Genomes and Genes
Experts and Doctors on introns in Sweden
- Bergström T, Josefsson A, Erlich H, Gyllensten U. Recent origin of HLA-DRB1 alleles and implications for human evolution. Nat Genet. 1998;18:237-42 pubmed....
- Landgren C, Beier D, Fassler R, Heinegard D, Sommarin Y. The mouse chondroadherin gene: characterization and chromosomal localization. Genomics. 1998;47:84-91 pubmed..The chondroadherin gene was mapped to mouse chromosome 11, near D11Mit14, by single-strand conformation polymorphism linkage analysis. ..
- Larsson J, Svensson M, Stenberg P, M kitalo M. Painting of fourth in genus Drosophila suggests autosome-specific gene regulation. Proc Natl Acad Sci U S A. 2004;101:9728-33 pubmed publisher..The chromosome specificity is determined at the species level and not by the amino acid sequence. We argue that POF is involved in a chromosome-specific regulatory function...
- Gowda N, Kaimal J, Masser A, Kang W, FriedlÃ¤nder M, AndrÃ©asson C. Cytosolic splice isoform of Hsp70 nucleotide exchange factor Fes1 is required for the degradation of misfolded proteins in yeast. Mol Biol Cell. 2016;27:1210-9 pubmed publisher..This study provides key findings for the understanding of the organization of protein quality control mechanisms in the cytosol and nucleus. ..
- Nilsson J, Hellquist M, Bjursell G. The human carboxyl ester lipase-like (CELL) gene is ubiquitously expressed and contains a hypervariable region. Genomics. 1993;17:416-22 pubmed..Several allelic variants can be resolved by polymerase chain reaction amplification of this region followed by sequencing using an automated laser fluorescent sequencer.(ABSTRACT TRUNCATED AT 250 WORDS) ..
- Persson K, Holm I, Heby O. Cloning and sequencing of an intronless mouse S-adenosylmethionine decarboxylase gene coding for a functional enzyme strongly expressed in the liver. J Biol Chem. 1995;270:5642-8 pubmed..e. it catalyzed the decarboxylation of S-adenosylmethionine, and its specific activity was comparable with that of recombinant human AdoMetDC purified according to the same procedure. ..
- Clauss A, Lilja H, Lundwall A. A locus on human chromosome 20 contains several genes expressing protease inhibitor domains with homology to whey acidic protein. Biochem J. 2002;368:233-42 pubmed....
- Bjorklund S, Hjortsberg K, Johansson E, Thelander L. Structure and promoter characterization of the gene encoding the large subunit (R1 protein) of mouse ribonucleotide reductase. Proc Natl Acad Sci U S A. 1993;90:11322-6 pubmed..One complex most likely contained Sp1, and another complex showed S-phase-specific binding, suggesting a direct role in the cell-cycle-dependent R1 gene expression. ..
- Mannila M, Silveira A, Hawe E, Eriksson P, Aillaud M, Juhan Vague I, et al. Plasma fibrinogen concentration predicts the risk of myocardial infarction differently in various parts of Europe: effects of beta-fibrinogen genotype and environmental factors. The HIFMECH Study. Thromb Haemost. 2004;92:1240-9 pubmed..7%). Thus, plasma fibrinogen concentration contributes differently to MI across Europe, and a disease-related stimulus is required to evoke allele-specific regulation of fibrinogen synthesis. ..
- Marklund S, Kijas J, Rodriguez Martinez H, Ronnstrand L, Funa K, Moller M, et al. Molecular basis for the dominant white phenotype in the domestic pig. Genome Res. 1998;8:826-33 pubmed..The EMBL accession numbers for porcine KIT1*0101, KIT1*0202, KIT2*0202, and KIT2*0101 are AJ223228-AJ223231, respectively.] ..
- Ulvsback M, Lundwall A. Cloning of the semenogelin II gene of the rhesus monkey. Duplications of 360 bp extend the coding region in man, rhesus monkey and baboon. Eur J Biochem. 1997;245:25-31 pubmed..However, another New World monkey, the cotton-top tamarin, carries only one semenogelin gene, but also has a gene that is similar to the mouse semenoclotin gene. ..
- Yue B, Akusjarvi G. A downstream splicing enhancer is essential for in vitro pre-mRNA splicing. FEBS Lett. 1999;451:10-4 pubmed..Also, splice site pairing occurs efficiently in the absence of exonic SR enhancers, emphasizing the significance of a downstream 5' splice site as the enhancer element in vertebrate splicing. ..
- Johanson U, Karlsson M, Johansson I, Gustavsson S, Sjovall S, Fraysse L, et al. The complete set of genes encoding major intrinsic proteins in Arabidopsis provides a framework for a new nomenclature for major intrinsic proteins in plants. Plant Physiol. 2001;126:1358-69 pubmed..The complete set of AtMIPs, together with the new nomenclature, will facilitate the isolation, classification, and labeling of plant MIPs from other species. ..
- Zhang X, Vuolteenaho R, Tryggvason K. Structure of the human laminin alpha2-chain gene (LAMA2), which is affected in congenital muscular dystrophy. J Biol Chem. 1996;271:27664-9 pubmed....
- Kårehed J, Groeninckx I, Dessein S, Motley T, Bremer B. The phylogenetic utility of chloroplast and nuclear DNA markers and the phylogeny of the Rubiaceae tribe Spermacoceae. Mol Phylogenet Evol. 2008;49:843-66 pubmed publisher..Notably, Oldenlandia is polyphyletic, the two subgenera of Kohautia are not sister taxa, and Hedyotis should be treated in a narrow sense to include only Asian species...
- Fällmar H, Sundstrom G, Lundell I, Mohell N, Larhammar D. Neuropeptide Y/peptide YY receptor Y2 duplicate in zebrafish with unique introns displays distinct peptide binding properties. Comp Biochem Physiol B Biochem Mol Biol. 2011;160:166-73 pubmed publisher..Zebrafish Y2-2 mRNA was detected by PCR in the intestine and the eye, but not in the brain. In conclusion, we have found a novel Y2-like NPY/PYY receptor that probably arose in early teleost fish evolution. ..
- Hessle V, von Euler A, González de Valdivia E, Visa N. Rrp6 is recruited to transcribed genes and accompanies the spliced mRNA to the nuclear pore. RNA. 2012;18:1466-74 pubmed publisher..These observations suggest that the quality control of pre-mRNA splicing is not based on the selective recruitment of the exoribonuclease Rrp6 to unprocessed mRNAs. ..
- Fernandez Rodriguez J, Andersson C, Laos S, Baeckstrom D, Sikut A, Sikut R, et al. The leukocyte antigen CD43 is expressed in different cell lines of nonhematopoietic origin. Tumour Biol. 2002;23:193-201 pubmed..As all cell lines expressed CD43, it is suggested that CD43 has a more fundamental function than previously believed and thus cannot be considered only as a specific leukocyte marker. ..
- Ruetschi U, Cerone R, Perez Cerda C, Schiaffino M, Standing S, Ugarte M, et al. Mutations in the 4-hydroxyphenylpyruvate dioxygenase gene (HPD) in patients with tyrosinemia type III. Hum Genet. 2000;106:654-62 pubmed..No correlation of the severity of the mutation and enzyme deficiency and mental function has been found; neither do the recorded tyrosine levels correlate with the clinical phenotype. ..
- Benson M, Mobini R, Barrenas F, Hallden C, Naluai A, Sall T, et al. A haplotype in the inducible T-cell tyrosine kinase is a risk factor for seasonal allergic rhinitis. Allergy. 2009;64:1286-91 pubmed publisher..Analysis of SNPs in TCR pathway genes revealed that a haplotype that covers a major part of the coding sequence of ITK is a risk factor for SAR. ..
- Thakur N, Tiwari V, Thomassin H, Pandey R, Kanduri M, Göndör A, et al. An antisense RNA regulates the bidirectional silencing property of the Kcnq1 imprinting control region. Mol Cell Biol. 2004;24:7855-62 pubmed..Double-stranded RNA (dsRNA)-mediated RNA interference is unlikely to be involved, as the ICR is active irrespective of the simultaneous production of dsRNA from the genes it silences. ..
- Lindqvist M, Sandstrom K, Liepins V, Stromberg R, Graslund A. Specific metal-ion binding sites in a model of the P4-P6 triple-helical domain of a group I intron. RNA. 2001;7:1115-25 pubmed..The interpretation is that U453 is so sensitive to structural disturbance that any change at this position hinders the proper formation of the triple helix...
- Eguchi H, Westin S, Strom A, Gustafsson J, Zaphiropoulos P. Gene structure and expression of the rat cytochrome P450IIC13, a polymorphic, male-specific cytochrome in the P450IIC subfamily. Biochemistry. 1991;30:10844-9 pubmed....
- Mörck C, Rauthan M, Wagberg F, Pilon M. pha-2 encodes the C. elegans ortholog of the homeodomain protein HEX and is required for the formation of the pharyngeal isthmus. Dev Biol. 2004;272:403-18 pubmed..The present report is the first to examine the expression and function of an invertebrate Hex homolog, that is, the C. elegans pha-2 gene...
- Tindberg N, Bengtsson I, Hu Y. A novel lipopolysaccharide-modulated Jun binding repressor in intron 2 of CYP2E1. J Neurochem. 2004;89:1336-46 pubmed..Future in vivo experiments will, however, be required for a full appreciation of the role of this repressor in the complex regulation of CYP2E1 during inflammatory conditions. ..
- Bylund J, Bylund M, Oliw E. cDna cloning and expression of CYP4F12, a novel human cytochrome P450. Biochem Biophys Res Commun. 2001;280:892-7 pubmed..Several CYP4F enzymes are important omega 1- and omega 2-hydroxylases of eicosanoids. The physiological function of CYP4F12 merits further investigation. ..
- Skogsberg J, Kannisto K, Roshani L, Gagne E, Hamsten A, Larsson C, et al. Characterization of the human peroxisome proliferator activated receptor delta gene and its expression. Int J Mol Med. 2000;6:73-81 pubmed..In addition, the chromosomal sublocalization of PPARD was determined by radiation hybrid mapping. The PPARD gene is located at 14 cR from the colipase gene and 15 cR from the serine kinase gene at chromosomal region 6p21.2. ..
- Bylund J, Finnstrom N, Oliw E. Gene expression of a novel cytochrome P450 of the CYP4F subfamily in human seminal vesicles. Biochem Biophys Res Commun. 1999;261:169-74 pubmed..1 and approximately 2.3 kb. The deduced protein showed 81.2 and 76.7% amino acid identity with the human enzymes CYP4F2 and CYP4F3. The novel CYP was designated CYP4F8. ..
- Bartschat S, Samuelsson T. U12 type introns were lost at multiple occasions during evolution. BMC Genomics. 2010;11:106 pubmed publisher..In addition, this distribution identifies a large number of instances during eukaryotic evolution where such splicing was lost. ..
- Mondal T, Rasmussen M, Pandey G, Isaksson A, Kanduri C. Characterization of the RNA content of chromatin. Genome Res. 2010;20:899-907 pubmed publisher..Our data suggest that ncRNA is an integral component of chromatin and that it may regulate various biological functions through fine-tuning of the chromatin architecture. ..
- Ingelman Sundberg M, Sim S. Intronic polymorphisms of cytochromes P450. Hum Genomics. 2010;4:402-5 pubmed....
- Sideras P, Muller S, Shiels H, Jin H, Khan W, Nilsson L, et al. Genomic organization of mouse and human Bruton's agammaglobulinemia tyrosine kinase (Btk) loci. J Immunol. 1994;153:5607-17 pubmed..The present analysis will significantly facilitate the mutational analyses of patients with XLA and the further characterization of the function and regulation of the Btk molecule. ..
- Andersson S, Lambertsson A. Evolution of the dec-1 eggshell locus in Drosophila. I. Restriction site mapping and limited sequence comparison in the melanogaster species subgroup. J Mol Evol. 1991;33:321-31 pubmed..teissieri and D. yakuba. ..
- Enerback S, Bjursell G. Genomic organization of the region encoding guinea pig lipoprotein lipase; evidence for exon fusion and unconventional splicing. Gene. 1989;84:391-7 pubmed....
- Berlin S, Lagercrantz U, von Arnold S, Ost T, Rönnberg Wästljung A. High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus. BMC Genomics. 2010;11:129 pubmed publisher..The marker positions in the two genomes were used to study genome evolution since the divergence of the two lineages some 45 mya...
- Klovins J, Haitina T, Ringholm A, Löwgren M, Fridmanis D, Slaidina M, et al. Cloning of two melanocortin (MC) receptors in spiny dogfish: MC3 receptor in cartilaginous fish shows high affinity to ACTH-derived peptides while it has lower preference to gamma-MSH. Eur J Biochem. 2004;271:4320-31 pubmed..The study indicates that many of the important elements of the MC system existed before radiation of gnathostomes, early in vertebrate evolution, at least 450 million years ago...
- Klopfstein S, Ronquist F. Convergent intron gains in hymenopteran elongation factor-1?. Mol Phylogenet Evol. 2013;67:266-76 pubmed publisher..The significant rate of convergent intron gain renders intron-exon structure unreliable as an indicator of orthology in eEF1A, and probably also in other protein-coding genes. ..
- Lind U, Järvå M, Alm Rosenblad M, Pingitore P, Karlsson E, Wrange A, et al. Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity. PLoS ONE. 2017;12:e0181192 pubmed publisher..Our study provides a base for future mechanistic studies on the role of aquaporins in osmoregulation. ..
- Sandegren L, Sjoberg B. Distribution, sequence homology, and homing of group I introns among T-even-like bacteriophages: evidence for recent transfer of old introns. J Biol Chem. 2004;279:22218-27 pubmed..These findings give further insight into the mechanisms of propagation and evolution of group I introns among the T-even-like bacteriophages...
- Strandberg L, Lawrence D, Ny T. The organization of the human-plasminogen-activator-inhibitor-1 gene. Implications on the evolution of the serine-protease inhibitor family. Eur J Biochem. 1988;176:609-16 pubmed..Evidence is presented supporting an intron loss model for the evolution of the SERPIN family. ..
- Grahn A, Barkhordar G, Larson G. Cloning and sequencing of nineteen transcript isoforms of the human alpha2,3-sialyltransferase gene, ST3Gal III; its genomic organisation and expression in human tissues. Glycoconj J. 2002;19:197-210 pubmed..Neural and muscular tissues showed the most complex patterns and were distinctly different from all other tissues examined. ..
- Teglund S, Olsen A, Khan W, Frängsmyr L, Hammarstrom S. The pregnancy-specific glycoprotein (PSG) gene cluster on human chromosome 19: fine structure of the 11 PSG genes and identification of 6 new genes forming a third subgroup within the carcinoembryonic antigen (CEA) family. Genomics. 1994;23:669-84 pubmed..Unlike any of the known CEA family genes, however, they seem to lack the exon for an IgV-like N-terminal domain. ..
- Sjoling A, Samuelson E, Adamovic T, Behboudi A, Röhme D, Levan G. Recurrent allelic imbalance at the rat Pten locus in DMBA-induced fibrosarcomas. Genes Chromosomes Cancer. 2003;36:70-9 pubmed....
- Olofsson B, Pajusola K, von Euler G, Chilov D, Alitalo K, Eriksson U. Genomic organization of the mouse and human genes for vascular endothelial growth factor B (VEGF-B) and characterization of a second splice isoform. J Biol Chem. 1996;271:19310-7 pubmed..The entirely different COOH-terminal domains in the two isoforms of vascular endothelial growth factor B imply that some functional properties of the two proteins are distinct. ..
- Aman P, Panagopoulos I, Lassen C, Fioretos T, Mencinger M, Toresson H, et al. Expression patterns of the human sarcoma-associated genes FUS and EWS and the genomic structure of FUS. Genomics. 1996;37:1-8 pubmed..These observations indicate that FUS and EWS belong to the housekeeping type of genes. This view is supported by the presence of the housekeeping gene type of promoter region in both genes. ..
- Aklillu E, Carrillo J, Makonnen E, Hellman K, Pitarque M, Bertilsson L, et al. Genetic polymorphism of CYP1A2 in Ethiopians affecting induction and expression: characterization of novel haplotypes with single-nucleotide polymorphisms in intron 1. Mol Pharmacol. 2003;64:659-69 pubmed....
- Finta C, Zaphiropoulos P. Intergenic mRNA molecules resulting from trans-splicing. J Biol Chem. 2002;277:5882-90 pubmed..Moreover, trans-splicing has been found not to interfere with polyadenylation. Heterologous expression of the chimeric species composed of CYP3A43 exon 1 joined to exons 2-13 of CYP3A4 revealed catalytic activity toward testosterone. ..
- Thelander M, Thelander L. Molecular cloning and expression of the functional gene encoding the M2 subunit of mouse ribonucleotide reductase: a new dominant marker gene. EMBO J. 1989;8:2475-9 pubmed..M2 genomic DNA should be a valuable dominant, selectable marker for identifying and isolating stable co-transformants. ..
- Hellman L, Steen M, Sundvall M, Pettersson U. A rapidly evolving region in the immunoglobulin heavy chain loci of rat and mouse: postulated role of (dC-dA)n.(dG-dT)n sequences. Gene. 1988;68:93-100 pubmed..These findings suggest that (dC-dA)n.(dG-dT)n sequences are potential targets for recombination events. ..
- Ekstrom U, Abrahamson M, Sveger T, Lombardi P, Nilsson Ehle P. An efficient screening procedure detecting six novel mutations in the LDL receptor gene in Swedish children with hypercholesterolemia. Hum Genet. 1995;96:147-50 pubmed..Six of the alterations, five single-base substitutions and one dinucleotide deletion, have not previously been described. DGGE detected six of the mutations and SSCP the seventh. ..
- Lee M, Bengt n E, Daggfeldt A, Rytting A, Pilstr m L. Characterisation of rainbow trout cDNAs encoding a secreted and membrane-bound Ig heavy chain and the genomic intron upstream of the first constant exon. Mol Immunol. 1993;30:641-8 pubmed..The sequence also contains possible enhancer-like and octamer-like motifs...
- Mathews C, Sjoberg B, Karlsson M. Cloning and sequencing of cDNAs encoding ribonucleotide reductase from zebrafish Danio rerio. Mol Mar Biol Biotechnol. 1996;5:284-7 pubmed..The zebrafish R1 shows 94% similarity and R2 shows 91% similarity to the human R1 and R2, respectively. The similarity extends to intron positions, of which the equivalent of mouse R2 intron 3 has been studied. ..
- Vogel J, Hess W. Complete 5' and 3' end maturation of group II intron-containing tRNA precursors. RNA. 2001;7:285-92 pubmed....
- Bengtsson T, Camper L, Schneller M, Lundgren Akerlund E. Characterization of the mouse integrin subunit alpha10 gene and comparison with its human homologue. Genomic structure, chromosomal localization and identification of splice variants. Matrix Biol. 2001;20:565-76 pubmed..In mouse, exon 26 was extended into the intron by 62 nt, generating a truncated alpha10-chain. In human, exon 25 consisted of 114 nt which were alternately spliced in or out. ..
- Panagopoulos I, Mertens F, Debiec Rychter M, Isaksson M, Limon J, Kardas I, et al. Molecular genetic characterization of the EWS/ATF1 fusion gene in clear cell sarcoma of tendons and aponeuroses. Int J Cancer. 2002;99:560-7 pubmed..In addition, topoisomerase I consensus sequences were found close to the junctions, suggesting that this enzyme may participate in the genesis of the EWS/ATF1 fusion...
- Zhao Y, Kacskovics I, Pan Q, Liberles D, Geli J, Davis S, et al. Artiodactyl IgD: the missing link. J Immunol. 2002;169:4408-16 pubmed..The presence of Cdelta genes in artiodactyls, possibly in most mammals, suggests that IgD may have some as yet unknown biological properties, distinct from those of IgM, conferring a survival advantage...
- Antonson P, Al Beidh F, Matthews J, Gustafsson J. The human RAP250 gene: genomic structure and promoter analysis. Gene. 2004;327:233-8 pubmed..Our data show that the RAP250 has a complex genomic structure with a promoter that is regulated by multiple transcription factors for its basal expression. ..
- Lundwall A, Malm J, Clauss A, Valtonen Andre C, Olsson A. Molecular cloning of complementary DNA encoding mouse seminal vesicle-secreted protein SVS I and demonstration of homology with copper amine oxidases. Biol Reprod. 2003;69:1923-30 pubmed..The species difference in size of SVS I is caused by tandem repeats of 18 amino acid residues in the central part of the molecule: The mouse has seven repeats, and the rat has 12 repeats. ..
- Holmström P, Dzikaite V, Hultcrantz R, Melefors O, Eckes K, Stål P, et al. Structure and liver cell expression pattern of the HFE gene in the rat. J Hepatol. 2003;39:308-14 pubmed..The pattern of tissue expression of the HFE gene is rather similar in humans and rodents. The finding of HFE gene expression in rat hepatocytes raises interesting questions regarding its role in the hepatocyte iron metabolism. ..
- Karlsson M, Reue K, Xia Y, Lusis A, Langin D, Tornqvist H, et al. Exon-intron organization and chromosomal localization of the mouse monoglyceride lipase gene. Gene. 2001;272:11-8 pubmed..The amino acid sequence derived from human MGL cDNA clones showed 84% identity with mouse MGL. The mouse MGL gene was mapped to chromosome 6 in a region with known homology to human chromosome 3q21. ..
- Engström L, Engblom D, Blomqvist A. Systemic immune challenge induces preproenkephalin gene transcription in distinct autonomic structures of the rat brain. J Comp Neurol. 2003;462:450-61 pubmed..These results demonstrated that enkephalin transcription is induced in central autonomic neurons during immune challenge, suggesting that enkephalins are involved in the centrally orchestrated response to such stimuli. ..
- Van Laere A, Nguyen M, Braunschweig M, Nezer C, Collette C, Moreau L, et al. A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature. 2003;425:832-6 pubmed..The result supports the long-held view that regulatory mutations are important for controlling phenotypic variation. ..