Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins-7

of 25 identified DSBH fold containing protein subgroups as indicated with protein family names on the right side. Scale bar represents the relative phylogenetic distance as determined with PHYLIP. Bootstrap values are shown for values <p><b>Copyright information:</b></p><p>Taken from "Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins"</p><p>http://www.biomedcentral.com/1471-2164/9/293</p><p>BMC Genomics 2008;9():293-293.</p><p>Published online 18 Jun 2008</p><p>PMCID:PMC2453528.</p><p></p

Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins-8

Ences, data processing approaches based on protein sequences are coloured green, and phylogenomic analysis methods based on DSBH protein domains are shown in blue. Initial queries are depicted as circles, databases as ovals, candidate gene and protein lists as cut-off boxes, and methods/analysis tools as normal boxes, respectively. Barrels indicate Perl script based analysis of retrieved results. Candidate lists of the individual workflows are shown and the final results of the analysis are depicted in bold. Arrows indicate the flow of information and the connections between different search routines and methods. Sources of queried databases and the analysis software used are given in the respective box elements.<p><b>Copyright information:</b></p><p>Taken from "Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins"</p><p>http://www.biomedcentral.com/1471-2164/9/293</p><p>BMC Genomics 2008;9():293-293.</p><p>Published online 18 Jun 2008</p><p>PMCID:PMC2453528.</p><p></p

Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins-6

Ologous proteins (Fig. 5). Annotation of the sequence identity onto the catalytic domain demonstrated the conservation of the critical residues within the active site of the Jmjd6-Fe(II)-2OG complex. Residues were shaded according to the heat map with dark red representing total conservation of residues (100% sequence identity across 54 analysed species), and blue colour representing 50% sequence identity.<p><b>Copyright information:</b></p><p>Taken from "Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins"</p><p>http://www.biomedcentral.com/1471-2164/9/293</p><p>BMC Genomics 2008;9():293-293.</p><p>Published online 18 Jun 2008</p><p>PMCID:PMC2453528.</p><p></p

Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins-1

S and its neighbouring genes using PipMaker. Green, blue and yellow overlays highlight the conservation of the annotated exons/coding sequences of the individual genes found in the reference sequence. The orange overlay indicates conserved sequences of the first exons of the and genes and sequences outside of the coding elements. The red overlay marks a high-scoring segment in all analysed mammalian species supporting the presence of at least one additional exon (No. 5) that is not included in the current Ensembl gene annotation (build 44). Transcriptional orientations of the genes, their exons, UTRs, repetitive elements, and CpG islands are in the symbol key at the figure bottom.<p><b>Copyright information:</b></p><p>Taken from "Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins"</p><p>http://www.biomedcentral.com/1471-2164/9/293</p><p>BMC Genomics 2008;9():293-293.</p><p>Published online 18 Jun 2008</p><p>PMCID:PMC2453528.</p><p></p

Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins-0

Ences, data processing approaches based on protein sequences are coloured green, and phylogenomic analysis methods based on DSBH protein domains are shown in blue. Initial queries are depicted as circles, databases as ovals, candidate gene and protein lists as cut-off boxes, and methods/analysis tools as normal boxes, respectively. Barrels indicate Perl script based analysis of retrieved results. Candidate lists of the individual workflows are shown and the final results of the analysis are depicted in bold. Arrows indicate the flow of information and the connections between different search routines and methods. Sources of queried databases and the analysis software used are given in the respective box elements.<p><b>Copyright information:</b></p><p>Taken from "Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins"</p><p>http://www.biomedcentral.com/1471-2164/9/293</p><p>BMC Genomics 2008;9():293-293.</p><p>Published online 18 Jun 2008</p><p>PMCID:PMC2453528.</p><p></p

Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins-7

of 25 identified DSBH fold containing protein subgroups as indicated with protein family names on the right side. Scale bar represents the relative phylogenetic distance as determined with PHYLIP. Bootstrap values are shown for values <p><b>Copyright information:</b></p><p>Taken from "Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins"</p><p>http://www.biomedcentral.com/1471-2164/9/293</p><p>BMC Genomics 2008;9():293-293.</p><p>Published online 18 Jun 2008</p><p>PMCID:PMC2453528.</p><p></p

Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins-3

Nserved sequence element identified using PipMaker in Figure 2 is shown in orange. 5'-untranslated regions (UTRs) are indicated in grey, and first exon coding sequences of the gene in green and of the gene in blue, respectively. The region indicated by two half arrows was used for promoter activity assays presented in (B). It was amplified and cloned to yield an 840 bp test fragment This putative bi-directional promoter fragment was used in a luciferase reporter gene assay to measure transcriptional activity. Basal promoter activity was found for both transcriptional orientations compared to a promoterless control (pGL3) vector. The 5'-3' orientation of the fragment (orientation, ) yielded only half of the transcriptional activity as it was measured for the 3'-5' orientation (orientation, ). The values reported for the transfection experiments are means ± standard deviation of three independent triplicate experiments. P value was determined using Student's t-test. *** P < 0.001.<p><b>Copyright information:</b></p><p>Taken from "Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins"</p><p>http://www.biomedcentral.com/1471-2164/9/293</p><p>BMC Genomics 2008;9():293-293.</p><p>Published online 18 Jun 2008</p><p>PMCID:PMC2453528.</p><p></p

Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins-5

Ve asparaginyl hydroxylase – 2636534 () and Jmjd2a (), respectively. Stereoview of the predicted structure of Jmjd6 presented as a ribbon model. The conserved eight-stranded DSBH core found in all Fe(II) and 2-oxoglutarate (2OG)-dependent dioxygenases is coloured in blue. Additional β-strands attached to the major β-sheet are shown in orange. Helices are depicted in green. View of the predicted active site of the Jmjd6-Fe(II)-2OG complex showing coordination of Fe(II) to 2OG, His187, Asp189, and His273. 2OG also ligates to Trp174, Asn197 and Lys204 with Thr285 stabilising Asn197 and Trp174. Additional important residues for putative interactions are shown in cyan and include hydrophobic interactions from Phe133 and Val275 as well as Thr184, which is involved in 2OG-binding in Hif1an. Interacting residues along with the 2OG co-substrate are shown as stick presentations, putative H-bond interactions as dotted lines. Fe(II) is depicted as an orange ball.<p><b>Copyright information:</b></p><p>Taken from "Genomic structure and expression of and evolutionary analysis in the context of related JmjC domain containing proteins"</p><p>http://www.biomedcentral.com/1471-2164/9/293</p><p>BMC Genomics 2008;9():293-293.</p><p>Published online 18 Jun 2008</p><p>PMCID:PMC2453528.</p><p></p