2. Nucleic Acids Research
vicinity of E. coli position 2350 (Gutell, unpublished results
and ref (3)) and when that evidence is favorable the interaction
is indicated on the f igures.
COMPARATIVE SEQUENCE ANALYSIS
For pragmatic reasons the primary tool used in constructing
the individual structures has been comparative (or phylogenetic)
analysis. This approach had its origin in the discovery of the
cloverleaf structure for tRNA (4). It first began to reach its
modern form with the analysis of 5S rRNA (5) and has emerged as
a well documented procedure (2,6-8) The underlying assumption is
that functionally equivalent regions of the large rRNAs from
phylogentically diverse sources will have biologically
equivalent structures. The procedure begins by aligning the
primary sequences using conserved sequence segments as a guide.
Next the various columns of bases are individually intercompared
to detect compensating base changes that maintain Watson-Crick
complementarity between the potential pairing regions. If an
individual helical element is independently tested several times
it is considered phylogenetically proven.
The comparative method has certain limitations that the
reader should appreciate in perusing the figures presented here.
First and foremost is the need for sequences that exhibit the
structure being studied. For highly conserved features this may
be the entire data base. In other cases features may be
extremely variable so that particular versions are only found in
individual phylogenetic groups, mammamalian mitochondria for
example. Secondly the feature must exhibit sequence variation
within the subset of sequences that contain the feature. Without
such variation a region can not be structured. Thirdly it should
be recognized that the approach necessarily produces minimal
structures. It is the nature of the method to allow the
identification of additional features as the data base grows.
Thus, for example, the continuing refinement of the E. coli
structure discussed above. Finally it should be appreciated that
it is very difficult to assess the significance of base pairs
that that can extend a particular helix in some organisms but
not all. Such base pairs are strongly supported by thermodynamic
arguements but conflict with the comparative concept. The proper
resolution in such circumstances may have to wait until such
time that more high resolution structure data is available.
CURRENT DATA BASE
As of late in 1987 there were 40 distinct complete large
subunit RNA sequences published and at least five extensive
partial sequences in which at least 500 bases of the large
subunit RNA have been sequenced (We have not exhaustively
searched for these). In addition in some instances sequence
information is available from more than one large subunit RNA
gene from the same organism. Multiple rRNA genes frequently
exhibit heterogeneity in sequence and this phenomenona may be of
more than academic interest. The present collection does not
address this matter however and in those few instances where
information from more than one large subunit rRNA gene is
available we have arbitrarily picked one sequence for inclusion
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3. Nucleic Acids Research
here. The 40 known sequences provide a diverse sample covering
the three major urkingdoms; eubacteria, archaebacteria and
eukaryotes as well as the organelles. Table 1 lists the
sequences, the common name of the RNAs involved, the total
length of the large subunit RNA inclusive of fragments such as
5.8S and 4.5S rRNAs, at least one relevant GENBANK/EMBL
accession numbers if the sequence is in the data bases, a highly
abbreviated reference and a key to the complete references that
accompany this text.
HOW TO READ THE DIAGRAMS
The structure diagrams were drawn to a single scale so that
they may be readily superimposed or intercompared. This was
accomplished by a computer program described elsewhere (6). Each
diagram encompasses two pages with a crossover point to the next
page indicated. In most bacterial cases a possible helical
structure exists between the 5'and 3' termini of the molecule.
It is uncertain whether this helix is present in the functional
RNA or is simply a remnant of processing. In any event the
reader needs to be aware that when it is possibly present it
appears on both halves of the figure. Extensive base numbering
occurs on the E. coli diagram. On the other sequence diagrams
only occasional numbers are included. These occasional numbers
refer to the specific sequence on which they appear. In those
cases in which more than one molecule is include (eg 5.8S and
28S RNAs) each is numbered separately.
When a region contains no known structure it is drawn by
the computer program as a circular loop. In order to maintain
the scale and layout of the drawings it is not always possible
to draw large uncharacterized regions as unstructured loops.
When this occurs the region of unknown structure is included as
a detached linear array listed from 5' to 3'. The Homo sapiens
and other eukaryotic cytoplasmic sequences contain many examples
of this, though the same phenomenon will also be seen on
mitochondrial and chloroplast diagrams. These linear arrays are
labeled with a bold letter and the positions included in the
array indicated. A second bold letter specifies where in the
sequence the linear array belongs. These bold letters are used
in a consistent fashion so that a large unstructured area at the
same location in several diagrams always receives the same bold
letter. In a few instances the uncharacterized array is small
enough to be shown as a loop in some but not all the diagrams.
In those instances a bold letter is used to label the loops so
that it is obvious that an equivalent unstructured region is
present.
The reader should not conclude that the regions assigned
bold letters are the only unstructured regions. Whenever room
exists the computer program draws the unstructured regions as a
large loop. A letter has only been assigned if the computer has
used the linear array display in at least one case. Many of the
unlabeled unstructured regions are rather large. Obvious
examples can be seen by examining any of the mammalian
mitochondria structures. Thus in many of the sequences presented
here local regions which are often substantial in size are shown
as unstructured. These regions clearly have a different
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5. Nucleic Acids Research
structure than is seen in E. coli or some of the other molecules
but we do not as yet know what it is.
This should not be seen as bothersome but rather as
defining an opportunity to obtain data from additional organisms
in order to allow resolution of the problem area. In many cases
the difficulty stems from the fact that too few sequences are
available or too little sequence variation has been displayed in
the known sequences to deduce a structure. In a few cases time
did not permit a though analysis and a recognizeable structulral
feature may have been overlooked. Also the reader should realize
that the comparative approach is a convergent one. The current
model should at best be perceived as a minimal one awaiting the
discovery of additional interactions. Thus small two and three
base helices may ultimately be found even in regions in which
considerable structure has already been identified as more data
accumulates.
5.8S RNA, 4.5S RNA AND OTHER LARGE SUBUNIT FRAGMENTS
It is one of the pecularities of the large subunit RNA that
it is sometimes genetically fragmented. The most well known
example is the 5.8S rRNA and its equivalents that are found in
most eukaryotic o.ganisms. This RNA has been shown (9,10) to be
homologous to approximately the first 150 positions of the E.
coli 23S rRNA. Although genetically distinct it interacts with
the large subunit RNA through base pairing. In effect then the
two together form a single RNA with a backbone nick in one of
its loops. The same phenomenon is also seen at the 3' end of
several chloroplast large subunit RNAs where the last 100 or so
bases are separately encoded as a 4.5S RNA (11). In this case
the homology to the E. coli 3' terminus is obvious but the the
mechanism by which the 4.5S rRNA and the main large subunit RNA
component are held together is not. The most extreme case of
this fragmentation phenomenon that is known is in Crithidia
fasciculata where the large subunit RNA is actually assembled
from six f-ragments plus a 5.8S rRNA (12). These various
fragmentation phenomenon are indicated on the diagram by labels
that indicate where the respective 5' and 3' ends are located.
The Crithidia fragments are labeled with the same lower case
letters that were used in the original publication (12) and
numbered as if they were a single large RNA.
OVERLAY DIAGRAMS AND COLLECTION ARRANGEMENT
It is very useful in comparing structures to produce
overlay diagrams that display one structure relative to another.
Several such diagrams are included here. In each case the
underlying structure is that of E. coli. Where the E. coli is
unique it can be seen as a light gray. The bold structure is
that of the other organism indicated in the legend. Base numbers
on these diagrams always refer to E. coli. These overlay figures
show immediately where the sites of structural variation between
the two RNAs are located. The overlay figures are used to
introduce the various sections of the collection. In each case a
particularly representative overlay is chosen so that the major
variations in the group relative to E. coli can be seen.
The collection begins with the five eubacterial sequences.
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6. Nucleic Acids Research
These are virtually identical structurally and therefore no
overlay figure is included. They are followed by the four
chloroplast figures which again follow the virtually identical
structural pattern. The Anacystis sequence used was arbitrarily
that of Douglas and Doolittle (13). The plant chloroplasts all
have a detached 4.5S at the 3' terminus but the alga, Chlorella
ellipsoidea does not. The C. ellipsoidea sequence also is unusal
in that it is claimed to contain an intron (14). We believe that
this assertion is not convincingly established and thus the
putative intron is shown on Figure 9a as an insertion region of
class D. Several large subunit sequences have an insertion at
this location. If the C. ellipsoidea insertion is in fact an
intron this would be very atypical as none of the known large
subunit introns correspond with common insertion regions. It is
possibile that experimental difficulties may have arisen due to
the propensity of large subunit RNAs such as E. coli 23S rRNA
(15) to readily fragment. The location of this fragmentation
site has been localized in E. coli (1) to the region of the RNA
that corresponds to that which contains the putative intron in
C. ellipsoidea.
The largest portion of the collection contains the
mitochondrial sequences. These are assembled into three groups
each prefaced by a separate overlay figure. The first and most
internally variable gLoup are those with large mitochondrial
RNAs as typified by the overlay of Zea mays, Fig. 10. These
mitochondrial RNAs resemble the eubacterial ones in size and
structure more than any of the other mitochondria do.
Nevertheless they are marked by considerable varibility even
within the group. One unifying feature is the presence of an
unstructured region H in the vicinity of E. coli position 1400
in all cases. Structures are provided for all of these RNAs
except Paramecium tetraaurelia which is virtually identical to
P. primaurelia, Fig. 15. and Schizosaccharomyces pombe which was
published after the structures were completed. The second major
mitochondrial group are the rather small 16S RNAs that are found
in most higher organisms. Although much smaller, as the human
overlay shows, Fig. 16, considerable structural similarity with
the eubacterial RNAs continues to exist. Finally the three
kinetoplast mitochondrial 12S rRNAs follow. Here as is indicated
by the overlay, Fig. 24, virtually none of the structure in the
5' half of the molecule is preserved, though considerable
structural conservation does exist in the 3' half of the
molecule.
The remaining figures are devoted to the archaebacteria and
eucaryotic cytoplasm. As indicated by the Halococcus morrhuae
structural overlay, Fig. 28, the archaebacteria exhibit
significant variation that exceeds anything that is seen among
the eubacteria alone. Close examination of the archaebacterial
figures also reveals that unlike the eubacteria, the
archaebacteria, do exhibit some variation within the group as a
whole. A figure is not included for Thermoproteus tenax because
this sequence was inadvertantly overlooked. The main theme from
the eucaryotic cytoplasmic sequences sems to be growth in size.
Although not all the RNAs exhibit the effect to the same extent
it is clear that several regions seem to be favored for
macroscopic insertions of new material. As indicated by the
Saccharomyces cerevisiae overlay, Fig. 34, the main theme of
rl 80
7. Nucleic Acids Research
secondary structure is again repeated in the eukaryotic
cytoplasmic RNAs. Excluding the large insertions, the eukaryotic
RNA structure is remarkably like that of the eubacteria and
archaebacteria. The sequence of S. carlsbergenesis 26S rRNA is
very similar to that of S. cerevislae and thus is not shown as a
separate figure. In the case of rat, the corrected sequence (16)
has been chosen for the figure presented here.
AVAILABILITY AND ACCURACY OF THE DATA
The sequences presented here are maintained in aligned data
bases according to phylogenetic type. Due to the numerous
macroscopic insertions and deletions no attempt is made to
maintain a single aligned data base of all the sequences. We
therefore cannot provide such an alignment on electronic medium.
We can however provide individual sequences. Alternatively the
interested reader may get sequences directly from the electronic
databases. When base ambiguity existed the IUPAC nomenclature
recommendations were followed. Post-transcriptional
modifications have not been indicated since these have not been
determined in most cases. The reader should be aware however
that the large rRNAs do have a number of such modified
nucleotides. In the case of the 5.8S rRNAs which mostly have
been sequenced at the RNA level the post-transcriptional
modifications are frequently known, though not indicated here.
The sequences presented here and the position number labels have
been extensively checked but nevertheless may contain an
occasional error. The structures themselves are the best we
currently have available. Although occasionally a helix
indicated may be in error it is far more likely that one will
have been overlooked. Readers are invited to inform us about
errors and ommissions of published sequences.
ACKNOWLEDGEMENTS
Dr. Robin Gutell's efforts in this undertaking were
supported by NIH grant #GM-17129 to Dr. Harry F. Noller of the
University of Santa Cruz and NASA grant NSG-7044 to Dr. Carl R..
Woese at the University of Illinois. Dr. George E. Fox's efforts
were supported by NASA grant NSG-7440 and NIH grant GM-37655.
*Present address: GENPROBE Inc., 9880 Campus Point Drive, San Diego, CA 92121, USA
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Secondary Structure of eubacterial 23S Ribosomal RNA: Escherichia coli
AAA tA
ACCAuCCAUCAu GAA^C ACC A A %CGCC Gu
GAUCGGUAGUA%XCIof IAtCCG AAAUI IC G
GA
c G5cA ... I. CACAC C
A01 AA,0A IUG
*oxo^C-C~~~~~~~~~~~~~~~g-CC A
A' CG CUACCC Gu C GCC Cu u CCu G C C C ^ '<o G C
OW
Gw .w
A
CA8 A
A UCG~~~~~~~~~~~~~~~~~~~~~~~
GoeU^uc .GxcGGc&s,
ACC AG`A A GAAAA :
A
~~~~~~~~~aAA~~~~~~~~~~~~~~~~~~~~~~
A A
AjA A'A ACA.A
AAAAC AAC AA AAAAAC GA c
A A ~~~~~~~~~~~~~~~~~~~~~~~~~AC
A:CC AACAAAAAAAAUC2:
EGAA cAWAAGAAA AAA
AG AA'AGA 3 A A0 UA "OGA-
AAAA A C U
AfA AGCCUCC AGUGGUC .G
v A AAI¼AA 'A
AAAG*GCJGAAAcc AACUCA uGA
%A A A9CCrGA
AAjGF 31 AACCAAAAA
ACAA- A-A ~~~~~~~~~~~~~~G
A
Fig. Ica
Esclwr,ch/o coil
rir84
11. Nucleic Acids Research
1870
GC AA
uGAU G
G *UUGCG
Ac GC-G*fu A-
C 2 e-G210
G 2 8i0
A-,g
AG UG
AG-C G GG AC UU -
ACUu GGAkU 2 20 Ai GA6TU-AA GU.A UA A' G GAGC AGG GGUGG C
UE : U CCACC U
J^GC 2110t- GAUG CGAA AGUU C 9130 U UU- UAA
UUCC A C -G
A UUA u GGA
AC2100 G C C
%ACGUGCCA2% Y-GU-A
U A C~~~~A 8 22
CCGGCU AGA G 220 C^^
UGAA:.AI GC CCGA
GGGUGCCGUCU_~CGCCCCUI <1.l
4--66161 A UA
GCUUGGGGCU A G
8GAG 'ACUUi
8
A AGAGUU-AG
G
A A
AUC U- A-4.au
G :8U
C
UG
G G
C
20,0A-AA C--
GA
0 GU G
^A-u
u ~~~~GGG
__ U~~~~~A~ A
AUUAGA2G7UA
-GAA GCA
A20MGAAA%UA
GU %G UA %U
AAc~~~~G
GCUGA UA CC GCC/
I AUL CG%UUGUGGCGG C
C 262 2610 A l CAG,
G C
ACAC-USA CAUG
A " AGGCC G.v>G §UG
GC .G G- AC CUGGGCUG
UCj,A U AA
G?UU8fAUGG(GAA(?CCUGGA0
276 C A 2120 tA' C8I?
GAG GAACC' 2260220
A Gm
kCG AA 0-G A G
27010 8 A
uAX%%% A ~ ~ A
A N~~~~~~A
Fig.Ib
£scherichic co/i
rl85
19. Nucleic Acids Research
Secondary Structure of eubacterial 23S Ribosomal RNA: 3'half
%
AXAG C - GA
'le a
-CACGGGUAo
U
A
11111 A
C U AUUGCCCACA
3 c-^ 2800
G-UA U
UG C
C U GA^
AAA
G
U: UAGA
UA- u
G^ cGA
Fig.5b
Anacystis nidulans
rl 93
21. Nucleic Acids Research
Secondary Structure of chloroplast 23S Ribosomal RNA: 3'half
AC-G%
o CC*g
UA0 U
GA
A GA
1895-C-C AcU8 CAG
A AG 6SPG AGGC
GACGG A A
UAUACU a#X0 G AGGUGG C
:1C2 OCAC
IIIIIIII I OACAAUCUCC G U
AGC
-a tl A
2O&C UAGAGUO ^°4 ^s
AAG C
CUU UGCGG A A
C
A 0A*u U UAG au
AGC A A U A GUG
eCAA-C A 1L
10(;Ac
A%~~~~~~~~~~~~~~~~~~~~~=A~~-A ACGCCCA ,
a8 GU u 00-G~~~~Zamay
UA U-AA 230020tU4 A~~.~CGCAGUGACCAG4:2 G CUdGUCAGAC S8
ikoAGoeau
~~A oi *llc111cc
UCAAUGCCCCGAUACGCUCAI c U- GAA4ACGGGCGC C- c
1800 1c AGU 8S
UG A A u .GGA
C-u.GGa U-A
U-A VSAG
AC-G C ~~~~~~~AG-: UA AAAUG
G GAu
u ACUGCAAGAU
U=A A c ~ ~~~~~~~~~~~ACGAGCUGCC
GAAAUAG GC
AGC20C CGGCGC
A= U-AAJGA
CAGACAUAUA A UI
U C
CCUIGCACc!'GGACAG
A
AAG
GGGUGUGGCCUACI.*ltl It C
U9 CG%bUUGGAAGGG CU ACC
AGA
U ~~~~~GC
ACG%%eAGAC A
",A AG'Gca CuUGuGau 2600
4.5S CUCU"% aUG&
A
CG,6GA
5CU3AAt
G
UC% %GCA
AUO 23S $
,
UC.4CC.GA
C- CAG AGAACCC9%ACCUU%%AGG Aj. U
9
G 1 11A
A
345S
'Gt
C AU CACCUGGAGCUGU
S
A A cUAAA~CA
G A A C C~~~~~~~, A C lllIU.
AGCA_ U C O 'C C UUGUM1CUGU
U = G C A A GAUcA
C U G~~ ~~~~AACA U
G
G C
COA AG AAAU,e.C
U-A-50 2QU
Zea mays
r195
22. Nucleic Acids Research
Secondary Structure of chloroplast 23S Ribosomal RNA: 5'half
'A~A0A c
1100 A
ACACA C CC A 'tCA AA~~UcCAUAUAAA%?CACAAA
C~~~~~~GGAACGACCA C,AGGCGtACCCA A CAAAU
AACG GUACUCo,A A oIl-fill fiA AGC
'A,CGUUUGGAu cuc~~~~~~~~~~~~~~~AA
A0 eCLCCA AAA CAG
A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~50A tI
CAIA C.
ACA a1400 -G
AG '~~~~~~~~~A' AC
Aic-dk~~ ~ ~ ~ ~ G A C C. A CG A
A AAGCAGAC GA GCCCAAAA C A -U
A G ACA A A"'~~~~~~~~~~~~~~~~~~~~~~~~~CA A ~~~~~~~~~ AGAA U-A
G-U ACC~~~~~~~~ACC
A U C 160
A G u2:CGGACAGGAA
cRcP GAC AAA0~ ~ ~ ~ ~ ~
Ad3~~~~~~GA AGAG A-
UA G
A- ACAeAA-CGGACG
IA A
ACCG GAAAC
A A-A~~~~~~~~~~C
A eC
OUAHAaCAAAAC
A 16007
Fig.7a
tobacco
rl96
c4
23. Nucleic Acids Research
Secondary Structure of chloroplast 23S Ribosomal RNA: 3'half
AUGAG-C
C-AAC-G
00p8-t
Ae U SC uC Cc
A "A U G
a C
U A G C
G A A a c7o
C- 0 A AA
A CA A AAG C
A u AG-CC
A6- A
C-G
A AU a. Ug AG . AUU A U GCUU AMAUU:'.A A A A Au
. toCGCGUCAC
CG-CUG
CAGC P.. G oilI A
18OO- 6. C UCACC c
G G *
AA CA Ga U Cu UAG UAGAGU
A AAACA ACGCC uAAGGU AC U - A
C .... 11CG U-A
CACUUUGUUGCCA U G C
ACC 2A C LA A G GG
GAGCA C U 7u
GC
U
GGC ACGCA^ %760 G^UGUA A A
U~~~~~~~~~..G50 ^
cu UuG-0 220078
UA~~~~UCU
GCGCAGUGA UGGU~A A j .
G BCCAGSCCUU,?GUCAG)5C
A
G C
UU1111-10 G A
1700GCUA 27GA Ad A
u-2000 C§C
AC G -U U A5
G A- GAGU C8170A-U U-AL A U7 AG
AC ~~~~~~~-ALA
u GFGcig. 7 A
AGACGAuLG%Uoa
8-A A A
-:UUAAACCA GA
CAG-G G C 2500
4.5SCUCU~~~~~~~~A~UUGGUG c
C GU C1AC/'UsCUUCG§
A~~~~ U~~~ %.uG U~~~~~ a U0-CA
u5~G~100~:S 23S~C'AAUAuG AU~ UA GAMGGA
G-ACGGGA GA:ACGCA.7
111 CCA U(A3A
4.5SA L~~ ~ ~~~~~~ACCA A *iG-i
uc %~C G U:U AU
a GCAU A U :
uAA%.G C cA C -GAU %U
AGCL U IF~~CA C G A
0 A A G ~ ~~ ~~~A UU
U 0 C A 2760LUGGAA
C U GAL C0~~~'o'LI'GUGUCUCC G
A 0 AA~~~~~~~J'. CCA
CG*AL
G c
u C 2 600 u~AC. 271
u AGUUG/G ig. l
A~~C%% tobacc
rl97
24. Nucleic Acids Research
Secondary Structure of chloroplast 23S Ribosomal RNA: 5'half
-,00
Fig.&o
Marchantiapolymorpha: liverwort
rl 98
26. Nucleic Acids Research
Secondary Structure of chloroplast 23S Ribosomal RNA: 5'half
intron!?
D: 1197 .1445
UUUuuACA UAOAA@ACUuAACUU
aUGCUCAA C:,AA,GUUAACOCA
CUGAAUUAUACCOUAAAUUUAUUUUU OUUCU C :gAUU^CUUCUGC
oacouoouucuucoAC uu
CA G
Fig.9a
Chlorella elllpsoidea
r200
27. Nucleic Acids Research
Secondary Structure of chloroplast 23S Ribosomal RNA: 3'half
C A
A
C-2
CAA
A
u
u A
2100C' ° .u
u *7
uGAA AAAACAC AC
C 11111
II
CAUUUGU UG
cA AA
-C
C-
,A
Au 3200 U a
A
~ ~ ~
A
A A AUGS GA AAc
G - ACAGUAA
A 11111 A
C fGUCAAuC
AG-CA U
A A
U Gb C
C U G
a ab
ACo , Au
U
0-C
AGAU-
Fig.9b
Chlorella ellipsoidea
r201
28. Nucleic Acids Research
Secondary Structure of mitochondinal 23S Ribosomal RNA: 5'half
Fig.1Oa
Zee mays over
Escherichia coi
r202
29. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 3'half
Fig.lOb
Zea mays over
Escherichia coli
r203
0
*no
I
31. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 3'half
OU
GAA
AG
G u
2495.UAA A OGA G
02
AA: aC A2A CA CA
A"AA8:8 ~~~%AA
AA...1 ACC
Uo--C^CCU
8~~~~~~~~-Ca^CAU 0GA
I:G U~AAA A A:
8-e U-A ~A-20
UA 0 A
eVcA-2600 AAOGUGO
cu:A -c^ ^c ^ccc ^o -
eo
8,6 Al-i
C
U UCACC
U
U GAAA°
A C eAeCUUUUUA C A U
A AAAACA ACACC AA U:8
UAUUUGUC UGUOG Sl
C A U uACC A
A UU AAy A UUA GU
a- AC-UC A%0CGCACC GAU
ema ayU
2400=CGG~~~~~~~~AAGGGGU UGA C~~~~~~~~~ACC u
OAA ~~A A0*GUS
CCA UGA ALAAC~~~~~t~. GAu 31
24W-A&AGQGGU1GI G~~~~~~~~Au
G
2f95 A ~~~~~~~~~~~aGCAC U
AAUeCCC'GUAAAAAUU ~~~~~~A- U=AiA
AGO AAGI JA AU A A A
A
U
GAC 2700A A C2 A
8-c A~~~~~~~~~~~~~~~~~~~~~~~~~~~~G-
GUG
AUUCCAJ'G U'e :'A
CAA 7 COU GAC
43A I-U~~~~~~G A GACACdI
A a 3100*GC_AAAAC
CCAACGJUAGACAAGG =A
A G ~~~~~~AC Ca :
A G ~~~~~~~~~CA A
3AA 200- U AA GU A
Gua CGk GCA
GA CA%JAGAUAG
~~JACAG% A ~~~~~~;S~*aGta A A%
AAGA C~~~~~uA l
A G-32A
A ~ ~ JAU~i~GSCAACGSRAA~CG 2AACAACCAGC
A CC~~~~~~~fiCA ill ,1"U U
2 G
GGUCAC AUGI
AA~~~~~~~~~~~~~ A
uU a c~~Za ay
r205
32. Nucleic Acids Research
Secondary Structure of mitochondral 23S Ribosomal RNA: 5'half
F: 1619-2022
LA GoG GA GC F
A II, .,
GCccA AGGACAGcc
1600 AU - G&
GA CA
U A
AUCU ACOCAOG c
A ....
IsI- A
AUGA UGCGUCUGU A
O GA A
C AAU^ALA AMA AGUA GA
-ACGAA 20
c6° 2070
,100
Fig.12a
Oenothera berteriana
r 206
COAUG"UACACGAAAGUGACOAAGUUGCUUUGACUACAOAACCAUGCCU
oucuouuo"ocaAAUUG"UGGUCG"CC"CUCUCGUCGCCUCUUCCC
CUCACUCUCCUUUCCCUAAUAUGAACCUUGAGUCAUCAAAGCCUUUCUGA
CUCOOCCUG"CCGGUCGCCCUAC"GACUGOCOCUUCAAAAGOCOAAAC
UCUCOUCOUAGUUUG"CUUUUGAAUCOACUGUUCUAGGGGG"CUAACG
UCUUUU"AACOAGUAGG"UCGCGA"GAGCAGGCGUACC"CCUGCCA
UAGUC"GAGUCUGUUUAUAGUCOCOACUGUUGUCAUAGUCAACAA4%GUU
"AACUUCUAGOAAAAAACUUCOAAUUGGGAGC4CC.AUCCUCCCGGUGAA
33. Nucleic Acids Research
Secondary Structure of mitochondfial 23S Ribosomal RNA: 3'half
311
Fig.12b
Oenothera berteriana
r207
a
3 ,'ACAAA
%~ A
39 A
34. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 5'half
A-U
Ua-GaUAU AC GA
UUUUGAUGUUAUUU UJ' 9
U I I ll ll I- r
GUAAAACUAAUUAUAAA UGU
1250
A
u - u oUAUAUAAUACUCUUAAAUAAUAAAUAAUAAAAAAUUU AAAAACC UUAAAAA
uaU ; UAUAAAAGGUUCUGGUAAAAUUUUUA A A CAAUAAUVAUAUAUAUAUUAUUAUUU
A AAGCCAUUAGGAAUCAAUUAUAUAA
A U UCUUAuUAAAAGUUUUCAAGAUu
UAUUAAUUAUUUAUUAA
UAUUUAUAAAAUAAUAAUAUUAUAUAUAAU
U
'Al A AC F': 1299-1512
:a AAUUAUA
aUA
U
ACAUAA
A
A
U
"
_Caa-FSu99tS
^_.CG 1561
Fig. 13a
Aspergillus nidulans
r208
35. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 3'half
A UU
AA CGUAGUAG
CG11IfA
AOCAUCACA
3,
,2605
Aspergillus nidulans
Fig. 13b
r209
36. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 5'half
F: 1409 -1543
59
Fig.14a
Saccharomyces cerevisiae
r210
37. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 3'half
I: 2438-2558
AAAUUGUAAGGAAAA
CAAUAAUAACUUUCU
CCUCUCUCGGUGGGO
GUUCACACCUAUUUU
UA AU A OGU GUGAA CC
CCUCUUCCGCCGUUCC
GOAACUUAAAUAAAA
AUCGAAAGAAUUAAA
U
AU
A A
Fig.14b
Saccharomces cerev,siae
r21 1
u
39
38. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 5'half
F: 1027- 1116
Fig. 15a
Paramecium primaurelia
r21 2
u5'u20
afi20S
8
g
Au
39. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 3'half
cGAAUUA A u
u A- U
c U-A AA
U A-U UUUAG G
U A A
UA UUAAAUCAUC
u
U
A-UA
-U
A A .G
U U-A
U U-A
A u -G
3 UUC UUu
c GCx c
GO C-G
G- G
U
U
A
G-C
AU0UU
2300
Fig.15b
Paramecium primaurelia
r213
u
A
40. Nucleic Acids Research
Secondary Structure of mitochondral 23S Ribosomal RNA: 5'half
Fig.16a
Homo saplens over
Escherichia cofi
r214
41. Nucleic Acids Research
Secondary Structure of mitochondral 23S Ribosomal RNA: 3'half
0
..........
:
Fig.16b
HMO sa s over
Escherichia coli
r215
42. Nucleic Acids Research
Secondary Structure of mitochondral 23S Ribosomal RNA: 5'half
oC4cocU GA AGAACoUAGCAGcCACCAA AUUA AGU
A
AACCGAUAU AACU CGAA
SOOC c
CAc
A
A CA
C C
cc~~~~~~~~~~fcA
AAUAAU CAUAUCUACAA^UCA
U A A
AcA
A
AC A
A AC
A 70f
A u~~~~~~~~~~~U
Ac~~~~~~~~~~~~~~
*U A- CA
U U ~ cs c
AAG CAGC A
A ~A-UU A
AAAAAAA
A60AAA
AUGUA|C UC A
AAUAAACUU AG
AGGAA U~~~G U
ucUcC 8-AUUACU^^ u^scCc^^
GA AAAA A
c c
~~GcccX
A G c0 0G Uc
A 2 C~~~~~~~~~~~~~~~~~~~~~-
AU A U A
CACU-A cc GUAAACCCCCAA
UcUcIlk c A C CU
400 A LA
cLce
AU-A-
A43 GCUA A C
U CCAC GAuGAc U A~~~U
uAAC WAU G
AACA
A
CA CA ACUGA78A
GAUA AeA
AGAA AG~~~~~~~~~~~~~~~AUAu u UU~~~~~~~~~~~~CUGAu C'', U~~~~~~~~~~~AC
uc A A~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
A a~~~~~~~~~~~~~~~AA
A~~~ ~ ~ ~ ~ ~ ~ ~~CA
A_-UCOAA100 % CCAGA
Fig.17a
HWomo sapiens
r216
43. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 3'half
cACCA C
AC A
C
CAU
A
A -UU C-G
C2-UA G *UX AC%C
C- C AG C
AAAAACA CACCGCCU 91 CAAGC C C AAG6C
CAUU GU*U C CO COO
CCAC U-UUACA G-CCACuc
C-G U'A
A iC cG - ^ c8^:o 3
AA al
AAAAACA C 900 AAAGG A/GC
c~~ ~ ~ ~ ~ ~ ^CIcI1I*a
A 0 C
CAUUUGU~ ~~~~~CcCG UCUCGUuC
ACACAGU
800-CA A CUAAACCC
ZCaA AGU G AA C A-C
A- CUUAAU0o
A-U U A 00 0 COCAC~~'uA
GA - A U
A-U U-AAA 6- A
AUUc C C
CCA-U U-ACUACGAA A UCAA0-1U00
UACCA cUAACC
80 A 0 0 U-A A G0C A U
A-C CGA CU A AU
A AG 0 U C
A-U UA-A GGGcAA AA c U AAG
A UA C c
COA6-A
A u u AU CA
Au U A G~~~~~~~~~~:S UZ~GCA UCC AG U CUAG U
AAA~ ~ ~ C~-CUU6AUA U
0 C 1G3000
A_ CA~~U
c1000 ~ C A~'G U-AUOC
G-C AU:CCAA0 ACGU
AAG C-G A cAAUU AAA CA
3,A GA U-A
AGUAA~A-UA CAC U UAG
UGA 0A AA:A A
ACJ -8A
At U~~~~~~~~~'
GCGtA
A A ~~~A CCA~~~~~~~~~~~~~~ A AG AC AUUC
IIII1UG6AUUACGCAACCUU0 G
C U
ll
uc GC UGGGiUU6
AU CC 1500~~~~~~~~u U AA A
CAACUCUACUAUAGUA ~ ~ L- % Au 40
UU
Fig.17b
Homo sapiens
r217
44. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 5'half
AGA.OCACCAA AAA
AAUCCGAIUGUA ACU CGAAP
c A
C CA
A A
u Au A
500-A u
A U
OCAAUAAUCACAC
C UCs 44A UAUU A C A
A A
c u AAU'
c
u
u
A
u
A^^
A
-600
795
Fig.18a
Mouse
r218
u
n
Cc
A
AUC
A
C
C
cU
C
uu
45. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 3'half
ACA 900
cOU^a
-ux
^^^^^C^ucu VA cAC^Ul u C-.
Co uA .Ut Ug
XCcAt.o10-c^"u
A AUc=UoU C
U gA g -A aA.JA9
UCA Ot UUCAC
C00 A A A
AACBC
AAAAAACA^AA A
AUA
AACAAUUUG'IA UUCACUAA UAAU%AoA
UfUO1 _U
O- %C CO C"¢sU
ACOAU.1 tiOOUCU A
Cza A AAAA
{~~~~10 C°40u^uou^uua^
A A A A 1200
A UUA
tAAAA~~~ ~ ~ ~ ~ ~~~~~~~~~d C
U
UCA 0 CUA -
UA~~% U-A UA
AA U=A AAA
8000AAUA C
-u 9-8 u A~ ~~~~~~~~~~u A
A5U0 A AA A
AA A- UAGCAUAGU
A-U UU 1^C OCA
%
CUA
A=U u~C A
c A
~~AAAA au U-A AA
A-u :iAC A A
AA-U AU U111 I CCAUCUAU AA a
AA
A-U ICluU~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~SIItII I
u U-A CAGUU-IJ~UCC UUGOUA C A
U U ~~~~~~~UACAU UCA A
U A
A
ioUGA~ ~ ~ A ACUUG UA c ACAA
AA AC AA d,AC,
U
/ ~~~~~~~~~~k AA =AU~
CCUUCAOUGaOA 1UGUUACA
u%'Be ~ ~ ig18
UUAAoA
A As0 A
UUG ~ ~ C aA
/ A
1550'AA%AAAUCUAA~~~~~~~A~zAl/
a c~Fg.8
u
K% Gcu ous
r219
46. Nucleic Acids Research
Secondary Structure of mitochondral 23S Ribosomal RNA: 5'half
pCAAGCCAUCAA A A
AkIt C aA
^^ *ucu AAtCAUA A
AA UI"GAUSU A Aoc^
A u
50u A
u
c
u
u
A
A
A c
c Ac c AUS
C 0A AAA
A cu
A S
U U CV _ C°
u u Avooc^ A
AACCA
A AA
A .uuc AA
AAA AA
A AA
G0a^@u V20X
C A up.c t c6
u~~ ~u
A Ag ACIA
A A A A
.A ACAA A AAACOUAA
A C A ~ ~~~A UUAC
A AG CGGAA
A AA AA:c A&-AA ~ ~~~~~~AA
.ACA A- AAc
AAA-A A
AA A iA
ACA AAA AV
A u ~ ~ ~ ~ ~ ~ ~ ~~~~~~~
A-600A GA ~~~~~~~A AG
AA A A 780~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
AOCUCI AACCCO u~~~~~~~~~~~~~~~~~U
uAAocuao, uCAAUU'Al ~ ~ ~ ~ ~ ~ ~ ~ A
cCOARA,:Uu c~~~~~~~~~~COAB
FAg. 1c9aRAUat
r220
47. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 3'half
ACA
UA A
u
u A-A u a
^^^CG. uA oc R- ooUo^? l lo
CCA
A U S A
G.UAa u
AAAACA CC
CAUUUGU~ ~ A eA02 1100lcCocuauo^U
uCG U UU C
C~~~ ~~~A I^UUAC UCUAA4^y
uC0 A A A
A§AAAACAAGAUCA. COA AAA-9c25
cIIfI11
AA
00~~~~~~~~~~~A
Ac A lUCA UU U
O(IC
A ACA c
AAQACCA CC Ae
CA^u A
u A~~~AU
At-U U-AUAC C Au
A- U AU A
CA too~~~~~~CGG2C A A
%CUA ~~~~~~AC UAU ~ L
AA.0 XLIUC~~ U~AAUOA't~UlAAA AAU A A
UU-A UA A
AU U- AG_CC U
A-C U.A UU
0 AC A
AGUQ CThJUA A:UAUUU CU
1000 A ~ QG CA AAUGa
AU u~~~~~~~A0 UA
A A to
C%CUU-A u~~~~
ac U-A CAG-IIICOCO CU AUUA U
UA CU UUAA AA CAG
UGAA i-UAUU U CAB A
ACAA CUA UU
3' C ACA~~UCA
A C%CoAos
AGG A
a
A C-0
UGAUUUGA
A A-U
AU ~~~~~~AUAU GCAaUA G
AUAAUUA 1500
olIICGOACCAU G
Fig.19b
Rat
r221
48. Nucleic Acids Research
Secondary Structure of mitochondral 23S Ribosomal RNA: 5'half
AGCACCCAUCAAA GA A u
A
..h It A
AAUCGAGAGAU ACU CG.,A
AC
C
C
AC a
A A A500-c u
AAA AUA
A
A
AAU CC
A
U
A
OP
CAt
U U
UGAA A
U A OO-t A
u ~~~~A'
A C C U
AA A~~~~~~G
U A-CC
c600
A A
C AUCAAAA A<"A
,
.
A°C
u
793
Ftg.20a o00
Bovine
r222
49. Nucleic Acids Research
Secondary Structure of mitochondral 23S Ribosomal RNA: 3'half
900
U A A CUU 0 AU
cA u C-G G*
C UA A-UU
0 U 0UU AU%U
_cU-8 1000U-AA
C-C-GAGC
A- U- 2 G- u C
C-G
CA CAAAAAACAU U C GA1C
UUGCC~~ ~ AOUAOC I GA^CU^U GAU
C
ilIIIIIAICAUUUGU GCCGG UGGU C
COCAUAA
co-c~~ ~ACUA CUA CCUUAA
ACC
AU A A A A
c~~I
A-U U-C AUA A A CAACAC uA A U A
c c £_G
CUC
A 1 00AGA /Ci00G AAACC
2-s-1000 C-G AAAA-U
C A A AA C A-U A
F 1200A-U
AICA-U C U G
A
0-CC AAGACUAG-u -~~~~~~~~C UG
A:A- A U UA LeCA: U:A~~~~~~~~~AC8 UU C
U A aCU- ACG8 0AAA C
UU IIc AA
~~~~~A0CU80A- A CU A1U-
ACA00-C U
0
A
A-CC U C CA AGUo S. A U U-AUU UAU A
AAAA A UA 03 ACAAA UCUCACuu
CA~U
A A
C
U 0 A 1300
l1111 CGCAAUCCUAUUCAGA0UCUAUCU CU III*1II1 I CAUU OCUOOUACUUAU U A AU
CAAO C
O CA C U
C AG0Gk'% oCA %% 0C CUAUGUAU A0 UACC0
U
A U-A
UUC,~A 8JG:C/~~~~~~~~~~~~~~~~~~~AU A AAUu%%At? 1400 A:
Ai AG AUC CUGAUGGUGC
A-U~~~~~
C U
ACUCUACAAUAOUAACCAACA ~ ~ U GG CU UCCA
/~~~~~~~~~~~~~~~~~~~~~~~~A A
A 2:U Fg.20
Bovine
r223
50. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 5'half
A GCCACCUG AGACACCGU
A ,,,II.,, i,,,
AA CGGGUGACU ACU CGAA
G cu
Au~~~~~~~~~~~~~~~~C
G A
uA~~~~~~~~~
UU
G C
500A AA
CU ^ UC~~~~~~~AC UAAU GA GA A AU^-
A C A-A
A Cu AAC U A AA
AUU
UA C CA
u U AAC A
u U-0 A c
AAA C A C
A A-AAU A-
A A A uAC AG
A A C U 8 2CAGACA
A AC'u^* C-C UA
Ca I'CUAACUU GACU^CA A A
^
G c U A2C tG
CtAAU AA CC
AC CAA C AC
A.CCAA A C G A
G~ A A CUAAUAUAAA
C
C--A400A AA A A A
A- A AA
A A C U G
GACC G AA
U G A A~ A
AGIA A G AG-C C
A -AC AUCAAUAUUC- A CCACG AGA -A
AAGAcG
AGA Ac
AA
G 2A CUAGC A
;AUUGAA A GCUAU
G A CU~~GA
GA GCUGAGAG U
FiC.AAA
G . C A
U
A'A?ZCCCU AC G~AAtCCA A
CGAA40 00 CAAAAAUAA
A,~~UAAAU Lf I AGAAAAU
u c "uc 87UA u~~~~~~~~~A
ucAU A 00-A~~~~~~~~~A A
A.~~~~~~~UAA~ ~ ~ AA4
AUU G UU GC u~~~~~~~~~~~AUUi
GACC~~~~~~~~~~~~~~~CAGA
AAA U 5~~~~~~~~~~~~~~~~UAG U
AUcUA u~~~~~~~~~~~CAACAAACC AG
GAUCAAU
UAAGC CUUACCU G
UA~~~~~~0
AiU.UAAXeou IaevA
r224
52. Nucleic Acids Research
Secondary Structure of mitochondinal 23S Ribosomal RNA: 3'half
500
UUAGCAAUUAUU AAAAAU
GACUUCGUAUUA A AU UA
U
A AA
u
U u
A A
A
A u
U A
u
UA
A
U
A u
A A U
A-
A A AU
U
A U UAUUAAU
A UU
U U A-
U U-
AA A AGAAA'62
A
A UUAAU /-0
AUUU A A
AI~~JU
U ~ ~ ~ ~~~~~~~U U-U A Au-UG
UAGGUAu U8- U Uu U_AuU X ^
A AGA
40 A AUAAGtU"A(AAAAUAA
AAs>UUAA
A?-% A uA
AA U UAAAUU A60
£AAA~~~~~~~
A UUAU=A30AU A U
A G A
U-A uUUAU
AUUUC U AcA UA
U-A A A
c
ze AJU A A
_A A
UiAU A%
e UA CAUU A £
-AAUU AuC A A
U A u~~~~~~~~~A A G U
A A u~~~~~~~~~~~A
U_YWAAAa u~~~AAA
A
UU:A UUAUAUUAAUUUU~~GUA2-U Auuu AAu
u~~~~~~~~~~~~~~~~A
U:A~ ~ ~ uAU A~~~~~~~~~~~AUp
Drosophila yakuba
r226
53. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 3'half
700 AAU
AUUUI A-U
G u AAUUUU A CUAA G_
uu_ Au' uu
UU AU
U-A AU A
C-G
A A
UCU C U
c
C^
A0AAACAUAACC ACAAGGUAGC
AAUUUGU GUUGG UU U
C G u A
CGA ACU
65'cu^ U
~ A ,GUAAGGUC
800A8 UU AGAUUA
u~~~~U
AAAA U - A ^^
UU UUA A
AU-A U
A:U X- GU u
AAU A U- U A
%CUU~-^UC %U-A UCAUJ
650O U U-A G.U A-U
A-u A:~~~~U- AAAAio0 AAc ~~~ ~~~~~U-AUUA AA A
U-^ C~~~~~~~-U AAU..AUUUU A
U A
A U- U-
GUA-U C UAUUUAA_t
A-u~ ~ Gcuu^^^^uoGuy
A-U~ ~ ^ CU-A A-U
U-A U-A G-CA C
U-A C-GA U-AAA
AAU U U A ':UA:UUA AAU- AGA A-UA A U A.. uG U
A A UC AAA %AA
AQUAU UA
JUAQuU U:AUCUCCCA
UA U UA A UG
AA GAAUA
A A -U A
A A Cu
AA CGAGG GGAG
UIUUAIICGAAUUUUU GA
u3 0
AU0 A0 Au
AA AU GCUGAAAACAU A AG A
A AGd'A
UAUUAAGCGA AAACAG
A11 L UACGUUUUU GGU
3 U ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~UGAGUICUG A
U A AU-A
A aUak9b-
C-G
A~~~~~~~~~~~A AG A AG
u ~~UUGAUUUAACUC
AU~~~~~~~~~~~~~GG
u A~C
A UU% AeA1300 7UuG
u % A CC C~~~Fig22A U A %%UA -AU DrsopAl yaub
r227
54. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 5'half
AU AAGUUAUCAU A AA UUU
A 1.1 A@
AA CGAAUGUAA A U UAAUU
500 A U
U U
U
A U
U~~~ ~ ~ ~ ~~~~~~A UU
U U
U U
U
U
G A
A U
A A
A u
U u
AA UU
AU U U-UU U UU
U A A-UAU A
U UU7AUXU UA U
5
Fig.23a
Aedes albopictus: mosquito
r228
55. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 3'half
~UUUA -A
700Q G U G -UA AUUU uU U-AA U
U--A oAC-
C-G -
GU U Gc
GUACA AAACAU UAACC GA AU GC
C II A
U A UUUGU GUUGG AUGA U
C .A A AUGACAA A CU
CA-U A U A A
A GAAUAAUUG AUGUUC%...,U AAUA
AA^UUA-U ~ ~ AA~U uA UU
CUU-O A-G A A;%A
'
~UUA A
A
AAUX
WG
UAA U
U C A A
AAAUUAU u u~~~~UU AU
65G A-UAUU
U A-U U A
U_ U-A U uCA-U U-A GA
G u u /1000~~~~~UA-
A5-U U- GAA-UU
UA U- A U U
UA U A AU UAA
G U U:AUUU U
G U AU UG A-U
A U U A%UUA-A-U U-AU UGAUAUA
GU Y1UA.CC-AUAGA UU A AC.U
A^G^^ AC AAA UUU U
U Us sUUAAUU-A U
UAGAA~ ~ AAUA U-
AAA A -CC AAA u
A A C^ GA AC1100~A
AUAAUUAAAGACGA G UUA GU
1 1 1 11111 II CGUAAUUuUUUUU AGA U
UAAUUUCU CU II* Ii I I C
A AUU GCGUUGAAAAAAUCU-U
u A % A U A A CG A
A G C%
G G C
ACU G
UA C UU AA~~~~~~~A
A U A~~~~~~~AA CU10
A u u G GUACGa G-U
A AUA G1UA0GG
lifilill1AUUAU GUAGGUGUU UU G
UAA p^A^U-AUUAUUCCUU GU
A AUU GCGUUAAUUUGAAAUUUGA
UUAU UA
A GU
U U~~~~~ A0oG0 UUAUG
Fig.23b
Aee aloitsUACGuito
r229
57. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 3'half
Fig.24b
Crithidla fasciculata kinetoplast over
Escherichia coli
r231
58. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 5'half
uu uUAAUC U AuA UUAAAUUUUU US UAU
AIII U ~ ~~~~I390A AAUUUUUGAA UA
CUUAUUUAUUUAAAUUGAA
U UAAUUUAACUACA AUGCUAA
A GUUGUGAUUUUUGUUUUUAG
U UAUAUUUUUAGAUAUUUAAU
U AAAAACAACGUUAAAUUUUAA AUAUUUAAUAUUUGUUAAAA
U AAAAAGUGACGAAUUCUAGUA AAAAAAAAUUAUUUUUAUAAA AUUUAUUUUUAAAAAUACAU
A AUAUAUUGUUAAUAAAAUUA
A UUA
u 592
u
AAA
u
u
G
U
U
U
A
U
G
A
U
u
u
u
u
UK Xc UUU^UGSUUUGUUUUUAUUU^
CaS.^ ' AAUUUUAUUUAUACAUAUUA
AG USGUUUASSAUUUSAUAUSU
uU U SAUUAUA^ACSAUUGUC _
UCUUGU GU 1 77
U U-200
U U
A AU
AU AUGUUG
~AU U U U U
UUs
AGUUUU
Fig.25a
Crithidia fasciculata
r232
59. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 3'half
uuCuAUUUAAUUA
A A A
u
C
uu
u uA C
UUU A A
700
U- U UU -A GU A
G UAA-UUA AU
U A
U-A AUA U
u
A A AUGCUU A UUCUu AUAAGUAGC
U AUUUGC AAGAC UUUAAGU
AA UA A G U
600 A -UU ~C UUUAA A
CA UUGU AA ACU
UA A A
GU U
u
A
UUA
U A
A- U
UA
C- UAC_G UU AA-U 900ooA U
A U
GGG C AG
G_c U-A
G U-A A
_AA-U -A U-A
A A UU:~A .AA- U ACU.GA
c GUU G A,
A A - U
u u A
A U -A A
A U-A A
UAAAUu~C-GU U A/-800 U U UAAGUU
AA C GC
U U -A
A AA C G
A UU A _CAAUUU AA U-A
AA% AA C G
UU A G A
A A c
AAAAUUAAAUA G A
111111111 ~~GCAUUAAUGAUUAAUUUAUA Au I I A
U Au U UGUAAAUC
U U G
A G U
1100' A U U
U UU U
U AGAU% UA
UG G-CA UA UUGUA G CA U A-U
G G-Cu
UUA AG U
GUU UA %U-A
A u
C-G
9
UG-CUAA3 AAU A
AA A UA AA
-C-U
C u
U UG
Fig.25b
Crithidia fasciculata
r233
60. Nucleic Acids Research
Secondary Structure of mitochondral 23S Ribosomal RNA: 5'half
AUU AAUCUGUUU A
UAhU
A if llio to
u
AAAUUUAACAA AAU AUA UA
u
Uu
A A
A
Auu
a
u
u
u
u
u
u
u
u
u
UA
u
u
u
A -U
u
A
U
A
U
A0
GU° u
u-
u-
U-
a-
A
ouu~~~~
391
-UAAUCUAAGUUAAUUUGAAU
AUUAAAAGUACAAGUAUAAU
UUGUAAUUCUAAAGUAUUUU
AAUGGUAUAUUUUUAOUAGO
UAAAUGAAAAGUAUAAAUGG
AUAUAACUUAAUAUUUAAUA
UUUGUUUAAU0AAAAGUAUU
UUAUUAUUAUAUUGUAUAGU
AUUAUUAUAGUGUAUAGUUU
UUUAAAAAUAUAAAAAUAUU
GUUAAUAAAAUUAUCO
-16016
AUUUUACCAAUUAAGAAGAA
UAUUAUAAUAAUGGGUGUCUUAUAUUUUAAAUAAAUAUUUAAAUU CoGUUAGUAAAUUUAUUAUUUGUAUUAUUUAUAUAAUAGGUGUAUUAUAUUUAA
AUUUUAAAUUUGUUGUUUUA
UAUUUAGAUACAUAUUUAUA
GAUUA AUA UAUUUAAAUAA
Fig.26a
Trypanosome txucei
r234
61. Nucleic Acids Research
Secondary Structure of mitochondral 23S Ribosomal RNA: 3'half
1000
LAu lap,u A %.
A A
A us
u
u UAAA %
A
3,
Fig.26b
Trypanosome brucei
r235
62. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 5'half
u ^Auuuu uU cA^UA^AU UAAAUUAUUU UA AICAA
A U
AA L"A;'G AAU AUAC
u
A 396U
A UAUAUAUAUAUAUUAAAUUG
A AAUAUUAAAAAUACAAAUUU
A AAUUUGUUAUUAAUACUAUU
A CUUUUAAAAAUGCAUAGAGA
U UAUAAUAUCACAUAUAAUUU
U AUUAUUUUAAUAUUUAAUAU
C UUGUUUAUACAAAAGUAACU
A UUAUUGAAUAAAAAGAAUUA
A UUUUUAUUAAUUAUUUUUUA
U AAAAUAUAAAAAUAUUGUUA
U AUAAAAUUAUCAA
C
A 6AUu
u
A
u
u
A
A
u
u
u
^^^
~
~~AU^AU^UUUGGUUUUAUAUUC s>U UAAAAAUAUUAUAUAUUUUA
U ~~~~~~~~~~GUUUU A AAUUU GU UGUU UUA
UG ~~~~~~UAUUUAGUUUAAUAUUUAUA
U UAUUAGUAAAUAAUAUAGAU
AUCUUG GU UUA
GAA
AU
A
U U
AUA%%UAAU
G~~~~~
UUU
Fig.27a
Leishmania tarentolae
r236
63. Nucleic Acids Research
Secondary Structure of mitochondrial 23S Ribosomal RNA: 3'half
700
AuUCUACAUA^ I
t.^ UU.AU-U
U GAA
UU
aUUU I}U
AG UAAA-U A A
A- UA U
AU A
AAA^UGCG UUCUU AUUOUAGC
U AA
UAUG AAGAU
UU
AAGA A AUAAA
U-A C U a
GAU u A
U U
A C A
AACG Uucu UA
UUAu u
U-A UAU
A _u u AU
A-UA
AG AG
0-AGC
PAA-U
G_
U-A
AA
U
-Ag U4-800
A
A-
U A A AU ^ 900 AX
AAA C_
-
A U A A A
,~~~~~A,^^ cu^
AAAAAU= u
AA A U U AAAG
A cA O
A A
AAAAAUAAAUA A u A
A UUU AAUUA U iA
,AUuAUUAAAu
0 UG000
A U U
U U%~~uU
A A GcA A
AAA t AAAA0 A~U
AUA~ ~ ~~~~~GAU A
A LIU .....ciU /U A 0-CAA
A 0UUAA UA
A u u~~~A
u A UU GUAA-Cu UG ~ C-
UtC -A
A UA% G A-U
A A ~ C
AUUA%%% UCU
Fig.27b
Leishmania tarentolae
r237
64. Nucleic Acids Research
Secondary Structure of archaebactenal 23S Ribosomal RNA: 5'half
Fig.28a
Hlococcue moffhua over
Escherdchia coi
r238
65. Nucleic Acids Research
Secondary Structure of archaebacteral 23S Ribosomal RNA: 3'half
Fig.28b
Halococcus morrhuae over
Escherichia cofi
r239
1720-
67. Nucleic Acids Research
Secondary Structure of archaebacterial 23S Ribosomal RNA: 3'half
2000
GG
AC GAG8 G A
-oaA A
0G:8 ACUCGUAG
,A 11111 A
3 C CUUGAGCAaA
AA-9
AX Ac-
A
6:8c cu
2900s,ccC °o Ac
c u GI
G a
AUU CAu
G-cA.G4
C-G
AC-G
Fig.29b
Halococcus morrhuae
r241
68. Nucleic Acids Research
Secondary Structure of archaebactenal 23S Ribosomal RNA: 5'half
cuGA A44,1AC GCUACCCU AA 160A0A off. Ill *g,t A
AUGGCAGoAAGCGAACAACOU
%-l U COACuAC G ~,UACUUA. - G A.
Fig.30a
Halobactenum halobium
r242
69. Nucleic Acids Research
Secondary Structure of archaebactenal 23S Ribosomal RNA: 3'half
3'
Fig.30b
Halobacterium halobium
r243
a
A
70. Nucleic Acids Research
Secondary Structure of archaebacterial 23S Ribosomal RNA: 5'half
-i200
Fig.31a
Methanococcus vanniellii
r244
71. Nucleic Acids Research
Secondary Structure of archaebacterial 23S Ribosomal RNA: 3'half
uCc
U-A
GC-C
8ac8CcAC
CUGC-G
GAA A A U-A
G G A U-A1890-UA U-A
C -¢ U G C-GCGU ~C A C-G
0UGAM ~~~~~~~~~~~~~AAA-UGA U UG-C G G
- CA A 2200-UA C-GA ACUA G~:A U G UA A UGUGU A:GU UAAA A A G A
UA AG-C UAA C GGUGG U
C a C A 11111 C
Uc-8G
i:UGUC U CCACC C
AAA a8 2G, 2000 G C A U
U U U A CCGI UG.CU CAGUG
U- ACAAACA ACGCC UUA AGCA
U IH A
cAUUUGU UGCGG U A
U-A
AGUU AGGA-
C
aA C''O, C A
G %ACCU C A
U AUG- A CG
AU a:8 c. CC-' UC
U A
A
18008:aCGCAGUGAUGACAC
CGAGGA%GU UCG ACCAGa- a,0 C C CCCUU G-C
IG* GGGUIIG* III U A-UG
UUAA
GCCUAACGGUUGA GGA GGAU
UCAAUGCCUC U CCA
GG~~~~~~~~~~A.U~~~ ~ ~ ~ ~ ~ ~ ~ ~ A A GUCAAA
AG G_u-:A
C UGAG
GGGU A &-AAGA-C ~~~~~~~~GUG G AC -CAAAC G-C-40
G_C0A GUG A- CC CUU
A A G A
_A G7~~~~~~230GGUA
G-C AU-AG L1 G-CZ S: 20AGCGGUGG
AA:aACA GC A G
CCA UA :GC A A
1750 AGAGA UCG C C CUU
uA 8 G u uG~~A
G A C
%A u `2300GUCCAGU%GAGGGZ8 U:AA 8:8C-G~~~~~CA
G-C U AAUAUU U QCG GCC CU A
A
c A-~~UA- GU CAAA
Ac~~~~~U G UUU U00aG:
A G GGCA GGC
CC%G~U G CUG
~~~GAGAA G C A',U ~AG, A U GACGAU A
AU
U-A~ ~ ~ ~ ~ GCGG A
A illi A C~~~~~ U GC G-
C UUUGGGCAGA UUCAGUGGAC AAUC GGGUCUGCG
A ,~~~~~ .~~~~. ..GAA UU GUC C G GI
%'LCGU IGU1A111C G~~~~~GAuGG C CG U1
A~~~~~~~ A~~~~ 2600 A
G A G 2805C~GG cCUU
G~~~~~~~~~~~~~~~~~
C GG~~~~~~~~~~~~~C,%A
C u 29 1
CA G
Fig.31b
Methanococcus vanniellii
r245
72. Nucleic Acids Research
Secondary Structure of archaebacterial 23S Ribosomal RNA: 5'half
Fig.32a
Methanobacterium thermoautotophicum
A:260 -314
r246
A
73. Nucleic Acids Research
Secondary Structure of archaebactenal 23S Ribosomal RNA: 3'half
3 uccc uuuuu
u
3u
.,UU .UC
2875
Fig.32b
Methanobacterium thermoautotrophicum
r247
74. Nucleic Acids Research
Secondary Structure of archaebacterial 23S Ribosomal RNA: 5'half
5'
Fig.33a
Desulfurococcus mobilis
A: 267-336
r248
75. Nucleic Acids Research
Secondary Structure of archaebactefial 23S Ribosomal RNA: 3'half
CCA
U-A
-c~~~~~~~~~U°c c
8~ uCoA a C-.
A A A A
a A A A -C
Fig.33b
Desulfurococcus mobilis
r249
76. Nucleic Acids Research
Secondary Structure of eucaryotic 23S Ribosomal RNA: 5'half
Fig.34a
Saccwhomyces cerevislse over
Escherichia coli
r250
77. Nucleic Acids Research
Secondary Structure of eucaryotic 23S Ribosomal RNA: 3'half
-70
B . .m
Fig.34b
Saccharomyces cerevlslae over
Escherichia coli
r251
-no6
79. Nucleic Acids Research
Secondary Structure of eucaryotic 23S Ribosomal RNA: 3'half
"GIUCGGGUAGUGAGGGCCUUGGUC A
AOGCGCCGOOCOUOCUUGUGGAC G A
UGCUUGGUGGOGCUUGCUCUGCUAG A - U
GCGGACUACUUGCGUGCCUU UUGU G-
AGACGGCCUUGGUAOGUCUCU U -UA
GACCGUCGOCUUGCUACAAUUA ACA
AUCAAC A C
G: 1945 - 2100 A c
AAA A A
A8 U8:o u a
G UG AU~
0 U AG-C
Al AG 8-A. ACUA U G
UA A GAAU2200-c u GC
U--AA G8'U AO A
as^^U-A A-cUoo^COGc^g c 30 u ^o-cs_AGUGH c
..|||| c ,AU ^a P ,
21Eio-&- o 81:-,f a 1I A
UAAAA
°^U CCA2490cUAA AG
AAAACA
AUUUC CUUGCOAG III
A U U CAAU UAUAG
AA~~~~~~~~UC°UUAG AUCC-OA o-
AAAGCAUUAU GUAA UUCAUUUUCC
A-U AG-CA U ACGUUCUAGC AGA
A U8CUU.COA CCCu U U C A^
A-U 8-8A 00 ~~~~~AC C CAAUUCAAGGUC C
aoocuto^U-A A G G CCAUUCGGGG A
ucuuucov A U
U-A A-1A8- CUGAUCOGG 'A'A
8GAGGCA88A A
UUGA :
0cA~U 2300 UuA CA
:
U CU'-A'UCAAUGC UAG AAAUA C UACUGAA : Uu UA
cAAG42AUA -o-H~~~~~~~~~~ACAAU
CUA~~ ~ ~ ~~~U~J1905 A:260 A
AC U V~~~~~~~~~ A
UA va~~~U GGGu.cG G U
'AU U UUG
a: Aa i
c8lAUGCG~ ~ ~ ~ ~ ~ ~ ~ ~ G~~~~cc~,: u Acc
CA G
UAGA 4 c20
AA AU-AA 87AG0CAA~~~~~~~~O G'AC 2U G, A
=X'COAAAc240 GA UA %AA
"
C :AA Cc80
UUCUUUGCUCCACACAAUAUAGAUG GC~~UA C- GA u UUAGUGCGGAUACGAAUAAGGCGUCCUUGGGGC ~~~~~~~AGUAGUC 0CCCAUU
GUCGCUGAACCAUAGCAGGCUAGCA
~ ~ ~ ~~GAUCGC%GAAUlU CAJUUCUAC
ACGGUGCACUUGGCGGAAAGGCCUU U CA
GGGUGCUUGCUGGCGAAUUGCAAUG A0UCAUUUUGCGUGG A U
K: 3148-3285 UA.8G?!.aGA
Fig.35b
Saccharomyces cerevisiae
r253
80. Nucleic Acids Research
Secondary Structure of eucaryotic 23S Ribosomal RNA: 5'half
D:2067 -- 2246
AGUCGAGAGUGGACGGGAGC
GGCGGGGGCGGCGGCGCGCG
CGCGCGUGUGGUGUGCGUCG
GAGGGCGGCGGCGGCCGCGGC
CGGCGGGGGUGUGGGGUCCU
UCC C CCGC CCC CCC CCC CA C
GCCUCCUCCCCUCCUCCCGC
CCACGCCCCGCUCCCCGCCC
CCGGAGCCCCGCGGAGCUAC
5.8S
'AX AGGCCGGCGCGCUCGCCGGC G
CC COAGOOUGGOAUCCCOCAGGCC d
UCCCCAGUCCOUCOCCGOGC elsu
ACCCOCCGOCCU
U
C
OG
CC: 1379- 1465
AO
GUAAACGGOUGGGGUCCGCGCAGUCCGCCCOGAGOAUUCAACCCGGCGGC
GGGuCCGGCCOUGUCGGCGGCCCGGCGOAUCUUUCCCOCCCCCCGUUCCU
CCCGACCCCUCCACCCGCCCUCCCUUCCCCCGCCGCCCCUCCUCCUCCUCCCCGGAOOGOGGCGGGCUCCGGCGGGUGCGGGGGUGGGCGGGCGGGGCCGG
GGGUGGGGUCOOCGGGGGACCGuCCCCCOGACCGGCGACCGGCCGCCGCC
OGGOCAC UUUCCAGOCOGUGCGCCGOAGCCGGCUCCOGACGCGCUGGGAA
GGC CCGOCGGGOAA^GGUGGC UCGGGGGGC CCCGUCCGOUC CGU CCGUCC UC
CUCCUCCCCCOUCUCCOCCCCCCGGCCCCGCOUCCUCCCUCGGGAGGGCG
CGC GGGUCGGGGCGGCGGC GGCGGC GGC GGUGGCGGCGGCGGCGGGGGCG
GCGGG:CCGAAACCCCCCCCGAGUGUUACAGCCCCCCCGGCAGCAGCACU
CGCCG AUCC GGCGC CoAGoGAGCGAGACCCGUCGCCGCGCUCUCCCCCCUCCCGGCGC CCCCCCGCCGGGAAUCCCCGCGAGGGGGGuCuCCCCCGG
CGC GGC GCC GC CGUCUCC UCCUCGGGGCGCCOCGCCCACC CC UCCC ACGGC
GCGACCGCUCUCCCACCCCUCCUCCCCGCGCCCCCGCCCCGGCGACGGGGG
GGGGUGCCGCGCGCGGGUCGGGGGGCGGGGCGGACUGUCCCCAGUGCGCCCCGGGC GGGUCGCGC CGU CGGGCC CGGCGGGAGGU UCU C UCGGGGC CA^CGC
GCGCG UCCCCCGAAGAGGGGGACGGCCGAGCGAGCGCACGGGGUCGGCGG
CGACGUCGGCUACCCACCCGACC
r254
5.8S
Homo sapiens B: 423-1295
Fig.36a
81. Nucleic Acids Research
Secondary Structure of eucaryotic 23S Ribosomal RNA: 3'half
G:2874- 3575
G00CUG0OUCGGUCOGOCUOG0GCG
COAAOCOOOOCUOGG0CCOCOCCOC
GOCU0GACOAOGCOCOCOCCCCCCC
CACOCCCOOGGCACCCCCCUCGC6O
CCCUCCCCCOCCCCACCCOCOCOCO
CCOCUCOCUCCCUCCCCACCCCC0 AA
CCCUCUCUCUCUCUCUCUCCCCCOC G
UCCCCOUCCUCCCCCCUCCCCOOGO A-uccccauccucceccuccccGoooA U37_
OA0COCCOCOUOCOOOCOCOGCGOG CJ 3700
O0GAOAAGOOUCOGOOCOOCAGGOO U A
CCGCOCGOCGOCCOCCOGGOCOGCC G -A
GCOGG0OCAOGUCCCCGCOGOGGG A U
GGCCCC6G6ACCC006606CCGOC A G
GGC606C6GGACUCUGGACOCOAGC CGG A A
CGOOCCCUUCCCOUOGAUCOCCCCA C C A
OCUOCOGCGOOCGUCOCOOCCOCCC Ge
CCOO0AGCCCGOCOOCOGCGCGGC U G
OC0CCCCCCACCCCCACCCCACGUC G _U GAC
UCOOUCOCOCOCOCOUCCCCUOGGG AU
GCOAOGCOOUCOGGCGGCGGCGOU G U c
COOCGGOCOOCGOOGGCOGOGCOGUU A u _
COUCCCCCCOCCCUACCCCCCCGGC A A0 8G ACUA
CCCOUCCOCCCCCCOUUCCCCCCUC GUA A
CUCCUCOOCOCGCGOCGCOCGCGGC I_
U-AA sGUGGCAGGCGOCOGAGOGGCCGCGGGC C_6 AG-C G
CGOUCCCCCCCOCCOOOUCCGCCCC U-A c G
COOOOCCOCOOUUCCGCGCOCGCCU A-U C-G G.'C
CGCCUCOOCCOOCOCCUAGCAOCCG 8 7 IUG-CG
AC A
u
GUAGU AAAUCA AUUUC UUAAG
G ^^ GU C
cIs Au *U
) A0UUU A A C GUAA
A-U
A-A U-A-300rUACC-CA4,AU
U-A 3600 A U%_. CU
C A A A
UAGG-AUUAUCGUCC A
U-dU^UACU^ G_ A
Er.AA UAGOC uGA-
2850
1AGC
A-^:AU390
18OG-C
A^U U
A A
CCAAQUU=j,
CGAAA6C%Cc
°°^UAGAA GG^
ACOOCAOCOCCOCGOAGCCUCO6UU OClii. III
"OCCUCO"AUAGCCOGUCCCCC6CC A0UAGUCACCAUU
UOUCCCCOCCOOCGOOCCOCCCCCC U U
CCUCCACOCOCCCCOCCGCOOOAGO U
OCOCOUOCCCCOCCOCOCOCCOOGA G
CCOGGUCCGUOCGG"GUGCCCUU A
COUCCU666AAACGOOGCOCOOCCO U.GAAAGOCGCCOCCCCCUCOCCCOU AGGs,CACGCACCOCACGUUCSUGGGAAC 4505S G~ ,cCA AU
CUOG
* uG
K:4689-4917 UUG%00Uo6ACG
GA- IC-G
UCAC G
,C-G
CA SU
cG CCC0AGCGGGU
UGGCGCCAAG C0 A
CC G CGU A
U C UGG C
G lit G
u UCACC G
G UC A U
A UACAA 2 AA
G8
A-CU H:4048-4128G G CC GGU GAGGC
88A-
X-U GGGGGGGC GA
C-GC GCCCAGAGGUA-U CUCUCGCUUC AGA
G-~U UGGCGCCAAG C A
G-YU CGCCCGCCCG _-CA U GCCGGOCGCG G-C
A- ACCCOCUCCO A-
Y-. GCG a-c,
j: GC Cf -5-A
A GU^UGYU A^CG^
A C-°A UA U
c
u
OCUUVUGGCGOCCAGCGU
I II C
UA%UUUUCOCUGCGCG UA
C
4400
Fig.36b
Homo sapiens
r255
83. Nucleic Acids Research
Secondary Structure of eucaryotic 23S Ribosomal RNA: 3'half
G: 2648-3260
GG:CUOGGUCGGUCGGGCUGOGGCGCGOAGCOGOOCUOGGCGCGCGCCGC
GGCUGGACOAGOCOCCOCCOCCCUC
UCCCACOUCCOOGGAGACCCCCCOU
CCUUUCCGCCCGGGCCCGCCCUCCC GUCa
CUCUUCCCCOCOGOOCCCCOUCOUC A 0oGCCCCOCOUCOUCOCCACCUCUCUUC G A C-O
CCCCCUCCUUCUUCCCOUCOGCOOO A-U CU
COGGUCOGGGGUCGGCGCGCGGCGc A- C U
GGOCUCCGGGCOOCOGGGUCCAACC U- C
CCoCoGGGGUUCCoGAGCGGAGoA .A
ACCAGCOGUCCCCOUGGGCOGOO AA
GGCCCGGACACUCGGOGGGCCGGCG A 0
GCGGCOOCOACUCUOGACGCGAGCC CG A
GOOCCCUUCCCOUGGAUCOCCUCAO CC tCC
cuocaocooocoucocooccocucc c_ c A
COGGOGAGCCCOOCGGuGCCGCGC§-o U
a
GGGUCCCCUCCCCOCOGGOCCUCOC G OU
UCCACCCCCCCAUCGCCUCUCCGA3G9A
UGUCCCGCGCGUGUG GCGGAAC A U t Cs:GG,CCOCOUCOOUOUUCCCCCOCCGGOU A AG 8 ACUA C
ccGccccCCoooccocGUuuuccG 0GUo A U GAAUAG Gc
cocoococccccoccucooccooco -c U_A u G A uAUG o °c 90
CCUAGCAoCCoAC c-G o-cC. u A oUGoC-39
u :G
~~~~~~UUCACC G
3300 a7 8 8 y GOu A AUAAAeAau ~~~~~~~~ACA
IAAAAAA *UGUU eGU AACA AUUUC UAA GUAUC H:372EU lUllo *l C CCGGUGAGG0C
(.) AAUUUGU AGUAGU CUCC AA U GGGGGCGA) A0- CA A GU-iA C F GCCCCGAGGGA- AU Au GCUCUCGCUU AGA
A-U C- C G CUGGCGCCAA CA
U--A 9ACOCGAU 3600-A-U GCGUCCGUCC A A
8c U:
oc
G.
uocooocouco
-cuCu°occo coocuo *o _ u ° =C-
U-A A-U Gu A cGCGCGUGCG GCCA A AUAGCGCC
c~~~~~A =°^ cAU A= ea u 4000
CGCUGCGGACG UA GC-AC ACCCGCUCCG 0:
A G7UGGCAG3:8 GCU 1GaVsC150lfA GGAUU A
a
.1
...... ~~CaG ACAG.o'-H A~A GUAGGC~~~CGOCUGA CU U-A
2600i-~ A A :2A C A AAC
A~U3500 u7 UG0 .
A-U~~~~~~~~~~~~~~~~~~~~~~~~ ~~~G-UUCa
AUAUC^OCtXOOOAUO CA
A GG*I
CCUCOU
CA G
A-UA-U UUCC
oucococcoctoocoococ,ooooucu 42 a5u c
CA A VUC A
'3:8 "U=AAACGA%GAAA GO cAl
GuCCCCCGCGGooucGGoCGcGGGUCU uu a
ooooccocccucucococoucoco (N u2° o AUG
o7
GUCCGGUGCGSASAGCCOUUCGUCu G A U~~~~~~~~~~~a7ula A A
UG@GAAACGGGUGCGCCGGAAAG ~ GCOAA AUA cU
GGGGccGcCCuCucGGu^cACCU U AGG Gcc ^ c
oGA.CGCACGUUCGU0U0GAACCuG A.'u'ouAU55,
K: 4379- 4604
39UGUU-AAUCGC
_8 AUUCoU a
UUCGUCC Al
A C
C-G
c-o
4700-t 8
A
- uc
UCAs-U ca,
I
AA
GU.A
C_u
u:U-A
. a
a
.
A
c_
o-¢
?"-c; FigM37b
Mouse
r257
85. Nucleic Acids Research
Secondary Structure of eucaryotic 23S Ribosomal RNA: 3'half
G: 2736-3330
ooCoGOGQUCoGUCoooCUOOOG
COCOAAOCOOOGCUOOOGCOCQc
CCOCOOCUGOACOAOOCOCCOCC
OCCCCCCUCCCACOUCCOOG"AO
AcccCcuccuuucccOCcooocc
CCCUCCCOUCUCCCCOCOUCGC OAAAccccoccoucccccocoucouco A A
ccousouccccuccucccucccu A- uc-
UCUUCCCCOGUCCOCOOGOOGOAC a- a
Goauc^^cciucocoacvcc N-A
;
ooOCoooUOcccoGocOcOcACOUCOAOCOCOOCCCCOOOGCCOA A
GUCCOUAACCCGCCGOCCCCC 3395
aoUaOOOOOOOOCCCOGACACCC CGO A Aa
GOOOOGOGCa COGOOCOAOA C G%
OCOOOCOUCOCOOCCOCUCCCOO O -0°
ACUCUGGACOCGAOCCOOOCCCU
OOAOCCCOOCOOAUCOCCCOGCO G 0 AU CGOA
~~~~~~~a
a
ooouuuuccuccoaccucouccu ° uU uo Cc gcC(cccccuucccccuccocaooouc A u ,_
CCU
CoUoCUCCCoCouucauu A A c- cu 3700-A
ccuccococoocoouuccccc _ 7oUAA^^o^^uOCuCOGUCCCCCOCAOA GAUA 0AGCCQuCoCCCoCCCOccCCCG U-0_ u- Au uouuuccc Cooccocccoccuco _- .o-c GU,,
u AoUoa c
"CGCOCOCUACOCAOCCOAC UIA ~ ~lfill aAccoccaccuocroccoacGU G o~c°o8'/ U UCACC a
A uG u
3500 GA UAA
UAAAACAA AUUUC 00UA 0Al38oe3A87G ) " III cG C UAOliii¢^ uu¢ A AOOuOAA CCOH:GU0AO38CAA( UOU ACUAUCUUCC A U OG°OOG OCGA
A0 C A COGU COC OCCCCOAGOOO
A-U O-A8. A. AG CUCUCOCUU AGAA-US.3A C||.@C A
AUc^^uO¢¢u^°O¢¢CCAcU ACOCOUCCOC A A
C"
A 2 A70 A-C0U | CCCOCc -C
CU-
A A AU A A= CA-CCAC a A
=ACUAC:°CUCC:Ga:8
GAA7GUGQU0CGGACCAOG u uGUA OGAUUCCO a
A-Uuu 0C C^ ^ U ^oAUU
'MC"COAACI 0 CAU 0U U=A GAGGC
AU 78 GOc&4ooL' 4000
uvococcoou^coocucccc A 0uou,4c¶uu .I II .I1 0
oUGo c
UG1
coooouccoouocvoooccouuc~~ ~ ~ ~ ~~~~~~1-o uLiugu
AUGooooccccccuccAUUUoAuAucAAAA^CAc"^¢^ a,10G,A,AU36000AC u
8
QUU=A aUUIF* AU cu 87
AAA UACA A00AaAA
U0GCCCCOOAUACCOGCUCCCCOU AOUAOUCAJCCAUA II C
COOGUCCOGUGCGAGAGCCAUGC 0~~~~~~~A GA
A-
OUCCCOOGAAACGGGU@CGGCC0O ~ ~ 41AUA^GAA UGUOCGCAACO
UAAOCCCCOCAACCUCUCCCCCOUC U GAU CAU 111 o
ACGCouUCCcAucoUUCOUGOAA A
%.C UAGUUOCOCAU
C"CUG 0'CG¶"oJAC0 000 0
Fig.38b
Rat
r259
87. Nucleic Acids Research
Secondary Structure of eucaryotic 23S Ribosomal RNA: 3'half
OGGGC UCOOUCOGOCUOOOOCG e A
CGAAOCOCOOCUOOOCCGCOCCOCO G A
GCUOOACOAAOOCOCCCCCOUOOCO A - U
CUCUUUCCCUCCUCCCOCCCCCCUC A-UC
UCUCUCCOOCCCCCCCUCOCOOOOU-
OCCOCOGOOOCOOOOOOOCOCGCOO G* A
GOCCOOAO^CGCCCOOCOOCOOCOA A U
CUCUOOACOCOCOCCOGOCCCUUCC A G
UGUOOAUCOCCCCAOCUOCOOCGCG AGO A A
COCCUCUCCCCCoCOCCOUCCCCCu a C
CCUOCOCCUCCCCCCOUCAOOGAOC C A
GOOOCOCGO OC GCGOOGOCOOCCGG _ U G-2900
GGCOOOCCCOOCCUCOOCCOOCOCC Au O
UAGCAGCUOAC o AU
G: 2432-2767 A U 7C
AAG ^G-C -'AcuAAAA A
UA AA
UA AACAAUUUC U-O
( ) 2ao^-i ouQ
CUCC
OGU^^OO^UUA G u
A- AAACAA AUUCA A -AAGUAA-U ... 3 - %ACoOCA III
Mc^^uocculncuo^AAUUUGU GUAe G UCC
A2 280 G-C A A
~~~% C
CA 8 _ A
2400 ~ ~ 0-
AGU U
GOUA
U0^^8 ^
2400 1'9~~~~~~0AC~~~~~~
3050AUAucAd
ACCOCAOCOCCOCOOAOCCUCOOUC * *11Ol
OOCCUCOOAUUAOCCOOCOCCCCCC AOUAOUC
CCOOOOOGCOCCOOCOOGCAOAOCCU
OCUCOCCUCOOOACC4OOOCOCOOA
COAAO4OOGOCCOCC VCUCUCCCO
CCo^OccccouooG o-3700K: 3856-4009 u
C AA C
o -UUCOUGAAA
cUUAOUCCAoC
A UC~
A -U CA GAA
OlU80 oUuuU3
~~~~G J
c~~~es~~
u-^~ ~ ~ ~ ~
CC-Q
UccA~ ~
fGuC,3150
CGA
8:8A
Fig.39b
Xenopus laevis
r261
89. Nucleic Acids Research
Secondary Structure of eucaryotic 23S Ribosomal RNA: 3'half
OGGCUGGUCUCUGGUGUCCGUCCCC A A
GAACCCGUCUUCUGCCUGCGUACUG U A
CuCGAUCUGCUCuCCCoUCGAAUGC A - U
OGOCCGCCGUCGOCCOGCCCGOGOA A:
COOCCOUGAACGCGCCCCUCGGOGG U-A
CCUUCCCCGUGCGUCOAACAQCCUA AA
C ~~~~~~~~~~~~~~~AC
G: 1940-2091 2CG2 A c
AA AUA
UC C AU
U t-a Cu
U-A G-CA
C UG AUG
C C
GC.U
AG UC
C-GAAACA C UA
G-C U-AAU C
U-A AG-C
U-GA -g GCSP,C-
U:A210 7 U- U^G C
UAAACAAAUUU U U A rC
C^~AAA 8GA-UGAuACGUCACAG UUAGG U A
UCA UCCU UCACU AA UC
A- C A
AA:819 :SA2300o_ ACcGCA<',C
-UA
a-A
a7GGAA u UACCC-AAAQ- U
GC G CGOCU,3A~~oo-UC
A U-C
A=U
UUCUCCOACOCCCOCCCCOACCCAC
GUUAGOOCOCACACCCCCAAOOCC
CUUGCCACCGUCCAAOCCCUUCCUU
CCoACGCGCCGCGGCCooCCoCCUU
CGAACUCCCUUCCCAACGGCUGC
K: 3142-3267
A A C
U AGUG¢ A
G I lilt A
UCACC
GAG A
A
U- CU
H:2505-2580G -U UCCOUGAGUC
U-A
U-AC GGAAGCGGGG
C-UC CCUAGCCCCC
A-U UCCUUUUGGC AGA
GU U UCUAAUOCCC C A
U-A A
A- U UAUCCCUCU
A-U GUCCGAUCCU G-C
A-U UOCOGA A-U
~XJAU U-C
8- Au^U UG
U-AC AU
UU GCA U-AACAA
UIAA -A 2800
A-:
IAAG
00 ~~~Aa A
C A C
° -U UUu
QAAUCAQF%UUAAA CAA
..II lo If OCUUGUBGCAOC UC
u
AUAGUC CCCAUU *11 I II C
AU u UAQJUUUUCGUUUCCU AU
A U
/
Cd4 ':UU
Fig.40b
Oriza sativa: RICE
r263
90. Nucleic Acids Research
Secondary Structure of eucaryotic 23S Ribosomal RNA: 5'half
1300 uA
GG 6666G AG66U...GAI''
C ..~~~~~~UA
cc
GUGGCAG-eCuC-A
UGGU AA ~ ~ ~~ 666 6 66
6;"C"CG
AA .6G
Azg 1800 u~~~~~~~68
6666~~~~~~~~~~~~~~~~~~~~~C,,Gu
UUAU_A666 666 66`C666
UA
/GC.CA A GC.C
U
GG8
C c~~~~~~~88
OG66 66 ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~~~~
GG-C G: uUA~~~~~~97
666 66~~~~~~~~~~~~~~~~~~~~~~~~~~~~
11666 6 1005AA UGA GCU 0C0UG
A, :U jp C
6666666 cu~~~~~~~~~~~~ 66
66'~~~~~~~F~~~~~ AU AA8If u"
6cA70AA0 AA.666 6666CUU U G G
666E666 GGGC6666666GCAAAC6 6U6GU
GU G1602c 165-6AuCA 6GU5.8AA3C
1006.~~~~6 ~ ~ Acu 66 666, C6 A3U86-6 66A5ZCGG6.It5
II 111 G A 6c 666666 =6 66'C
AA, ~ ~64o ~666u6 8 88 d6.6 6
U%6..~6,.J666666666UG66AC6UGCA66U.A
u A I UG
A
G~~~6 6 6 6?U66u CU., ~ ~ ~ ~ 666 6 ~ , .
6 666666666CUC 6.. 6 66 66
AAGG,1G66 6G
/~~~~~~~~~~~~uGUAU66 1400 6C6C666C6G.6666'A 6
88' CC666666666l666C66 6 6 6 6 6 6 6~~~~~~~~~
c: A7G-22A 68 8
I'CCAAC~~~~~-~-9 AA~~CC: 666 66 6
200-%"A 8.U :A A:~~~~~~~66 6 6 II,, 6666
66666666666666666666666666666 6A '66 66G6 l
c A
r00,,AGUAG~~~~~~~~~~~~66 0~68 6
,GAGAACG G~ ~~~~~~~~~~6 6>1 G6" I'llA
16 6 .6 .6
Fig.41a
Caenorhabditis elegans
r264
91. Nucleic Acids Research
Secondary Structure of eucaryotic 23S Ribosomal RNA: 3'half
UGGUUGGAACGGUUGOCCAGUUGGU
UGAUGCUUUUCCGGCOCAGUUCUOGU
CUGCUUGAUACUUUCGOOUUOAUUG
CGUACUAGUGAUUGUOCCUUGCUUGC
GGACGCUUUCUGOUUUGUUCUUUUA
CCUC GUUCUAUA UCCUGAUCGCU
CAUCUAAACAACCOUA
G: 2039-2204
G UU A AAA
G u ,
G-C
U
U-C
C
GG'A g_AUCG GGUACCGGA
uUCAAUGCCUAGA UCAAA
2000
AAAAUUUCUUGCUUCCCOGUGUCGG
GAGGCAUCUCUAUCUCOUGOCAACA
CGAGAGCUUAUGCCCUAUGUAUGOC
CUUUGCGUCGUAGUUAAUUCUUCUA
CGCUUGCCAACGCCAGAUCACUCUG
GUUCAAUGUCOGOOG
K: 3261-3399
3,
Fig.41b
Caenorhabditis elegans
r265
92. Nucleic Acids Research
Secondary Structure of eucaryotic 23S Ribosomal RNA: 5'half
E: 1622-1719
-A A GAUGA
,,,. a
CUCGAC
2033
26S
AAAQCACCCAOOOCOAOCCU
A UOCOOACCCCOCAA UOCU
CUCCUAACCOOOCUCUCOG
C-
B: 420-674
Fig 42a
Physarum polycephalum
r266
A*AACQ"AAAUCUAUACQWIACUC:UCGAAA ocuo"coaauucauc
CCCUGCCAUACOOCOCUCAOUAC. OCACAOCUGC"CUGAGGC"COCUO
G"AAGOUOACCUAACG"CAA UCUCOCUUACGG"GAG"CO"CAA"
ACACCG"Accocaa"ccuc UCCOUCUA"GCUUACACUCACOCOU"AU
G"UUCGCCCCAUAACCOU"GAC4UACACCOUGUCAGAOCUUAGUUUAC--- -- -- -- -- - -- - - -
93. Nucleic Acids Research
Secondary Structure of eucaryotic 23S Ribosomal RNA: 3'half
AGOCU:GGUGUCGCUGGCUGGGUA A
AOGCU OCOGGAUGUGCUUUAGUAA AA
UGOCCoAGOCoCUUUCGoGUGCCOA u
GAGCOUAACOOOCCOCUCGGGCU O-c
GAAAACUABAUCAUUGCGGAOGUUC U-A
OCCCOAGUGOUGAAAACCOOCACAC A A
CoCUAACAoCUAAC A c
G: 2103-2266 AAA c
GCA U A
UG t- 2
U AA U
U A CI
U AAAACAU 0U A
A A UAUGU
UUAGO
2300 A UA AA
S S-(CI ACGC
H: 2683-2914
U0CU0UAACIAACOAACOGA
ACCOCOUCCCUCU CACCGUA
AAAGOUOGGOOAAGOGAUAG
OCAAUCCAAAUUCUAGCOCU
UUCCOCOCUCAUACOACGAG
UU0GCUCCCCUG0GUGAGUA
CCOUGGAACCAC0A0CUGG0
CUUCCOAUCCGGCGAOUGC
U0UUUCCGC000AACCA0AG
ACGOUCUUCUCOOCCUCUOU
GOOCUUCAUGCCGOUACGUA
AUUGCGUGUAGC
3000
AGA
C A
G-C
C-G
GZUG-C
COCAAUCAAAGAUACOCUUGC UUUU
AAGUCUGGCAACOCOGUCUUUUACC
AUCAACA0CCAGUCAACU0A0CA0O
ACOCOAUGCAAA0A0OUC0AAAUUA
OCCCGUAAAAAGOUCAGUUCCUCGU
UAA0CCOCCCCCACOGGOOCAUCAA
COOCOCUCCOCCU0CAUCA0GCUCO
QUAUUC
K: 3496-3676
FigA2b
Physarum polycephalum
r267
u
a
95. Nucleic Acids Research
Secondary Structure of eucaryotic 23S Ribosomal RNA: 3'half
G:2124- 2342
GGGCAAAGUCAG2AGAAAACCGGAGG A
GCCAGUGUCCCUCCACGUGCAGCCG
AuCuuCAGAUUUGouuuAGCGCuC c u
GCCGCCUA:ACACGCAGUUAGCGACA
uucccoocouou^^c cc o_ c
CUCACUCuGGCACGooCCoGGCuuG c c
OCOGGUUCACOCUCOUCUUGUGCCG A 0
H: 2752-3012
H
K:3426-3541
GAAAAAGCGAGAAAAAGAUUAUCCG
GC AAAAC OGA C UC GGCCGACUAU
GGGOCCU GGCGAGCGGUGGOAGA
AGUAACGCCAUCACCGUGAGAUU
GAGAAGGGAACUCGCA
"6f"1 39 /59'"1"
CCC UCA ACGAAUACGC CACCUAUCAC
ACA GGA GOCAUGC 0CC CUAC UCGGC C
_UCA A GA AUA UUCA AGA UCACA A GG
AACAACGUCCCUCACCAAACGAGAG
OGGGGCACUAACGUCCCGAGGCGCAG
AACCAA GA GGCC UGA AAUUA CA AGC
UCAGOGACA
L: 3698-3906
AG'
UAAG%GCacu
uc 'cG 3650
c G
COCAA
Fig.43b
Crithidia fasciculata
r269
L'/
