c28b00ca6c39b734b0034705ac3f3b57335b5a91 markd Wed Apr 17 21:42:07 2024 -0700 added files from RR from caludron paper diff --git src/hg/htdocs/cauldron/breakTable.html src/hg/htdocs/cauldron/breakTable.html new file mode 100644 index 0000000..12e5938 --- /dev/null +++ src/hg/htdocs/cauldron/breakTable.html @@ -0,0 +1,229 @@ +<HTML> +<HEAD> +<META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=windows-1252"> +<META NAME="Generator" CONTENT="Microsoft Word 97"> +<TITLE>Evolution's Cauldron Supplement</TITLE> +<META NAME="Template" CONTENT="C:\Program Files\Microsoft Office\Templates\Outline.dot"> +</HEAD> +<BODY LINK="#0000ff" VLINK="#800080"> + +<B><FONT FACE="Arial" SIZE=5><P ALIGN="CENTER">Supplemental Information for </P> +<P ALIGN="CENTER"></P> +</FONT><FONT FACE="Arial" SIZE=5><P>Evolution’s Cauldron: Duplication, Deletion, and Rearrangement in the Mouse and Human Genomes.</P> +</FONT><FONT FACE="Arial" SIZE=5><P ALIGN="CENTER"></P></B></FONT> +<TABLE BORDER CELLSPACING=1 BORDERCOLOR="#000000" WIDTH=571> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P> Breaks </B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P>Position </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P> aligned </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P> span </B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P> breakPerMb </B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>Genes in region</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>759</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr19:52283288-55023011 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>355617</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>2739723</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>277.04</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>Sialic acid binding (ig like cluster) and Zinc finger cluster</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>307</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr19:11912709-12980044 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>123180</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>1067335</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>287.63</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>KRAB C2H2 Zinc finger cluster</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>282</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr19:57924332-58994674 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>163649</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>1070342</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>263.47</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>KRAB C2H2 Zinc finger cluster</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>228</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr2:129802976-130894216 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>284128</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>1091240</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>208.94</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>Ptpn18, cryptic (gene poor)</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>215</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr22:19036955-20094010 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>132206</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>1057055</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>203.4</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>Contains Ig lambda light chain locus and Rhabdoid tumor deletion region</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>212</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr19:9294092-10142345 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>100712</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>848253</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>249.93</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>KRAB C2H2 Zinc finger cluster</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>209</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr8:6948129-8102614 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>205566</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>1154485</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>181.03</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>Ig region (defensin cluster)</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>199</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr6:28560342-29380273 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>99588</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>819931</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>242.7</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>Olfactory receptor cluster</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>164</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr12:11050382-11876400 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>124173</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>826018</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>198.54</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>6 Taste receptors and 5 salivary gland genes</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>160</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr3:19755611-22829219 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>94791</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>3073608</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>52.06</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>HMGB1, mostly gene desert</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>158</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr1:153813433-154249175 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>48153</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>435742</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>362.6</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>CD1, immune response cluster</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>140</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr11:90897985-91367162 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>75731</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>469177</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>298.39</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>RNF18, gene poor region</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>124</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr17:21859306-22267186 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>116716</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>407880</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>304.01</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>TL132 protein, gene poor region</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>120</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr19:15050464-15453575 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>38600</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>403111</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>297.68</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>KRAB C2H2 Zinc finger, olfactory cluster</B></FONT></TD> +</TR> +<TR><TD WIDTH="8%" VALIGN="TOP"> +<B><FONT SIZE=2><P>115</B></FONT></TD> +<TD WIDTH="30%" VALIGN="TOP"> +<B><FONT SIZE=2><P> chr18:13919892-15073531 </B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>145639</B></FONT></TD> +<TD WIDTH="11%" VALIGN="TOP"> +<B><FONT SIZE=2><P>1153639</B></FONT></TD> +<TD WIDTH="16%" VALIGN="TOP"> +<B><FONT SIZE=2><P>99.68</B></FONT></TD> +<TD WIDTH="23%" VALIGN="TOP"> +<B><FONT SIZE=2><P>2 melocortin GPCRs</B></FONT></TD> +</TR> +</TABLE> + +<FONT SIZE=2> +</FONT><P> </P> +<P>Table S1 – Long runs of short chains in the top level of the net. "Breaks" gives the number of short chains in the region, "Position" the location in the human genome (November 2002 freeze), "aligned" the number of aligned bases in the region, "span" the total length of the region (in human genome coordinates). "BreaksPerMb" the average number of breaks between chains in each megabase in the region, and "Genes in region" lists the properties of or accessions of human RefSeq genes from the region. This table lists only the top few "hotspots" with the most consecutive short chains, excluding pericentormeric and telomeric regions , matches to human chromosome Y (since little sequence is available from mouse chromosome Y), and one region with extensive simple repeats of longer period than we masked. Hotspots of this type cover 5-10% of the human genome. Some are associated with clusters of mobile genes in the olfactory or zinc finger families (see text). Others are associated with immune genes. One of the largest of these regions (5<SUP>th</SUP> entry in the table) is on chromosome 22 near the Ig Lambda light chain locus. This locus rearranges somatically during B-cell maturation . Possibly a low level of the RAG proteins responsible for this somatic rearrangement are expressed in germ cells and occasionally cause recombination in germ cell lines in this region in mammals as well as other vertebrates . There are a number of RAG ESTs isolated from cells not in the B-cell lineage, including GenBank accession <A HREF="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&term=N92955&doptcmdl=GenBank&tool=genome.ucsc.edu">N92955</A>.</P> +</BODY> +</HTML>