Systematic analysis and evolution of 5S ribosomal DNA in metazoans

(Joaquín Vierna, Stefanie Wehner, Christian Höner zu Siederdissen, Andrés Martínez-Lage and Manja Marz)


Query sequences from Rfam and Literature
Databases used for this work
GFF, FA, STK Alignment files and Constraints for RNAfold
5s rDNA clusters
Paralogous Groups Data: Consensus sequences, SplitsTree files and pictures
Promotor analysis with MEME
Terminator analysis with MEME
Alignment of NTS regions <500nt
Linkage between 5S rRNA and other ncRNAs

Query sequences from Rfam and Literature


Databases used for this work

f-chromosom; s-scaffold/superscaffold; c-contig/supercontig
Organism AssemblyCoverage real genomesize (Mbp) Mbp expected Download date Download
Homo sapiens f 3096 3423 26.11.10 Download link
Pongo pygmaeus f 6X 3447 3703 28.01.10 Download link
Macaca mulata f 5.1X 3097 3291 28.01.10 Download link
Callithrix jacchus Marmoset c 6X 2927 3355 28.01.10 Download link
Tarsius syrichta s 1.82X 3187 5144 28.01.10 Download link
Otolemur garnettii s 1.5X 3429 3531 28.01.10 Download link
Mus musculus f 2717 3216 26.11.10 Download link
Rattus norvegicus f 2719 3286 26.11.10 Download link
Dipodomys ordii s 1.85X 2165 4377 28.01.10 Download link
Spermophilus tridecemlineatus s 1.90X 3499 3932 28.01.10 Download link
Cavia porcellus s 2X 2723 3751 28.01.10 Download link
Ochotona princeps s 1.93X 4782 3107 28.01.10 Download link
Oryctolagus cuniculus s 7.48 3474 3107 28.01.10 Download link
Tupaia belangeri s 2X 3670 3472 28.01.10 Download link
Felis catus s 1.87X 4056 3040 28.01.10 Download link
Canis familiaris f 7.6X 2532 3051 28.01.10 Download link
Vicugna pacos s 2.51X 2968 3169 28.01.10 Download link
Tursiops truncatus s 2.59X 2522 3081 28.01.10 Download link
Bos taurus f 9.5X 2918 3537 28.01.10 Download link
Sus scrofa f 4X 2263 3059 28.01.10 Download link
Equus caballus f 6.8X 2475 3149 28.01.10 Download link
Myotis lucifugus s 7X 2859 2248 28.01.10 Download link
Pteropus vampyrus s 2.63X 2000 2318 28.01.10 Download link
Erinaceus europaeus s 1.86X 3378 3579 28.01.10 Download link
Sorex araneus s 1.9X 2944 2846 28.01.10 Download link
Loxodonta africana s 7X 4181 4181 28.01.10 Download link
Echinops telfairi s 2X 3834 4919 28.01.10 Download link
Procavia capensis s 2.19X 2993 3971 28.01.10 Download link
Dasypus novemcinctus s 2X 4824 5291 28.01.10 Download link
Choloepus hoffmanni s 2.05X 2467 4137 28.01.10 Download link
Monodelphis domestica f 6.8X 3606 4592 28.01.10 Download link
Macropus eugenii s 2X 2956 4224 28.01.10 Download link
Ornithorhynchus anatinus f 1.84 2073 2993 26.11.10 Download link
Taeniopygia guttata f 6X 1233 1222 28.01.10 Download link
Gallus gallus f 6.6X 1100 1222 28.01.10 Download link
Xenopus tropicalis s 7.65X 1511 3978 28.01.10 Download link
Tetraodon nigroviridis f 6X 359 421 28.01.10 Download link
Takifugu rubripes s 8.5X 393 391 28.01.10 Download link
Gasterostreus aculeatus s 6X 61 626 28.01.10 Download link
Oryzias latipes f 10.6X 869 1010 28.01.10 Download link
Danio rerio f ~30X 1481 1817 28.01.10 Download link
Callorhinchus mili c 1.4X 769 1897 28.01.10 Download link
Petromyzon marinus c 5.9X 1027 2020 28.01.10 Download link
Branchiostoma floridae s 8.1X 522 577 28.01.10 Download link
Ciona intestinalis f 11X 173 196 28.01.10 Download link
Ciona savignyi c 12X 177 196 28.01.10 Download link
Oikopleura dioica s 10X 70 68 28.01.10 Download link
Saccoglossus kowalevskii s 7X 776 800 27.03.10 Download link
Drosophila melanogaster f 169 168 27.03.10 Download link
Drosophila simulans s 9.5X 138 142 27.03.10 Download link
Drosophila sechellia s 167 166 27.03.10 Download link
Drosophila erecta f 153 147 27.03.10 Download link
Drosophila yakuba s 166 170 27.03.10 Download link
Drosophila ananassae s 231 199 27.03.10 Download link
Drosophila pseudoobscura s 153 168 27.03.10 Download link
Drosophila persimilis s 188 192 27.03.10 Download link
Drosophila willistoni s 236 220 27.03.10 Download link
Drosophila virilis s 206 362 27.03.10 Download link
Drosophila mojavensis s 194 179 27.03.10 Download link
Drosophila grimshawi s 200 240 27.03.10 Download link
Anopheles gambiae s 10X 236 264 31.01.10 Download link
Aedes aegypti c 8X 1384 942 31.01.10 Download link
Bombyx mori s 6X 481 513 27.03.10 Download link
Tribolium castaneum c 7X 200 202 27.03.10 Download link
Apis mellifera s 7.5X 235 229 11.11.10 Download link
Nasonia vitripennis f 7X 357 333 27.03.10 Download link
Pediculus humanus c 8.5X 111 108 31.01.10 Download link
Acyrthosiphon pisum s 6.2X 464 303 27.03.10 Download link
Daphnia pulex s 8.7X 197 289 27.03.10 Download link
Ixodes scapularis s 4X 1765 2357 31.01.10 Download link
Caenorhabditis remanei c 9.2X 145 101 11.11.10 Download link
Caenorhabditis briggsae f 10X 108 117 11.11.10 Download link
Caenorhabditis brenneri c 9.5X 190 101 11.11.10 Download link
Caenorhabditis elegans f 100 93 11.11.10 Download link
Caenorhabditis japonica c 6.3X 163 101 11.11.10 Download link
Haemonchus contortus c 2-3X 298 59 11.11.10 Download link
Ancylostoma canium c 10X 75 166 31.01.10 Download link
Pristionchus pacificus c 8.92X 170 166 11.11.10 Download link
Strongyloides ratti c 396 225 11.11.10 Download link
Meloidogyne incognita c 82 49 11.11.10 Download link
Meloidogyne hapla c 10.4X 53 44 11.11.10 Download link
Brugia malayi c 11X 96 108 11.11.10 Download link
Trichinella spiralis c ~35X 3061 254 31.02.10 Download link
Echinococcus multilocularis 10 440 11.11.10 Download link
Schistosoma mansoni s 3X 381 254 27.03.10 Download link
Schistosoma japonicum c 369 254 11.11.10 Download link
Schmidtea mediterranea c 11.6X 902 704 27.05.10 Download link
Helobdella robusta c 3090 303 31.02.10 Download link
Capitella sp c ~7.9X 3592 235 02.02.10 Download link
Alvinella pompejana c 290 729 31.01.10 Download link
Lottia gigantea s 8.87X 360 421 11.11.10 Download link
Aplysia californica s 9.86X 716 1858 31.01.10 Download link
Biomphalaria glabrata c 23X 202 929 31.01.10 Download link
Euprymna scolopes c 47 3668 11.11.10 Download link
Acropora palmata c 9 225 31.01.10 Download link
Acropora millepora c 5X 11 225 31.01.10 Download link
Porites lobata 10 1114 11.11.10 Download link
Nematostella vectensis s 7.8X 357 225 27.03.10 Download link
Reniera spez c ~9X 2882 359 11.11.10 Download link
Trichoplax adhaerens s 8X 106 39 27.03.10 Download link

GFF, FA, STK Alignment files and Constraints for RNAfold

5S rRNA U1 snRNA
Organism GFF FA STK Constraints GFF FA STK Constraints
Homo sapiens hsa.5S.gff hsa.5S.fa hsa.5S.stk hsa.5S.constraints hsa.U1.gff hsa.U1.fa hsa.U1.stk hsa.U1.constraints
Pongo pygmaeus ppy.5S.gff ppy.5S.fa ppy.5S.stk ppy.5S.constraints ppy.U1.gff ppy.U1.fa ppy.U1.stk ppy.U1.constraints
Macaca mulata mac.5S.gff mac.5S.fa mac.5S.stk mac.5S.constraints mac.U1.gff mac.U1.fa mac.U1.stk mac.U1.constraints
Callithrix jacchus Marmoset cjc.5S.gff cjc.5S.fa cjc.5S.stk cjc.5S.constraints cjc.U1.gff cjc.U1.fa cjc.U1.stk cjc.U1.constraints
Tarsius syrichta tsy.5S.gff tsy.5S.fa tsy.5S.stk tsy.5S.constraints tsy.U1.gff tsy.U1.fa tsy.U1.stk tsy.U1.constraints
Otolemur garnettii oga.5S.gff oga.5S.fa oga.5S.stk oga.5S.constraints oga.U1.gff oga.U1.fa oga.U1.stk oga.U1.constraints
Mus musculus mmu.5S.gff mmu.5S.fa mmu.5S.stk mmu.5S.constraints mmu.U1.gff mmu.U1.fa mmu.U1.stk mmu.U1.constraints
Rattus norvegicus rno.5S.gff rno.5S.fa rno.5S.stk rno.5S.constraints rno.U1.gff rno.U1.fa rno.U1.stk rno.U1.constraints
Dipodomys ordii dor.5S.gff dor.5S.fa dor.5S.stk dor.5S.constraints dor.U1.gff dor.U1.fa dor.U1.stk dor.U1.constraints
Spermophilus tridecemlineatus str.5S.gff str.5S.fa str.5S.stk str.5S.constraints str.U1.gff str.U1.fa str.U1.stk str.U1.constraints
Cavia porcellus cpo.5S.gff cpo.5S.fa cpo.5S.stk cpo.5S.constraints cpo.U1.gff cpo.U1.fa cpo.U1.stk cpo.U1.constraints
Ochotona princeps opr.5S.gff opr.5S.fa opr.5S.stk opr.5S.constraints opr.U1.gff opr.U1.fa opr.U1.stk opr.U1.constraints
Oryctolagus cuniculus ocu.5S.gff ocu.5S.fa ocu.5S.stk ocu.5S.constraints ocu.U1.gff ocu.U1.fa ocu.U1.stk ocu.U1.constraints
Tupaia belangeri tbe.5S.gff tbe.5S.fa tbe.5S.stk tbe.5S.constraints tbe.U1.gff tbe.U1.fa tbe.U1.stk tbe.U1.constraints
Felis catus fca.5S.gff fca.5S.fa fca.5S.stk fca.5S.constraints fca.U1.gff fca.U1.fa fca.U1.stk fca.U1.constraints
Canis familiaris cfa.5S.gff cfa.5S.fa cfa.5S.stk cfa.5S.constraints cfa.U1.gff cfa.U1.fa cfa.U1.stk cfa.U1.constraints
Vicugna pacos vpa.5S.gff vpa.5S.fa vpa.5S.stk vpa.5S.constraints vpa.U1.gff vpa.U1.fa vpa.U1.stk vpa.U1.constraints
Tursiops truncatus ttr.5S.gff ttr.5S.fa ttr.5S.stk ttr.5S.constraints ttr.U1.gff ttr.U1.fa ttr.U1.stk ttr.U1.constraints
Bos taurus bta.5S.gff bta.5S.fa bta.5S.stk bta.5S.constraints bta.U1.gff bta.U1.fa bta.U1.stk bta.U1.constraints
Sus scrofa ssc.5S.gff ssc.5S.fa ssc.5S.stk ssc.5S.constraints ssc.U1.gff ssc.U1.fa ssc.U1.stk ssc.U1.constraints
Equus caballus eca.5S.gff eca.5S.fa eca.5S.stk eca.5S.constraints eca.U1.gff eca.U1.fa eca.U1.stk eca.U1.constraints
Myotis lucifugus mlu.5S.gff mlu.5S.fa mlu.5S.stk mlu.5S.constraints mlu.U1.gff mlu.U1.fa mlu.U1.stk mlu.U1.constraints
Pteropus vampyrus pva.5S.gff pva.5S.fa pva.5S.stk pva.5S.constraints pva.U1.gff pva.U1.fa pva.U1.stk pva.U1.constraints
Erinaceus europaeus eeu.5S.gff eeu.5S.fa eeu.5S.stk eeu.5S.constraints eeu.U1.gff eeu.U1.fa eeu.U1.stk eeu.U1.constraints
Sorex araneus sar.5S.gff sar.5S.fa sar.5S.stk sar.5S.constraints sar.U1.gff sar.U1.fa sar.U1.stk sar.U1.constraints
Loxodonta africana laf.5S.gff laf.5S.fa laf.5S.stk laf.5S.constraints laf.U1.gff laf.U1.fa laf.U1.stk laf.U1.constraints
Echinops telfairi ete.5S.gff ete.5S.fa ete.5S.stk ete.5S.constraints ete.U1.gff ete.U1.fa ete.U1.stk ete.U1.constraints
Procavia capensis pca.5S.gff pca.5S.fa pca.5S.stk pca.5S.constraints pca.U1.gff pca.U1.fa pca.U1.stk pca.U1.constraints
Dasypus novemcinctus dno.5S.gff dno.5S.fa dno.5S.stk dno.5S.constraints dno.U1.gff dno.U1.fa dno.U1.stk dno.U1.constraints
Choloepus hoffmanni cho.5S.gff cho.5S.fa cho.5S.stk cho.5S.constraints cho.U1.gff cho.U1.fa cho.U1.stk cho.U1.constraints
Monodelphis domestica mdo.5S.gff mdo.5S.fa mdo.5S.stk mdo.5S.constraints mdo.U1.gff mdo.U1.fa mdo.U1.stk mdo.U1.constraints
Macropus eugenii meu.5S.gff meu.5S.fa meu.5S.stk meu.5S.constraints meu.U1.gff meu.U1.fa meu.U1.stk meu.U1.constraints
Ornithorhynchus anatinus oan.5S.gff oan.5S.fa oan.5S.stk oan.5S.constraints oan.U1.gff oan.U1.fa oan.U1.stk oan.U1.constraints
Taeniopygia guttata tgu.5S.gff tgu.5S.fa tgu.5S.stk tgu.5S.constraints tgu.U1.gff tgu.U1.fa tgu.U1.stk tgu.U1.constraints
Gallus gallus gga.5S.gff gga.5S.fa gga.5S.stk gga.5S.constraints gga.U1.gff gga.U1.fa gga.U1.stk gga.U1.constraints
Xenopus tropicalis xtr.5S.gff xtr.5S.fa xtr.5S.stk xtr.5S.constraints xtr.U1.gff xtr.U1.fa xtr.U1.stk xtr.U1.constraints
Tetraodon nigroviridis tni.5S.gff tni.5S.fa tni.5S.stk tni.5S.constraints tni.U1.gff tni.U1.fa tni.U1.stk tni.U1.constraints
Takifugu rubripes tru.5S.gff tru.5S.fa tru.5S.stk tru.5S.constraints tru.U1.gff tru.U1.fa tru.U1.stk tru.U1.constraints
Gasterostreus aculeatus gac.5S.gff gac.5S.fa gac.5S.stk gac.5S.constraints gac.U1.gff gac.U1.fa gac.U1.stk gac.U1.constraints
Oryzias latipes ola.5S.gff ola.5S.fa ola.5S.stk ola.5S.constraints ola.U1.gff ola.U1.fa ola.U1.stk ola.U1.constraints
Danio rerio dre.5S.gff dre.5S.fa dre.5S.stk dre.5S.constraints dre.U1.gff dre.U1.fa dre.U1.stk dre.U1.constraints
Callorhinchus mili cmi.5S.gff cmi.5S.fa cmi.5S.stk cmi.5S.constraints cmi.U1.gff cmi.U1.fa cmi.U1.stk cmi.U1.constraints
Petromyzon marinus pma.5S.gff pma.5S.fa pma.5S.stk pma.5S.constraints pma.U1.gff pma.U1.fa pma.U1.stk pma.U1.constraints
Branchiostoma floridae bfl.5S.gff bfl.5S.fa bfl.5S.stk bfl.5S.constraints bfl.U1.gff bfl.U1.fa bfl.U1.stk bfl.U1.constraints
Ciona intestinalis cin.5S.gff cin.5S.fa cin.5S.stk cin.5S.constraints cin.U1.gff cin.U1.fa cin.U1.stk cin.U1.constraints
Ciona savignyi csa.5S.gff csa.5S.fa csa.5S.stk csa.5S.constraints csa.U1.gff csa.U1.fa csa.U1.stk csa.U1.constraints
Oikopleura dioica odi.5S.gff odi.5S.fa odi.5S.stk odi.5S.constraints odi.U1.gff odi.U1.fa odi.U1.stk odi.U1.constraints
Saccoglossus kowalevskii sko.5S.gff sko.5S.fa sko.5S.stk sko.5S.constraints sko.U1.gff sko.U1.fa sko.U1.stk sko.U1.constraints
Drosophila melanogaster dme.5S.gff dme.5S.fa dme.5S.stk dme.5S.constraints dme.U1.gff dme.U1.fa dme.U1.stk dme.U1.constraints
Drosophila simulans dsi.5S.gff dsi.5S.fa dsi.5S.stk dsi.5S.constraints dsi.U1.gff dsi.U1.fa dsi.U1.stk dsi.U1.constraints
Drosophila sechellia dse.5S.gff dse.5S.fa dse.5S.stk dse.5S.constraints dse.U1.gff dse.U1.fa dse.U1.stk dse.U1.constraints
Drosophila erecta der.5S.gff der.5S.fa der.5S.stk der.5S.constraints der.U1.gff der.U1.fa der.U1.stk der.U1.constraints
Drosophila yakuba dya.5S.gff dya.5S.fa dya.5S.stk dya.5S.constraints dya.U1.gff dya.U1.fa dya.U1.stk dya.U1.constraints
Drosophila ananassae dan.5S.gff dan.5S.fa dan.5S.stk dan.5S.constraints dan.U1.gff dan.U1.fa dan.U1.stk dan.U1.constraints
Drosophila pseudoobscura dps.5S.gff dps.5S.fa dps.5S.stk dps.5S.constraints dps.U1.gff dps.U1.fa dps.U1.stk dps.U1.constraints
Drosophila persimilis dpe.5S.gff dpe.5S.fa dpe.5S.stk dpe.5S.constraints dpe.U1.gff dpe.U1.fa dpe.U1.stk dpe.U1.constraints
Drosophila willistoni dwi.5S.gff dwi.5S.fa dwi.5S.stk dwi.5S.constraints dwi.U1.gff dwi.U1.fa dwi.U1.stk dwi.U1.constraints
Drosophila virilis dvi.5S.gff dvi.5S.fa dvi.5S.stk dvi.5S.constraints dvi.U1.gff dvi.U1.fa dvi.U1.stk dvi.U1.constraints
Drosophila mojavensis dmo.5S.gff dmo.5S.fa dmo.5S.stk dmo.5S.constraints dmo.U1.gff dmo.U1.fa dmo.U1.stk dmo.U1.constraints
Drosophila grimshawi dgr.5S.gff dgr.5S.fa dgr.5S.stk dgr.5S.constraints dgr.U1.gff dgr.U1.fa dgr.U1.stk dgr.U1.constraints
Anopheles gambiae aga.5S.gff aga.5S.fa aga.5S.stk aga.5S.constraints aga.U1.gff aga.U1.fa aga.U1.stk aga.U1.constraints
Aedes aegypti aae.5S.gff aae.5S.fa aae.5S.stk aae.5S.constraints aae.U1.gff aae.U1.fa aae.U1.stk aae.U1.constraints
Bombyx mori bmo.5S.gff bmo.5S.fa bmo.5S.stk bmo.5S.constraints bmo.U1.gff bmo.U1.fa bmo.U1.stk bmo.U1.constraints
Tribolium castaneum tca.5S.gff tca.5S.fa tca.5S.stk tca.5S.constraints tca.U1.gff tca.U1.fa tca.U1.stk tca.U1.constraints
Apis mellifera ame.5S.gff ame.5S.fa ame.5S.stk ame.5S.constraints ame.U1.gff ame.U1.fa ame.U1.stk ame.U1.constraints
Nasonia vitripennis nvi.5S.gff nvi.5S.fa nvi.5S.stk nvi.5S.constraints nvi.U1.gff nvi.U1.fa nvi.U1.stk nvi.U1.constraints
Pediculus humanus phu.5S.gff phu.5S.fa phu.5S.stk phu.5S.constraints phu.U1.gff phu.U1.fa phu.U1.stk phu.U1.constraints
Acyrthosiphon pisum api.5S.gff api.5S.fa api.5S.stk api.5S.constraints api.U1.gff api.U1.fa api.U1.stk api.U1.constraints
Daphnia pulex dpu.5S.gff dpu.5S.fa dpu.5S.stk dpu.5S.constraints dpu.U1.gff dpu.U1.fa dpu.U1.stk dpu.U1.constraints
Ixodes scapularis isc.5S.gff isc.5S.fa isc.5S.stk isc.5S.constraints isc.U1.gff isc.U1.fa isc.U1.stk isc.U1.constraints
Caenorhabditis remanei cre.5S.gff cre.5S.fa cre.5S.stk cre.5S.constraints cre.U1.gff cre.U1.fa cre.U1.stk cre.U1.constraints
Caenorhabditis briggsae cbr.5S.gff cbr.5S.fa cbr.5S.stk cbr.5S.constraints cbr.U1.gff cbr.U1.fa cbr.U1.stk cbr.U1.constraints
Caenorhabditis brenneri cbe.5S.gff cbe.5S.fa cbe.5S.stk cbe.5S.constraints cbe.U1.gff cbe.U1.fa cbe.U1.stk cbe.U1.constraints
Caenorhabditis elegans cel.5S.gff cel.5S.fa cel.5S.stk cel.5S.constraints cel.U1.gff cel.U1.fa cel.U1.stk cel.U1.constraints
Caenorhabditis japonica cja.5S.gff cja.5S.fa cja.5S.stk cja.5S.constraints cja.U1.gff cja.U1.fa cja.U1.stk cja.U1.constraints
Haemonchus contortus hco.5S.gff hco.5S.fa hco.5S.stk hco.5S.constraints hco.U1.gff hco.U1.fa hco.U1.stk hco.U1.constraints
Ancylostoma canium acn.5S.gff acn.5S.fa acn.5S.stk acn.5S.constraints acn.U1.gff acn.U1.fa acn.U1.stk acn.U1.constraints
Pristionchus pacificus ppa.5S.gff ppa.5S.fa ppa.5S.stk ppa.5S.constraints ppa.U1.gff ppa.U1.fa ppa.U1.stk ppa.U1.constraints
Meloidogyne incognita min.5S.gff min.5S.fa min.5S.stk min.5S.constraints min.U1.gff min.U1.fa min.U1.stk min.U1.constraints
Meloidogyne hapla mha.5S.gff mha.5S.fa mha.5S.stk mha.5S.constraints mha.U1.gff mha.U1.fa mha.U1.stk mha.U1.constraints
Brugia malayi bma.5S.gff bma.5S.fa bma.5S.stk bma.5S.constraints bma.U1.gff bma.U1.fa bma.U1.stk bma.U1.constraints
Trichinella spiralis tsp.5S.gff tsp.5S.fa tsp.5S.stk tsp.5S.constraints tsp.U1.gff tsp.U1.fa tsp.U1.stk tsp.U1.constraints
Schistosoma mansoni sma.5S.gff sma.5S.fa sma.5S.stk sma.5S.constraints sma.U1.gff sma.U1.fa sma.U1.stk sma.U1.constraints
Schistosoma japonicum sja.5S.gff sja.5S.fa sja.5S.stk sja.5S.constraints sja.U1.gff sja.U1.fa sja.U1.stk sja.U1.constraints
Schmidtea mediterranea sme.5S.gff sme.5S.fa sme.5S.stk sme.5S.constraints sme.U1.gff sme.U1.fa sme.U1.stk sme.U1.constraints
Helobdella robusta hro.5S.gff hro.5S.fa hro.5S.stk hro.5S.constraints hro.U1.gff hro.U1.fa hro.U1.stk hro.U1.constraints
Capitella sp cca.5S.gff cca.5S.fa cca.5S.stk cca.5S.constraints cca.U1.gff cca.U1.fa cca.U1.stk cca.U1.constraints
Alvinella pompejana apo.5S.gff apo.5S.fa apo.5S.stk apo.5S.constraints apo.U1.gff apo.U1.fa apo.U1.stk apo.U1.constraints
Lottia gigantea lgi.5S.gff lgi.5S.fa lgi.5S.stk lgi.5S.constraints lgi.U1.gff lgi.U1.fa lgi.U1.stk lgi.U1.constraints
Aplysia californica aca.5S.gff aca.5S.fa aca.5S.stk aca.5S.constraints aca.U1.gff aca.U1.fa aca.U1.stk aca.U1.constraints
Biomphalaria glabrata bgl.5S.gff bgl.5S.fa bgl.5S.stk bgl.5S.constraints bgl.U1.gff bgl.U1.fa bgl.U1.stk bgl.U1.constraints
Euprymna scolopes esc.5S.gff esc.5S.fa esc.5S.stk esc.5S.constraints esc.U1.gff esc.U1.fa esc.U1.stk esc.U1.constraints
Acropora palmata apa.5S.gff apa.5S.fa apa.5S.stk apa.5S.constraints apa.U1.gff apa.U1.fa apa.U1.stk apa.U1.constraints
Acropora millepora ami.5S.gff ami.5S.fa ami.5S.stk ami.5S.constraints ami.U1.gff ami.U1.fa ami.U1.stk ami.U1.constraints
Nematostella vectensis nve.5S.gff nve.5S.fa nve.5S.stk nve.5S.constraints nve.U1.gff nve.U1.fa nve.U1.stk nve.U1.constraints
Reniera spez rsp.5S.gff rsp.5S.fa rsp.5S.stk rsp.5S.constraints rsp.U1.gff rsp.U1.fa rsp.U1.stk rsp.U1.constraints
Trichoplax adhaerens tad.5S.gff tad.5S.fa tad.5S.stk tad.5S.constraints tad.U1.gff tad.U1.fa tad.U1.stk tad.U1.constraints

5s rDNA clusters

green=plus strand; blue=negative strand; filled=A-type; not filled=Q-type;

Organism *.ps
Homo sapiens hsa.5S.gff.10000.cluster.eps
Pongo pygmaeus ppy.5S.gff.10000.cluster.eps
Macaca mulata mac.5S.gff.10000.cluster.eps
Callithrix jacchus Marmoset cjc.5S.gff.10000.cluster.eps
Tarsius syrichta tsy.5S.gff.10000.cluster.eps
Otolemur garnettii oga.5S.gff.10000.cluster.eps
Mus musculus mmu.5S.gff.10000.cluster.eps
Rattus norvegicus rno.5S.gff.10000.cluster.eps
Dipodomys ordii dor.5S.gff.10000.cluster.eps
Spermophilus tridecemlineatus str.5S.gff.10000.cluster.eps
Cavia porcellus cpo.5S.gff.10000.cluster.eps
Ochotona princeps opr.5S.gff.10000.cluster.eps
Oryctolagus cuniculus ocu.5S.gff.10000.cluster.eps
Tupaia belangeri tbe.5S.gff.10000.cluster.eps
Felis catus fca.5S.gff.10000.cluster.eps
Canis familiaris cfa.5S.gff.10000.cluster.eps
Vicugna pacos vpa.5S.gff.10000.cluster.eps
Tursiops truncatus ttr.5S.gff.10000.cluster.eps
Bos taurus bta.5S.gff.10000.cluster.eps
Sus scrofa ssc.5S.gff.10000.cluster.eps
Equus caballus eca.5S.gff.10000.cluster.eps
Myotis lucifugus mlu.5S.gff.10000.cluster.eps
Pteropus vampyrus pva.5S.gff.10000.cluster.eps
Erinaceus europaeus eeu.5S.gff.10000.cluster.eps
Sorex araneus sar.5S.gff.10000.cluster.eps
Loxodonta africana laf.5S.gff.10000.cluster.eps
Echinops telfairi ete.5S.gff.10000.cluster.eps
Procavia capensis pca.5S.gff.10000.cluster.eps
Dasypus novemcinctus dno.5S.gff.10000.cluster.eps
Choloepus hoffmanni cho.5S.gff.10000.cluster.eps
Monodelphis domestica mdo.5S.gff.10000.cluster.eps
Macropus eugenii meu.5S.gff.10000.cluster.eps
Ornithorhynchus anatinus oan.5S.gff.10000.cluster.eps
Taeniopygia guttata tgu.5S.gff.10000.cluster.eps
Gallus gallus gga.5S.gff.10000.cluster.eps
Xenopus tropicalis xtr.5S.gff.10000.cluster.eps
Tetraodon nigroviridis tni.5S.gff.10000.cluster.eps
Takifugu rubripes tru.5S.gff.10000.cluster.eps
Gasterostreus aculeatus gac.5S.gff.10000.cluster.eps
Oryzias latipes ola.5S.gff.10000.cluster.eps
Danio rerio dre.5S.gff.10000.cluster.eps
Callorhinchus mili cmi.5S.gff.10000.cluster.eps
Petromyzon marinus pma.5S.gff.10000.cluster.eps
Branchiostoma floridae bfl.5S.gff.10000.cluster.eps
Ciona intestinalis cin.5S.gff.10000.cluster.eps
Ciona savignyi csa.5S.gff.10000.cluster.eps
Oikopleura dioica odi.5S.gff.10000.cluster.eps
Saccoglossus kowalevskii sko.5S.gff.10000.cluster.eps
Drosophila melanogaster dme.5S.gff.10000.cluster.eps
Drosophila simulans dsi.5S.gff.10000.cluster.eps
Drosophila sechellia dse.5S.gff.10000.cluster.eps
Drosophila erecta der.5S.gff.10000.cluster.eps
Drosophila yakuba dya.5S.gff.10000.cluster.eps
Drosophila ananassae dan.5S.gff.10000.cluster.eps
Drosophila pseudoobscura dps.5S.gff.10000.cluster.eps
Drosophila persimilis dpe.5S.gff.10000.cluster.eps
Drosophila willistoni dwi.5S.gff.10000.cluster.eps
Drosophila virilis dvi.5S.gff.10000.cluster.eps
Drosophila mojavensis dmo.5S.gff.10000.cluster.eps
Drosophila grimshawi dgr.5S.gff.10000.cluster.eps
Anopheles gambiae aga.5S.gff.10000.cluster.eps
Aedes aegypti aae.5S.gff.10000.cluster.eps
Bombyx mori bmo.5S.gff.10000.cluster.eps
Tribolium castaneum tca.5S.gff.10000.cluster.eps
Apis mellifera ame.5S.gff.10000.cluster.eps
Nasonia vitripennis nvi.5S.gff.10000.cluster.eps
Pediculus humanus phu.5S.gff.10000.cluster.eps
Acyrthosiphon pisum api.5S.gff.10000.cluster.eps
Daphnia pulex dpu.5S.gff.10000.cluster.eps
Ixodes scapularis isc.5S.gff.10000.cluster.eps
Caenorhabditis remanei cre.5S.gff.10000.cluster.eps
Caenorhabditis briggsae cbr.5S.gff.10000.cluster.eps
Caenorhabditis brenneri cbe.5S.gff.10000.cluster.eps
Caenorhabditis elegans cel.5S.gff.10000.cluster.eps
Caenorhabditis japonica cja.5S.gff.10000.cluster.eps
Haemonchus contortus hco.5S.gff.10000.cluster.eps
Ancylostoma canium acn.5S.gff.10000.cluster.eps
Pristionchus pacificus ppa.5S.gff.10000.cluster.eps
Meloidogyne incognita min.5S.gff.10000.cluster.eps
Meloidogyne hapla mha.5S.gff.10000.cluster.eps
Brugia malayi bma.5S.gff.10000.cluster.eps
Trichinella spiralis tsp.5S.gff.10000.cluster.eps
Schistosoma mansoni sma.5S.gff.10000.cluster.eps
Schistosoma japonicum sja.5S.gff.10000.cluster.eps
Schmidtea mediterranea sme.5S.gff.10000.cluster.eps
Helobdella robusta hro.5S.gff.10000.cluster.eps
Capitella sp cca.5S.gff.10000.cluster.eps
Alvinella pompejana apo.5S.gff.10000.cluster.eps
Lottia gigantea lgi.5S.gff.10000.cluster.eps
Aplysia californica aca.5S.gff.10000.cluster.eps
Biomphalaria glabrata bgl.5S.gff.10000.cluster.eps
Euprymna scolopes esc.5S.gff.10000.cluster.eps
Acropora palmata apa.5S.gff.10000.cluster.eps
Acropora millepora ami.5S.gff.10000.cluster.eps
Nematostella vectensis nve.5S.gff.10000.cluster.eps
Reniera spez rsp.5S.gff.10000.cluster.eps
Trichoplax adhaerens tad.5S.gff.10000.cluster.eps

Paralogous Groups Data: Consensus sequences, SplitsTree files and pictures

ALL.consens.aln.nex (for SplitsTree)

MAMMALIA.consens.aln.nex (for SplitsTree)
mammals - with taxon names (pdf)

Promotor analysis with MEME

MEME results (-35nt- -25nt)
shuffled MEME results (-35nt- -25nt)

Terminator analysis with MEME

MEME results (+30nt)
shuffled MEME results (+30nt)

Evolutionary boxplot of distances between 5S rRNA coding region and first occurrence of the downstream located TTTT motif

Figure 5

Alignment of NTS regions <500nt


Linkage between 5S rRNA and other ncRNAs

mir-562 (Figure 7)

5.8S rRNA
Histone 3
sno U13
sno U85