 and might be useful in investigation of the significance of O-glycosylation of mucins in respiratory virus infections. ..
  6. Dong Z, Zhang J, Ji X, Zhou F, Fu Y, Chen W, et al. Molecular cloning, characterization and expression of cathepsin D from grass carp (Ctenopharyngodon idella). Fish Shellfish Immunol. 2012;33:1207-14 pubmed publisher
    ..The fact that the bacterial infection can obviously improve the cathepsin D expression in immune-related organs, may suggest that cathepsin D plays an important role in the innate immune response of grass carp. ..
  7. Bathige S, Whang I, Umasuthan N, Wickramaarachchi W, Wan Q, Lim B, et al. Three complement component 1q genes from rock bream, Oplegnathus fasciatus: genome characterization and potential role in immune response against bacterial and viral infections. Fish Shellfish Immunol. 2013;35:1442-54 pubmed publisher
    ..These data collectively suggest that the RbC1qs may play defense roles as an innate immune response to protect the rock bream from bacterial and viral infections. ..
  8. Dutkiewicz M, Stachowiak A, Swiatkowska A, Ciesiołka J. Structure and function of RNA elements present in enteroviral genomes. Acta Biochim Pol. 2016;63:623-630 pubmed
    ..This review considers the RNA structures in enteroviral genomes identified and characterized to date. ..
  9. Chen B, Piel W, Gui L, Bruford E, Monteiro A. The HSP90 family of genes in the human genome: insights into their divergence and evolution. Genomics. 2005;86:627-37 pubmed
    ..Phylogenetic analyses based on both nucleotide and protein data demonstrated that HSP90(AA+AB+B) formed a monophyletic clade, whereas TRAP is a relatively distant paralogue of this clade. ..
  10. Vandamme J, Volkel P, Rosnoblet C, Le Faou P, Angrand P. Interaction proteomics analysis of polycomb proteins defines distinct PRC1 complexes in mammalian cells. Mol Cell Proteomics. 2011;10:M110.002642 pubmed publisher
    ..Finally, we suggest that differences in CBX protein interactions would account, at least in part, for distinct subnuclear localization of the CBX family members. ..
  11. Roach J, Glusman G, Rowen L, Kaur A, Purcell M, Smith K, et al. The evolution of vertebrate Toll-like receptors. Proc Natl Acad Sci U S A. 2005;102:9577-82 pubmed publisher
    ..In addition, we have produced >70 gene models, including sequences from the opossum, chicken, frog, dog, sea urchin, and sea squirt...
  12. Williford A, Demuth J. Gene expression levels are correlated with synonymous codon usage, amino acid composition, and gene architecture in the red flour beetle, Tribolium castaneum. Mol Biol Evol. 2012;29:3755-66 pubmed publisher
    ..These changes in gene architecture are only in partial agreement with selection favoring reduced cost of biosynthesis. ..
  13. Singh S, Suzuki T, Uchiyama A, Kumada S, Moriyama N, Hirose S, et al. Mutations in the NHLRC1 gene are the common cause for Lafora disease in the Japanese population. J Hum Genet. 2005;50:347-52 pubmed
    ..Our study, in addition to documenting the genetic and molecular heterogeneity observed for LD, suggests that mutations in the NHLRC1 gene may be a common cause of LD in the Japanese population. ..
  14. Mulley J, Holland P. Parallel retention of Pdx2 genes in cartilaginous fish and coelacanths. Mol Biol Evol. 2010;27:2386-91 pubmed publisher
    ..The Pdx2 gene has been lost independently in ray-finned fish and in tetrapods. ..
  15. Katafuchi T, Yasue H, Osaki T, Minamino N. Calcitonin receptor-stimulating peptide: Its evolutionary and functional relationship with calcitonin/calcitonin gene-related peptide based on gene structure. Peptides. 2009;30:1753-62 pubmed publisher
    ..In this regard, it is important to elucidate the physiological roles of CT, CGRP and CRSP from the viewpoint of the CT/CGRP/CRSP family even in Euarchontoglires. ..
  16. Iuchi S, Koyama H, Iuchi A, Kobayashi Y, Kitabayashi S, Kobayashi Y, et al. Zinc finger protein STOP1 is critical for proton tolerance in Arabidopsis and coregulates a key gene in aluminum tolerance. Proc Natl Acad Sci U S A. 2007;104:9900-5 pubmed
    ..There was no induction of AtALMT1 by Al(3+) treatment in the stop1 mutant. These results indicate that STOP1 plays a critical role in Arabidopsis tolerance to major stress factors in acid soils. ..
  17. Zhang F, Lu C, Li Z, Xie P, Xia Y, Zhu X, et al. Partial deletions are associated with an increased risk of complete deletion in AZFc: a new insight into the role of partial AZFc deletions in male infertility. J Med Genet. 2007;44:437-44 pubmed
    ..The susceptibility of partial AZFc deletions to complete AZFc deletion deserves further examination, especially in the populations or Y haplogroups abundant in partial AZFc deletions. ..
  18. Ehrlich M, Jackson K, Tsumagari K, Camaño P, Lemmers R. Hybridization analysis of D4Z4 repeat arrays linked to FSHD. Chromosoma. 2007;116:107-16 pubmed
    ..Furthermore, we show that the D4Z4-like sequences present elsewhere in the genome are not tandemly arranged, like those at 4q35 and 10q26. ..
  19. Wang Q, Bao B, Wang Y, Peatman E, Liu Z. Characterization of a NK-lysin antimicrobial peptide gene from channel catfish. Fish Shellfish Immunol. 2006;20:419-26 pubmed publisher
  20. Larsen K, Bendixen C. Characterization of the porcine FBX07 gene: the first step towards generation of a pig model for Parkinsonian pyramidal syndrome. Mol Biol Rep. 2012;39:1517-26 pubmed publisher
    ..Real-time quantitative RT-PCR analysis revealed that FBXO7 mRNA is differentially expressed in many tissues and organs, and that FBXO7 transcript can be detected early in embryo development. ..
  21. Parducci L, Suyama Y, Lascoux M, Bennett K. Ancient DNA from pollen: a genetic record of population history in Scots pine. Mol Ecol. 2005;14:2873-82 pubmed
    ..This retrieval of ancient DNA from pollen has major implications for plant palaeoecology in conifer species by allowing direct estimates of population dynamics in space and time. ..
  22. Arockiaraj J, Vanaraja P, Easwvaran S, Singh A, Othman R, Bhassu S. Bioinformatic characterization and gene expression pattern of apoptosis inhibitor from Macrobrachium rosenbergii challenged with infectious hypodermal and hematopoietic necrosis virus. Fish Shellfish Immunol. 2011;31:1259-67 pubmed publisher
    ..The collective results of this study indicate that the MrIAP is an essential immune gene and influences the immune response against IHHNV infection in M. rosenbergii...
  23. Wei H, Xuling H, Yusong X. Molecular cloning of the Robl gene from Bombyx mori and studies of its developmental and physicochemical regulation. Mol Biol Rep. 2012;39:6439-47 pubmed publisher
    ..This indicated that UV and vanadate might down-regulate BmRobl synergetically. It was further speculated that BmRobl may function as a positive regulator of the dynein complex during cellular transport. ..
  24. Wan Y, Yan Z, Liu K, Zheng Y, D Ovidio R, Shewry P, et al. Comparative analysis of the D genome-encoded high-molecular weight subunits of glutenin. Theor Appl Genet. 2005;111:1183-90 pubmed
    ..The implications of these results for HMW subunit evolution and wheat quality improvement are discussed. ..
  25. Sasaki T, Yukawa Y, Wakasugi T, Yamada K, Sugiura M. A simple in vitro RNA editing assay for chloroplast transcripts using fluorescent dideoxynucleotides: distinct types of sequence elements required for editing of ndh transcripts. Plant J. 2006;47:802-10 pubmed
    ..These results suggest that distinct editing mechanisms are present in chloroplasts. ..
  26. Richards M, Poch S, McMurtry J. Characterization of turkey and chicken ghrelin genes, and regulation of ghrelin and ghrelin receptor mRNA levels in broiler chickens. Gen Comp Endocrinol. 2006;145:298-310 pubmed publisher
    ..These results offer new information about the avian ghrelin and ghrelin receptor genes and the potential role that this system might play in regulating feed intake and energy balance in poultry...
  27. Bengtsson H, Epifantseva I, Abrink M, Kylberg A, Kullander K, Ebendal T, et al. Generation and characterization of a Gdf1 conditional null allele. Genesis. 2008;46:368-72 pubmed publisher
    ..This indicates that the transcript level is regulated by a negative feedback-loop, sensing presence of either the protein or the mRNA region encoded by Gdf1 exon 2. ..
  28. Chang N, Hsu L, Lin Y, Lai F, Sheu H. WW domain-containing oxidoreductase: a candidate tumor suppressor. Trends Mol Med. 2007;13:12-22 pubmed
    ..We propose that suppression of WWOX expression by overexpressed hyaluronidases might contribute in part to the development of hormone independence in invasive cancer. ..
  29. Song W, Zou Z, Xu F, Gu X, Xu X, Zhao Q. Molecular cloning and expression of a second zebrafish aldehyde dehydrogenase 2 gene (aldh2b). DNA Seq. 2006;17:262-9 pubmed
    ..Taken together, our results reveal that zebrafish has two orthologues of aldh2 gene and the two genes share similar expression patterns during early development and in adult tissues. ..
  30. Endo Y, Ishiwata Endo H, Yamada K. Cloning and characterization of chicken α5 integrin: endogenous and experimental expression in early chicken embryos. Matrix Biol. 2013;32:381-6 pubmed publisher
    ..Availability of these α5 integrin tools should facilitate studies of its functions in early embryonic development. ..
  31. Di Pierro E, Brancaleoni V, Moriondo V, Besana V, Cappellini M. Co-existence of two functional mutations on the same allele of the human ferrochelatase gene in erythropoietic protoporphyria. Clin Genet. 2007;71:84-8 pubmed
    ..By RNA and long polymerase chain reaction analysis, we identified a deletion of 5576 bp (g12490_18067), including exons 3 and 4, in cis with the -250G>C mutation in the promoter. ..
  32. Nakamura J, Kanno S, Kimura E, Matsui K, Nakamatsu T, Wachi M. Temperature-sensitive cloning vector for Corynebacterium glutamicum. Plasmid. 2006;56:179-86 pubmed
    ..Pro-47 is conserved among the Rep proteins of the pIJ101/pJV1 family of plasmids. This temperature-sensitive cloning vector will be useful for disrupting genes in this industrially important bacterium. ..
  33. Stoltzfus J, Massey H, Nolan T, Griffith S, Lok J. Strongyloides stercoralis age-1: a potential regulator of infective larval development in a parasitic nematode. PLoS ONE. 2012;7:e38587 pubmed publisher
    ..elegans dauer larvae. Understanding the mechanisms by which infective larvae are formed and activated may lead to novel control measures and treatments for strongyloidiasis and other soil-transmitted helminthiases...
  34. Roche J, Louis J, Grishaev A, Ying J, Bax A. Dissociation of the trimeric gp41 ectodomain at the lipid-water interface suggests an active role in HIV-1 Env-mediated membrane fusion. Proc Natl Acad Sci U S A. 2014;111:3425-30 pubmed publisher
  35. Hu Y, Deng T, Sun L. The Rab1 GTPase of Sciaenops ocellatus modulates intracellular bacterial infection. Fish Shellfish Immunol. 2011;31:1005-12 pubmed publisher
    ..These results provide the first indication that a fish Rab1 GTPase, SoRab1, regulates intracellular bacterial infection and thus is likely to play a role in bacteria-induced host immune defense. ..
  36. Kim S, Soltis P, Wall K, Soltis D. Phylogeny and domain evolution in the APETALA2-like gene family. Mol Biol Evol. 2006;23:107-20 pubmed
    ..Our expression studies show that the euAP2 homologue from Amborella trichopoda, the putative sister to all other angiosperms, is expressed in all floral organs as well as leaves. ..
  37. Mauri I, Roher N, MacKenzie S, Romero A, Manchado M, Balasch J, et al. Molecular cloning and characterization of European seabass (Dicentrarchus labrax) and Gilthead seabream (Sparus aurata) complement component C3. Fish Shellfish Immunol. 2011;30:1310-22 pubmed publisher
  38. Gu S, Hu J, Song P, Gong W, Guo M. Identification of a new transcript specifically expressed in mouse spermatocytes: mmrp2. Mol Biol Rep. 2005;32:247-55 pubmed
    ..The structure of the predicted protein and the expression pattern of the mRNA suggest that the new isoform could have an important role in meiosis. We temporarily named it mmrp 2 (Mouse Meiosis Related Protein 2). ..
  39. Lange C, Hemmrich G, Klostermeier U, López Quintero J, Miller D, Rahn T, et al. Defining the origins of the NOD-like receptor system at the base of animal evolution. Mol Biol Evol. 2011;28:1687-702 pubmed publisher
    ..These results add substantially to our understanding of the ancestral innate immune repertoire as well as providing the first insights into putative cytoplasmic defense mechanisms at the base of animal evolution. ..
  40. Geric Stare B, Fouville D, Širca S, Gallot A, Urek G, Grenier E. Molecular variability and evolution of the pectate lyase (pel-2) parasitism gene in cyst nematodes parasitizing different solanaceous plants. J Mol Evol. 2011;72:169-81 pubmed publisher
    ..quot;mexicana", a close relative of G. pallida that is unable to develop on cultivated potato varieties. ..
  41. Ueda N, Okamoto Y, Morishita J. N-acylphosphatidylethanolamine-hydrolyzing phospholipase D: a novel enzyme of the beta-lactamase fold family releasing anandamide and other N-acylethanolamines. Life Sci. 2005;77:1750-8 pubmed
    ..The existence of NAPE-PLD specifically hydrolyzing NAPEs to NAEs emphasizes physiological significance of NAEs including anandamide in brain and other tissues. ..
  42. Shui Y, Guan Z, Zhang S. Molecular characterization of cytokine TWEAK and its receptor Fn14 in pig (Sus scrofa). Vet Immunol Immunopathol. 2008;126:396-402 pubmed publisher
    ..It will be helpful for investigation on the biological role of the TWEAK/Fn14 system in this important animal model. Furthermore, it provides insight into the molecular evolution of the emerging TWEAK and Fn14 families. ..
  43. Mirabeau O, Joly J. Molecular evolution of peptidergic signaling systems in bilaterians. Proc Natl Acad Sci U S A. 2013;110:E2028-37 pubmed publisher
    ..In addition to shedding light on the function of human G protein-coupled receptor PSs, this work presents orthology markers to study ancestral neuron types that were probably present in the last common bilaterian ancestor. ..
  44. Song L, Takamune K, Sugawara Y, Fujii T. cDNA cloning of a mannose-binding lectin-associated serine protease (MASP) gene from hagfish (Eptatretus burgeri). Zoolog Sci. 2005;22:897-904 pubmed
    ..This evidence strongly suggests that the hagfish defends itself against pathogens at least by the complement system composed of lectin pathway. ..
  45. Omi T, Brenig B, Spilar Kramer S, Iwamoto S, Stranzinger G, Neuenschwander S. Identification and characterization of novel peroxisome proliferator-activated receptor-gamma (PPAR-gamma) transcriptional variants in pig and human. J Anim Breed Genet. 2005;122 Suppl 1:45-53 pubmed
    ..We hypothesize that there are three promoters, which differentially regulate PPAR-gamma1 and PPAR-gamma2 gene expression, depending on the specific localization of the fat tissue. ..
  46. He M, Pei Z, Mohsen A, Watkins P, Murdoch G, Van Veldhoven P, et al. Identification and characterization of new long chain acyl-CoA dehydrogenases. Mol Genet Metab. 2011;102:418-29 pubmed publisher
  47. Klein R, Klein P, Mullet J, Minx P, Rooney W, Schertz K. Fertility restorer locus Rf1 [corrected] of sorghum (Sorghum bicolor L.) encodes a pentatricopeptide repeat protein not present in the colinear region of rice chromosome 12. Theor Appl Genet. 2005;111:994-1012 pubmed
  48. Davis J, Mittel L, Lowman J, Thomas P, Maney D, Martin C, et al. Haplotype-based genomic sequencing of a chromosomal polymorphism in the white-throated sparrow (Zonotrichia albicollis). J Hered. 2011;102:380-90 pubmed publisher
    ..Overall, these results provide important insights into the genomic attributes of an inversion polymorphism linked to mate choice and variation in social behavior. ..
  49. Cho J, Kim H, Kim C, Hahn T, Jeon J. Identification and characterization of the duplicate rice sucrose synthase genes OsSUS5 and OsSUS7 which are associated with the plasma membrane. Mol Cells. 2011;31:553-61 pubmed publisher
    ..These results suggest that two redundant genes, OsSUS5 and OsSUS7, evolved via duplication of a chromosome region and through the transposition of transposable elements. ..
  50. Mechaly A, Viñas J, Piferrer F. Gene structure analysis of kisspeptin-2 (Kiss2) in the Senegalese sole (Solea senegalensis): characterization of two splice variants of Kiss2, and novel evidence for metabolic regulation of kisspeptin signaling in non-mammalian species. Mol Cell Endocrinol. 2011;339:14-24 pubmed publisher
  51. Anderson J, Bhandari R, Kumar J. A genetic screen identifies putative targets and binding partners of CREB-binding protein in the developing Drosophila eye. Genetics. 2005;171:1655-72 pubmed
    ..Of particular interest is the identification that the CREB transcription factor appears to function with CBP at multiple stages of retinal development. ..
  52. Haaning A, Quinn M, Ware S. Heterotaxy-spectrum heart defects in Zic3 hypomorphic mice. Pediatr Res. 2013;74:494-502 pubmed publisher
    ..Our data do not support a direct role for Zic3 in the myocardium via regulation of Nppa and Tbx5 and suggest that the primary effect of Zic3 on cardiac development occurs during left-right patterning. ..
  53. Mao X, Jia D, Li A, Zhang H, Tian S, Zhang X, et al. Transgenic expression of TaMYB2A confers enhanced tolerance to multiple abiotic stresses in Arabidopsis. Funct Integr Genomics. 2011;11:445-65 pubmed publisher