$URL = '/SRGD'; $html = $URL ; $SRGD = $URL ; $SRGDhtml = $URL ; $CGI = '/SRGD/cgi-bin'; $SRGDcgi = $CGI; $ATGDB = '/AtGDB'; $ATGDBcgi = '/AtGDB/cgi-bin'; $AtGDBcgi = $ATGDBcgi; $DBID = 0; //The following are global variables that indicate the locations of the PlantGDB phplib directory: $phplibDIR = '/Product/phplib'; $phplibURL = '/phplib'; $footer_path = $phplibDIR.'/footer.php' ; # $USER = 'bbwang'; # $PASS = 'mysqlbbwang'; # $HOST = 'grinch6'; $USER = 'bbwang'; $PASS = ''; $HOST = 'localhost'; $DB = 'SRGD'; $ASRG = 'ASRG3'; $AtsnRNA = 'AtsnRNA'; $SRGgroup = array ('1.1' => 'Sm core', '1.2' => 'U1 snRNP specific', '1.3' => 'U2 snRNP specific', '1.4' => 'U5 snRNP specific', '1.5' => 'U4/U6 snRNP specific', '1.6' => 'Tri-snRNP Specific (U4/U6.U5)', '1.7' => '18S U11/U12 snRNP Specific', '2.1' => 'Splice site selection', '2.2' => 'SR', '2.3' => '17S U2 associated', '2.4' => '35S U5 associated', '2.5' => 'BDU1 specific', '2.6' => 'Exon junction complex (EJC)', '2.7' => 'Second step splicing', '2.8' => 'Other known splicing', '3.1' => 'SR kinase', '3.2' => 'Glycine-Rich RNA binding', '3.3' => 'hnRNP A/B family', '3.4' => 'Other hnRNP (with animal homologs)', '3.5' => 'Other plant hnRNPs', '4.1' => 'other processes', '4.2' => 'Poly A binding', '4.3' => 'DEAD/H box helixase', '4.4' => 'cis-trans prolyl isomerases', '4.5' => 'Related to spliceosome', '5.1' => 'Splicing factor like', '5.2' => 'Nucleotide Binding', '5.3' => 'Other multiple functional', '5.4' => 'Glycine rich' ); ?> //Following function will transform gene structure from GenBank location format to Exon (Intron) Exon format function transform_gst($GST) { $reverse=0; $thisIntron=""; $thisExon=""; $theIntron=""; if (strpos($GST, "complement") !== false) { $GST=preg_replace("/complement\((.+)\)/i", "\\1", $GST); $reverse=1; } $GST=preg_replace("/join\((.+)\)/i", "\\1", $GST); $exons=preg_split ("/\D+/", $GST, -1, PREG_SPLIT_NO_EMPTY); $exonN=count($exons)/2; $GST=""; for ($i=0; $i0) { return "$exonN exons: $GST"; }else { return "see annotation in version 3"; } } ?> //MySQL database query $QueryColumn="Gene, GeneID, Chr, Strand, LStart, LStop, len, eVal, Similarity, GenBank, Note"; $link = mysql_connect($HOST,$USER,$PASS) or die("Connect Error: ".mysql_error()); mysql_select_db($DB , $link) or die("Couldn't open $db: ".mysql_error()); if ($Class) { $result = mysql_query( "SELECT $QueryColumn FROM $AtsnRNA where Class=\"$Class\" order by Chr, Lstart" ) or die("SELECT Error: ".mysql_error()); }else { $result = mysql_query( "SELECT $QueryColumn FROM $AtsnRNA order by Chr, Lstart" ) or die("SELECT Error: ".mysql_error()); } $num_rows = mysql_num_rows($result); /* while ($get_info = mysql_fetch_row($result)){ print "\n"; foreach ($get_info as $field) print "\t$field\n"; print "\n"; } */ mysql_close($link); //Prepare the link array $li=0; $LinkArray=array(); while ($li<$num_rows) { $Chr=mysql_result($result, $li, "Chr"); $From=mysql_result($result, $li, "LStart"); $To=mysql_result($result, $li, "LStop"); if ($From>$To) { $Temp=$From; $From=$To; $To=$Temp; } $TheLink=$ATGDBcgi."/getRegion.pl?chr=$Chr&l_pos=$From&r_pos=$To&dbid=$DBID"; array_push($LinkArray, $TheLink); $li++; } ?> SRGD Help Feedback PlantGDB Site Search Sequence ID Sequence Keyword at PlantGDB Home Sequence -Overview - Download Search -Overview- Select Species... Arabidopsis thaliana Brassica napus Brassica oleracea Chlamydomonas reinhardtii Cucumis sativus Glycine max Gossypium hirsutum Hordeum vulgare Medicago truncatula Oryza sativa Physcomitrella patens Setaria italica Sorghum bicolor Triticum aestivum Vitis vinifera Zea mays EST Assemb -Overview - Select Species... Arabidopsis thaliana Brassica napus Brassica oleracea Chlamydomonas reinhardtii Cucumis sativus Glycine max Gossypium hirsutum Hordeum vulgare Medicago truncatula Oryza sativa Physcomitrella patens Setaria italica Sorghum bicolor Triticum aestivum Vitis vinifera Zea mays GSS Assemb FTP Server Genomes -Overview- Dicots AtGDB - Arabidopsis thaliana BrGDB - Brassica rapa CpGDB - Carica papaya CsGDB - Cucumis sativus GhGDB - Gossypium hirsutum GmGDB - Glycine max LjGDB - Lotus japonicus MeGDB - Manihot esculenta MtGDB - Medicago truncatula MgGDB - Mimulus guttatus PeGDB - Prunus persica PtGDB - Populus trichocarpa RcGDB - Ricinus communis SlGDB - Solanum lycopersicum StGDB - Solanum tuberosum VvGDB - Vitis vinifera Monocots BdGDB - Brachypodium distachyon HvGDB - Hordeum vulgare OsGDB - Oryza sativa SbGDB - Sorghum bicolor SiGDB - Setaria italica TaGDB - Triticum aestivum ZmGDB - Zea mays Other CrGDB - Chlamydomonas reinhardtii PpGDB - Physcomitrella patens SmGDB - Selaginella moellendorffii VcGDB - Volvox carteri Tools -Overview- BioExtract BLAST DAS GeneSeqer GenomeThreader MuSeqBox PatternSearch ProbeMatch TE nest yrGATE Datasets - Overview - Ac/Ds maize Overview Browse Insertions Gene Distance ASIP PLEXdb RescueMu RFLP/FLIS SRGD UniformMu Outreach Plant Genome Outreach Portal (PGROP) Outreach to Native Americans Help Help Community Annotation Genome Browsers TableMaker Tutorials Annotation Tutorial Annotation Lessons GeneSeqer Tutorial About Us News Tour F.A.Q. Site Map Publications Links Acknowledgments Overview Data & Methods BLAST Old Version Database Overview Human Drosophila Yeast small nuclear RNA 395 Splicing Related Genes 10 Plant Species Arabidopsis Glycine max Lotus japonicus Medicago truncatula Oryza sativa Physcomitrella patens Populus trichocarpa Sorghum bicolor Vitis vinifera Zea mays Species Comparisons Overview Arabidopsis thaliana Glycine max Lotus japonicus Medicago truncatula Oryza sativa Physcomitrella patens Populus trichocarpa Sorghum bicolor Vitis vinifera Zea mays Gene Groups Overview 1. Small nuclear Ribonucleoprotein 1.1 Sm core proteins 1.2 U1 snRNP specific proteins 1.3 17S U2 snRNP specific proteins 1.4 U5 snRNP specific proteins 1.5 U4/U6 snRNP specific proteins 1.6 Tri-snRNP specific proteins (U4/U6.U5) 1.7 18s U11/U2 snRNP specfic proteins 2. Splicing factors 2.1 Splice site selection 2.2 SR protein 2.3 17S U2 associated proteins 2.4 35S U5 associated proteins 2.5 Proteins specific for BDU1 complex 2.6 Exon junction complex (EJC) proteins 2.7 Second step splicing factors 2.8 Other known splicing factors 3. Splicing regulation 3.1 SR protein Kinase 3.2 Glycine-Rich RNA binding protein 3.3 hnRNP A/B family 3.4 Other hnRNP proteins (with animal homologs) 3.5 Other plant hnRNPs 4. Novel spliceosome proteins 4.1 Proteins involved in other processes 4.2 Poly A binding protein 4.3 DEAD/H box helicase 4.4 cis-trans prolyl isomerases 4.5 Related to spliceosome 5. Possible splicing related proteins 5.1 Splice factor like 5.2 Nucleotide Binding proteins 5.3 Possible multiple function proteins 5.4 Glycine Rich protein Novel Splicing-related Proteins Overview Novel Splicing-related Proteins Specific Proteins Overview Arabidopsis Specific Proteins Dicots Specific Proteins Missing Proteins in Pp Search Group CIWOG Gene hHomologs SeHomologs Gene Name Chr Domains Group Name HID GB Accession in Any species Arabidopsis thaliana Glycine max Lotus japonicus Medicago truncatula Oryza sativa Physcomitrella patens Populus trichocarpa Sorghum bicolor Vitis vinifera Zea mays Human Drosophila Yeast PrintPicture($Class, $LinkArray); ?> Gene GeneID Chr str From To len eVal Similarity GenBank $i=0; while ($i<$num_rows) { $Gene=mysql_result($result, $i, "Gene"); $GeneID=mysql_result($result, $i, "GeneID"); $Chr=mysql_result($result, $i, "Chr"); $str=mysql_result($result, $i, "Strand"); $From=mysql_result($result, $i, "LStart"); $To=mysql_result($result, $i, "LStop"); $len=mysql_result($result, $i, "len"); $eVal=mysql_result($result, $i, "eVal"); $Similarity=mysql_result($result, $i, "Similarity"); $GenBank=mysql_result($result, $i, "GenBank"); $Note=mysql_result($result, $i, "Note"); $Homologs=$Chr ; if ($Homologs == $PrevHomo) { ////////////////////////// Set the backgound color $BGCOLOR=$PrevBGColor; }else { $PrevHomo=$Homologs; if ($i<$num_rows-1) { $NextHomo=mysql_result($result, $i+1, "Chr"); }else { $NextHomo=""; } if ($Homologs==$NextHomo) { $detColor++; if ($detColor % 2) { $BGCOLOR="#c0c0c0"; }else { $BGCOLOR="#969696"; } }else { $BGCOLOR="#FFFFFF"; } // Determine the background color $PrevBGColor=$BGCOLOR; } //////////////////////////////////////////////////////////////////// if ($GeneID == $Query) { ///////////////////////////// set the font color to highlight the query $fontcolor="ff0000"; }else { $fontcolor="000000"; } ///////////////////////////////////////////////////////////////////////// ?> HEIGHT="16">">&DB=ATsnRNA.fsa&Retrieve">> echo"$Gene"; ?> echo"$Note"?> HEIGHT="16">">> echo"$GeneID"?> HEIGHT="16">> echo"$Chr"?> HEIGHT="16">> echo"$str"?> HEIGHT="16">> echo"$From"?> HEIGHT="16">> echo"$To"?> HEIGHT="16">> echo"$len"?> HEIGHT="16">> echo"$eVal"?> HEIGHT="16">> echo"$Similarity"?> HEIGHT="16">> if ($GenBank) {echo"$GenBank"; }?> $i++; }// end while loop ?> * used as query sequence. 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