Snippets 6
When looking at the previous “Snippets” it became apparent that the HIV-1, HIV-2 kissing loop sequences were somehow similar or derived from the same sequence.
If one compared HIV-1 where it actually “kissed” or docked, the sequence was CACACGUG, (and CUGAGG-but we will get back to this second sequence later) (Paillart et. al. PNAS 93, pp5572-5577, May 1996) and the HIV-2 kissing loop sequence was CCAUGG.
One could see they were similar to one another in the following way; they looked like a variant of CACACTGTG., and it was obvious that these sequences were found in many molecules, not associated with HIV disease.
How this important sequence was derived is unknown, but empirically it looks as though it was derived from a simple double stranded cross over of either DNA or RNA. For instance, if one went back to a simple double-stranded sequence of
CACACA or CACACACA and there was a crossover, you might
GTGTGT GUGUGUGU
Arrive at a sequence such as
CACACTGTGT
GTGTGACACA etc
Or CAGTGTG etc.
In the DNA world, it is known that CACACA and GTGTGT repeats exist as microsatellite DNAs and are used as markers for DNA analysis when trying to locate certain genes in a genome. But to continue…
Supposing, instead of CACACA and GTGTGT we hypothesized that there might be a parallel sequence derived from CTCTCTCT and GAGAGAGA….and, in keeping with the “cross over” we might look for some sequence like CTCTGAG or GAGAGTCT etc. It turns out, that in searching for this sequence it was found that not only does it occur, but in many instances it occurs in tandem, or overlapping with CACAGTG. Of course each “cross over sequence” was found at many different locations, but the places where they occurred in tandem or overlapping seemed to be important in the world of molecular biology.
But first a digression:
When looking for these “cross-over like” sequences some arbitrary, but useful, ground rules were set, figuring that the sequences would not always appear perfectly.
CACAGTGG could be made to CACAGTGtG.
I didn’t do any statistical analysis as to whether this was ok, but I usually worked with conserved sequences which meant that they were significant in the world of molecular biology.
The following are some of the locations where the sequences were found:
When antibodies are made from DNA there is usually more than one choice of a V gene, D gene or J gene to be transcribed.. The DNA sequences that are used for the immunoglobulin mRNA are brought together by an RSS (recombination signal sequence) which consists of a heptamer separated by either 12 or 23 bases from a nonamer.
The heptamer previously has been the sequence CACACGTG, or GTGTGCAC, but on further inspection I found that some Ig genes had another sequence nearby; a variant of CTCTCAG. What seemed important was, that the 12 mer for the J gene also carried the variant of CTCTCAG. Below is a detail of at least 7 V genes and one J Gene from the immunogolulin lambda light chain.
Homo sapiens
lambda locus on Chromosome 22 |
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Locus
NG-000002 |
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alignment
of 3' RSS for V genes |
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HEPTAMER |
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23 MER |
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NONAMER |
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IGLV8-61
(77316-77611) |
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C |
A |
C |
A |
G |
T |
G |
a |
t |
t |
t |
a |
a |
a |
c |
c |
t |
a |
t |
g |
a |
g |
g |
a |
a |
g |
t |
g |
c |
a |
A |
C |
T |
A |
A |
A |
A |
C |
C |
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IGLV6-5
(174370-174665) |
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C |
A |
C |
A |
G |
T |
G |
c |
t |
c |
c |
a |
g |
a |
c |
c |
c |
a |
t |
g |
g |
g |
g |
a |
a |
g |
t |
g |
a |
g |
A |
C |
A |
G |
A |
A |
A |
C |
T |
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IGLV11-55
(180233-180544) |
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C |
A |
C |
A |
G |
T |
G |
a |
g |
a |
c |
a |
g |
a |
t |
g |
a |
g |
g |
a |
a |
g |
t |
c |
g |
g |
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A |
C |
A |
A |
A |
A |
A |
C |
C |
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IGLV10-54
(19355-193650) |
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C |
A |
C |
A |
G |
T |
G |
c |
c |
t |
c |
a |
g |
g |
c |
c |
a |
g |
t |
g |
g |
g |
g |
a |
a |
g |
t |
g |
a |
g |
A |
T |
A |
A |
A |
A |
A |
C |
T |
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IGLV5-52
(297254-297570) |
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C |
A |
C |
A |
G |
T |
G |
c |
t |
c |
c |
a |
g |
a |
c |
c |
c |
a |
t |
g |
a |
g |
g |
a |
a |
g |
t |
a |
a |
g |
A |
C |
A |
A |
A |
A |
C |
C |
C |
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IGLV1-51
(301019-301314) |
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C |
A |
C |
A |
G |
T |
G |
c |
t |
c |
c |
a |
g |
g |
c |
c |
c |
a |
g |
g |
g |
g |
g |
a |
g |
g |
t |
t |
a |
t |
A |
C |
A |
A |
G |
A |
A |
C |
C |
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IGLV1-50
(305865-306163) |
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C |
A |
C |
A |
G |
T |
G |
c |
t |
c |
c |
a |
g |
g |
c |
c |
c |
a |
g |
g |
g |
g |
g |
a |
g |
g |
t |
t |
a |
t |
A |
G |
A |
A |
G |
A |
A |
C |
C |
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3'-5' |
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5' RSS
for J gene |
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12 MER |
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IGLJ1 5
(859945-859982) |
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G |
T |
G |
T |
C |
A |
C |
t |
g |
a |
c |
t |
c |
c |
g |
a |
g |
t |
c |
T |
G |
G |
T |
T |
T |
C |
C |
T |
G |
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Not only is the heptamer conserved at this particular site, but it seems to also carry the ctctgagag sequence which is complementary to at least one of the 5’RSSs for J. Also, please note in the first sequence of IGLV8-61, the hairpin sequence TTTAAA similar to the one found in Donor site 3632 of HPV 16. (see below) and serves to bring the CCTA(t)GAG sequence closer to the CACAGTG.
When looking for these sequences one could make a case that they were also found at
And the GT-AG rule
At the 5’ and 3’ junctions of introns, there are the following conserved nucleotides:
(5’)GT…………………………………………AG (3’) which are found 100 percent of the time.
The textbook consensus (Found on the ncbi.nlm website) sequence makes a pretty good case for the two “crossover” sequences discussed above.
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A/C |
A |
G |
5' |
G |
U |
A/G |
A |
G |
U |
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A |
C/U |
Pyr rich region |
n |
C |
A |
G |
3' |
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Molecular
Cell Biology ncbi.nlm.gov/books |
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C |
A |
G |
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G |
U |
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C |
A |
G |
u |
G |
U |
G |
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C/U |
C/U |
C/U |
C/U |
n |
C |
A |
G |
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Which are conserved sequences found at the excison sites of introns.
One could make an observation that the GU at the 5’ end of the intron might be part of a larger sequence; CAGUGU and AG is part of a sequence like CUCUCUnGAG or some pyrimidine variant thereof.
After looking at many sequences in these regions, it seemed, on closer inspection that although one could find a variant of CACGTGTG there was actually an overlap between the two sequences CACAGTG and CTCTGAG which might say more about the history of the junction rather than the enzymatic activity.
Below is listed the donor and acceptor sites of Human Papilloma Virus 16. Please note that donor sites 880 and 226 give rise to early protein transcripts. Donor site1302 gives rise to L1.
GT is the donor pair in red. Light brown highlights the sequences that may be derived from CTCTGAG and beige might be sequences derived from CAGTGTG. Of note; the sequences can be either 5’ to 3’ or 3’ to 5’. The sequences around the donor 880 are very similar to HIV-2 kissing loop. However, since no connection with disease etiology is implied, the sequence will be labeled H-2.
Donor 880 |
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c |
t |
a |
c |
c |
t |
g |
c |
a |
g |
G |
T |
a |
c |
c |
a |
a |
t |
g |
g |
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C |
A |
G |
G |
T |
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c |
c |
t |
g |
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a |
g |
g |
t |
a |
c |
c |
a |
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(t) |
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(a) |
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c |
c |
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g |
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a |
g |
g |
t |
a |
c |
c |
a |
a |
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g |
g |
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H-2 |
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The bases in the beige squares appear to be a variant of CAGtGT or ACaCATG and the light brown bases might be construed to be part of CtCTG(c)GAG
The second donor site might also have an overlap of the two different “cross-over” sequences.
Donor 226 |
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c |
t |
g |
c |
g |
a |
c |
t |
g |
a |
g |
G |
T |
a |
t |
a |
t |
g |
a |
c |
t |
t |
t |
g |
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a |
c |
t |
g |
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g |
g |
t |
? |
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c |
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g |
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(a) |
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g |
g |
u |
a |
u |
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Donor 1302 also shows a similar pattern if you are willing to accept that the bases in light brown were once part of a cTGAGAG sequence
Donor
1302 |
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g |
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t |
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a |
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G |
T |
a |
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a |
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g |
g |
g |
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(t) |
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t |
a |
g |
a |
a |
g |
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c |
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(g) |
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Donor 3632, involved in the transcription of a late protein does not really fit the above sequence scheme., but if one is willing to accept the TTT-AAA hairpin configuration, than GT is part of a ACAGtGTG sequence. The sequences in lavender and green are discussed below.
Donor
3632 |
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t |
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g |
G |
T |
g |
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g |
c |
t |
a |
a |
t |
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u |
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G |
T |
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In quick passing it was noticed that this junction resembled the sequences in the paper entitled “Frequent Use of the Same Tertiary Motif by Self-Folding RNAs”, (1995) The EMBO Journal, vol 14, #6, pp1276-1285 by Maria Costa and Francois Michel. And to quote from their paper…”A copy of the (CCUAAG…UAUGG) motif which is present in domain I of many group II introns is shown to interact with the GAAA terminal loop that caps domain V.”
Another place that these tandem sequences or overlapping sequences were observed was in a recent article by Stern-Ginosar et. al. who made a case that human cytomegalovirus codes for an miRNa (hcmv-miR-UL112) which targets MICB the stress-induced ligand of NKG2D. When it combines with MICB, the NK cell activating receptor, it decreases the NK cell’s ability to kill virus-infected cells and tumor cells. See below. Of note is that the miRNA has both “cross over “ sequences whereas the cell MICB does not.
Noam
Stern-Ginosar et. Al. " Host Immune System Gene Targeting by a Viral
miRNA", 2007, Science Magazine Vol 317 p.376 20 July |
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"MICB stress induced ligand of of the natural
kill cell activating receptor MKG2D and is critical for the NK cell killing
of virus-infected cells and tumor cells.". |
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3' UTR
MICB |
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miR-UL112 - SPECIFICALLY BINDS TO micb 3'utr |
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U |
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C |
A |
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C |
G |
G |
A |
C |
C |
U |
A |
G |
A |
G |
U |
G |
G |
|
|
G |
U |
G |
A |
A |
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G |
C |
C |
U |
G |
G |
A |
U |
C |
U |
C |
A |
C |
C |
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C |
A |
C |
U |
U |
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U |
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A |
G |
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MICB |
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miR-UL112 |
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U |
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G |
C |
A |
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C |
G |
G |
A |
C |
C |
U |
A |
G |
A |
G |
U |
G |
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G |
U |
G |
A |
A |
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G |
C |
C |
U |
G |
G |
A |
U |
C |
U |
C |
A |
C |
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C |
A |
C |
U |
U |
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U |
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A |
A |
G |
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MICA |
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In the following, I might be trying to show too much at once. So, by way of disclaimer, I do not mean to demonstrate that the HNF binding site is somehow related by way of biological action to the MIRs listed underneath it. What is listed are the tandem sequences that seem similar. (The mir sequences are from Matthew Jones-Rhoades and David P. Bartel, “Computational Identification of Plant micro RNAs and Their Targets Including a Stress-Induced miRNA”, (2004) Molecular Cell vol 14, 787-799)
Gulam et.
Al. Interaction between STAT-3 and HNF-3 Leads to the Activation of Liver
Specific Hepatitis B Virus Enhancer 1 Function Journal of Virology 2002 2721
2729 |
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Cytokine
mediated |
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T |
A |
C |
A |
A |
G |
G |
C |
C |
T |
T |
T |
C |
T |
A |
A |
G |
T |
A |
A |
A |
C |
A |
G |
T |
A |
C |
A |
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Stat 3
binding |
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HNF
Binding site |
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c |
u |
a |
g |
u |
u |
a |
c |
g |
C |
U |
A |
G |
G |
G |
A |
A |
A |
C |
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MIR 393A |
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mir 393a
binds with DNA of F-box proteins |
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ASD2
Copper superoxide dismutase target of 398a |
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|||||||||||||
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g |
c |
g |
g |
g |
u |
g |
a |
c |
C |
U |
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G |
G |
g |
A |
A |
C |
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mir 398 |
u |
u |
c |
c |
c |
a |
c |
u |
g |
g |
a |
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c |
u |
c |
u |
u |
g |
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mir
phosphate transporter |
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mir 399c |
|
|
G |
U |
C |
C |
C |
G |
U |
U |
U |
A |
G |
A |
G |
G |
A |
A |
A |
C |
G |
U |
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3' |
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||
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u |
u |
a |
g |
a |
g |
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a |
a |
c |
g |
u |
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c |
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c |
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MIR 399A |
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||
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G |
U |
C |
C |
C |
G |
U |
U |
G |
A |
G |
A |
G |
G |
A |
A |
A |
C |
G |
U |
c |
c |
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But |
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It became clear that these similarities were being found in promoter sites, because the action of the miRNAs was at the 5’untranslated regions of mRNA. So I decided to look at promoter sites. But first, one more look at viroids:
If we take another look at the conserved central region of viroids we can show that what looks like the HIV 2 kissing loop sequence seems to have the overlapping sequences CTGAGAG and ACACTG.
Diener,
Theodor, Subviral Pathogens of Plants: Viroids and Viroid Like Satellite
RNAs, (1991)FASEB J 5: 2808-2813 |
||||||||||||||||||
from figure #3 Central Viroid
Region Upper Strand PSTVd Group Palindrome |
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|
5' |
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3' |
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a |
c |
c |
|
t |
g |
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c |
|
t |
g |
g |
a |
g |
|
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|
PstVd |
G |
G |
A |
A |
A |
C |
C |
|
U |
G |
G |
A |
G |
C |
|
|
|
|
TASVd |
G |
G |
A |
A |
A |
C |
C |
|
U |
G |
G |
A |
G |
|
|
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|
|
TPMVd |
G |
G |
A |
A |
A |
C |
C |
|
U |
G |
G |
A |
G |
C |
|
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|
|
CEVd |
G |
G |
A |
A |
A |
C |
C |
|
U |
G |
G |
A |
G |
C |
|
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|
|
CLVd |
G |
G |
A |
A |
A |
C |
C |
|
U |
(C) |
G |
A |
|
C |
C |
G |
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A |
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|
HIV2 KL |
G |
G |
A |
A |
A |
C |
C |
A |
U |
G |
G |
A |
G |
C |
C |
G |
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These overlaps also occur in ASBVD, and it is important to note that the ribozymal conserved sequence CTGATGAG might also be a region of overlap between the two sequences, ACACTG and CTGAGAG.
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A |
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C |
G |
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C |
G |
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A |
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U |
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A |
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C |
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A |
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U |
G |
U |
U |
C |
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G |
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A |
C |
A |
A |
G |
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5' |
G |
A |
C |
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C |
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C |
T |
G |
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U |
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A |
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G |
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G |
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U |
A |
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Although, not quite as clear, CSVd viroids seem to have remnants of the overlap too.
Haseloff
and Symons, Chrysanthemum Stunt Viroid: Primary sequence and Secondary
Structure (1981) NAR 9 (12) 2741-2751 |
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from fig. 1 |
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4 |
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19 |
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G |
A |
C |
T |
(T) |
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A |
C |
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T |
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T |
G |
T |
(G) |
G |
T |
T |
C |
CSVd.16,
CSVd.15, CSVd.01 |
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G |
A |
C |
T |
C |
C |
A |
C |
G |
T |
G |
T |
G |
T |
C |
G |
T |
T |
C |
HIV-1 KL
complement |
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5’ Untranslated region of ORFs.
In 1987 Dr. Marilyn Kozak assembled a compendium of
sequences of 5’ UTRs before the ATG codon in a number of unrelated protein
ORFs. [(1987) An Analysis of
5' Non Coding Sequences from 699 Vertebrate Messenger RNAs, NAR Vol 15 #20 ]
After going through them all and looking for tandem or overlapping “crossover sequences” I found that about 17% of them fit the criteria of the two “crossover” sequences together, and they appeared vaguely similar to the sequences found in RSSs. I’ve included the original references listed in Dr. Kozak’s article, but have not checked them all. Also if the sequence looked like H2 or H1 I included that also.
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Sequence
for the initiation of translation ((Kozak Consensus Sequence) |
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g |
c |
c |
g |
c |
c |
a/g |
c |
c |
a |
t |
g |
g |
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c |
a |
c |
c |
a |
t |
g |
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a |
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Acetylcholine
receptors |
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#2 |
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Boulter
'86 Nature 319, 368 |
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alpha
nicotinic, rat, neural |
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c |
g |
g |
g |
t |
c |
t |
t |
a |
g |
a |
c |
A |
T |
G |
g |
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#4 |
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Shibahara
'85 EJB 146, 15 |
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gamma
nicotinic, hu muscle |
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a |
g |
c |
t |
g |
a |
g |
g |
c |
a |
c |
c |
A |
T |
G |
c |
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Actins |
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#10 Hu
'86 MCB 6, 15 |
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Alpha
skeletal, mouse |
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a |
a |
a |
c |
t |
a |
g |
a |
c |
a |
c |
c |
A |
T |
G |
t |
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Aldolase |
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#39 |
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Burgess
'85 JBC 260, 4604 |
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aldolase
B, ch |
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c |
a |
a |
t |
a |
a |
g |
t |
c |
a |
c |
c |
A |
T |
G |
a |
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ADH |
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#32 |
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Ikuta '86
PNAS 83, 634 |
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alpha
subunit, hu class I |
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g |
a |
c |
a |
g |
a |
a |
t |
c |
a |
a |
c |
A |
T |
G |
a |
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#34 |
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Hoog '86
EJB 159, 215 |
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gamma
subunit, hu Class I |
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g |
a |
c |
a |
g |
a |
a |
t |
c |
a |
a |
t |
A |
T |
G |
a |
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#90 |
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Putkey
'83 JBC 258, 11864 |
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Calmodulin
ch |
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c |
c |
g |
a |
g |
c |
c |
a |
c |
c |
A |
T |
G |
g |
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#95 |
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Ferrari
'87 JBC 262, 8325 |
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Calcyclin
(S100-related) human |
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a |
g |
c |
c |
c |
t |
c |
a |
g |
c |
c |
A |
T |
G |
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#55 |
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Davies
'84 JBC 259, 8063 |
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Antifreeze
protein flounder |
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c |
a |
a |
g |
t |
t |
c |
t |
a |
a |
a |
A |
T |
G |
g |
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#57 |
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Haraguchi
'87 PNAS 84, 412 |
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Arginase,
hu liver |
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a |
a |
g |
t |
g |
t |
c |
a |
g |
a |
g |
c |
A |
T |
G |
a |
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#73 |
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Shull '86
JBC 261, 16788 |
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ATPase
h,K, rat |
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c |
a |
c |
c |
t |
a |
g |
c |
c |
a |
c |
c |
A |
T |
G |
g |
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#84 |
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Jonas '85
PNAS 82, 1994 |
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Calcitonin,
hu |
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c |
a |
g |
a |
g |
a |
g |
g |
t |
g |
t |
c |
A |
T |
G |
g |
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#102 |
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Yu-Lee,
86 NAR 14, 1883 |
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alpha
casein rat |
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a |
t |
c |
t |
t |
a |
g |
c |
a |
a |
c |
c |
A |
T |
G |
a |
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|||
beta-casein
rat Jones '85 JBC 260, 7042 |
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g |
a |
c |
t |
t |
g |
a |
c |
a |
g |
c |
c |
A |
T |
G |
a |
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#105 |
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gamma
casein rat |
|
Hobbs '82
NAR 10 8079 |
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g |
a |
t |
c |
a |
a |
g |
t |
a |
a |
c |
c |
A |
T |
G |
a |
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COAGULATION
FACTORS |
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#115 |
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||||
Factor
VII, hu (coag) |
Hagan '86
PNAS 83, 2412 |
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a |
g |
a |
g |
a |
t |
t |
t |
c |
a |
t |
c |
A |
T |
G |
g |
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#123 |
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||||
procollagen
alpha2 ch Vogeli '81 PNAS 78, 5334 |
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? |
|
||||||||||||||||
t |
a |
g |
c |
a |
a |
g |
t |
a |
g |
a |
c |
A |
T |
G |
c |
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#120 |
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Protein
C, hu |
|
|
Plutsky
'86 PNAS 83, 56 |
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||||||||||||
a |
g |
t |
g |
c |
c |
t |
c |
c |
a |
g |
a |
A |
T |
G |
t |
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#121 |
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Protein S
hu |
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Hoskins
'87 PNAS 84, 349 |
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g |
c |
g |
c |
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t |
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c |
g |
a |
a |
A |
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G |
a |
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#123 |
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proCollagen,
alpha 2 (I), ch |
Vogeli,
'81 PNAS 78 5334 |
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a |
g |
c |
a |
a |
g |
t |
a |
g |
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A |
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c |
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#124 |
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proCollagen,
alpha1 (I), ch Yamada '83 JBC 258, 14914 |
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a |
a |
t |
a |
t |
t |
t |
a |
g |
a |
c |
A |
T |
G |
t |
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complement
components and modulators: |
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#127 |
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preC1r
hu Journet '86 Bio.
J. 240, 783 |
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g |
g |
g |
c |
c |
t |
t |
g |
a |
g |
a |
a |
A |
T |
G |
t |
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#128 |
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pre C2hu |
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Bently
'86 Bio J. 239,339 |
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a |
g |
g |
g |
a |
g |
g |
a |
c |
a |
c |
c |
A |
T |
G |
g |
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#131 |
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preC4,
mu Nonaka '86 PNAS 83, 7883 |
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g |
a |
t |
c |
c |
t |
c |
c |
a |
g |
c |
c |
A |
T |
G |
c |
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#142 |
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alpha
B-Crystallin, ha Quax-Jeuken '85 PNAS 82, 5819 |
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c |
a |
c |
c |
t |
a |
g |
c |
c |
a |
c |
c |
A |
T |
G |
g |
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#145 |
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beta
B1-Crystallin, rat Dunnen '86 PNAS 83,
2855 |
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g |
c |
a |
t |
c |
a |
g |
a |
a |
a |
c |
c |
A |
T |
G |
t |
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g |
a |
a |
a |
c |
c |
a |
t |
g |
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H2 |
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#155 |
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Cytochrome
C oxidase IV bovine Lomax '84 PNAS 81 6295 |
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g |
g |
t |
g |
g |
c |
a |
t |
c |
a |
g |
a |
A |
T |
G |
t |
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Cytochrome
P-450 Proteins |
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#160 |
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P450c21,
human Higashi '86 PNAS 83, 2841 |
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g |
g |
g |
c |
g |
t |
c |
t |
c |
g |
c |
c |
A |
T |
G |
c |
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#163 |
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P-450
(M-1), male rat liver |
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g |
a |
g |
a |
a |
g |
g |
c |
t |
g |
c |
c |
A |
T |
G |
g |
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#164 |
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P-450 MC
rat Yabusaki '84 NAR 12, 2929 |
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g |
c |
c |
a |
c |
c |
t |
a |
g |
a |
t |
c |
A |
T |
G |
c |
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#169 |
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P-450s,
ch Hobbs '86 JBC 261, 9444 |
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c |
c |
t |
c |
t |
g |
c |
c |
c |
a |
c |
c |
A |
T |
G |
g |
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#172 |
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Cytokeratin
Endo A, mu Vasseur '85 PNAS 82, 1155 |
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a |
g |
a |
c |
t |
t |
c |
a |
c |
c |
a |
A |
T |
G |
t |
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#173 |
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Cytokeratin
Endo B, mu Singer '86 JBC 261, 538 |
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t |
c |
t |
c |
c |
a |
g |
a |
c |
a |
a |
g |
A |
T |
G |
a |
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#174 |
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Cytokeratin-Xp
Franz '86 PNAS 83, 6475 |
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c |
a |
c |
a |
g |
c |
t |
c |
c |
a |
c |
c |
A |
T |
G |
t |
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#184 |
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Endothelial
cell GF, hu Jaye '86 Science 233,541 |
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a |
g |
c |
t |
g |
c |
t |
g |
a |
g |
c |
c |
a |
T |
G |
g |
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#185 |
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preproEnkephalin
A, hu Noda '82 Nature 297, 431 |
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a |
g |
c |
g |
t |
c |
a |
a |
c |
t |
c |
c |
A |
t |
g |
g |
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# 186 |
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preproEnkephalin
B hu Horikawa '83 Nat 306 611 |
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t |
g |
c |
t |
g |
a |
g |
a |
c |
a |
g |
g |
A |
T |
G |
g |
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#188 |
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Enolase,
non-neuron, rat Sakimura ' 85 NAR 13, 4365 |
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c |
a |
g |
a |
a |
c |
t |
t |
c |
a |
c |
c |
A |
T |
G |
g |
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#193 |
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Epoxide
hydrolase, rat Falany'87 JBC 262, 5924 |
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c |
a |
g |
t |
c |
a |
g |
g |
a |
g |
t |
c |
A |
T |
G |
t |
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#202 |
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Ferritin,
L-chain rat Leibold '87 JBC 262, 7335 |
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t |
c |
c |
g |
g |
a |
t |
c |
a |
g |
c |
c |
A |
T |
G |
a |
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#208 |
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PreFibrinogen-gamma,
hu Rixon '85 Biochem 24, 2077 |
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c |
a |
c |
t |
c |
a |
g |
a |
c |
a |
t |
c |
A |
T |
G |
a |
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#209 |
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PreFibrinogen
alpha rat Crabtree '85 JMB 185, 1 |
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c |
a |
a |
t |
c |
a |
g |
a |
a |
a |
c |
t |
A |
T |
G |
c |
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g |
a |
a |
a |
c |
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a |
t |
g |
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#210 |
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PreFibrinogen
beta rat Fowlkes '84 PNAS 81, 2313 |
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a |
a |
a |
t |
c |
t |
g |
a |
a |
a |
c |
c |
A |
T |
G |
a |
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g |
a |
a |
a |
c |
c |
a |
t |
g |
a |
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g |
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#213 |
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Fibronectin,
hu Dean '87 PNAS '84, 1876 |
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c |
a |
c |
c |
g |
t |
c |
t |
c |
a |
a |
c |
A |
T |
G |
c |
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#211 |
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preFibrinogen-gamma
rat Morgan '87 NAR 15, 2774 |
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c |
a |
c |
c |
c |
a |
g |
a |
c |
a |
c |
t |
A |
T |
G |
a |
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#223 |
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GAP-43,
rat neuronal Karns '87 Science 236, 597 |
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g |
a |
a |
g |
a |
t |
a |
c |
c |
a |
c |
c |
A |
T |
G |
c |
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#233 |
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duck,
adult, major alpha a Erbil '82 Gene 20, 211 |
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g |
g |
a |
g |
c |
t |
g |
c |
a |
a |
c |
c |
A |
T |
G |
g |
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g |
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a |
a |
c |
c |
a |
t |
g |
g |
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H2 |
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#235 |
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a |
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Hu fetal
gamma (beta globulin) Slightom '80 Cell 21, 627 |
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a |
g |
t |
c |
c |
a |
g |
a |
c |
g |
c |
c |
A |
T |
G |
g |
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#238 |
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rabbit
embryonic beta globin (beta3)Hardison '81, JBC 256,11780 |
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#252 |
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gamma
glutamyl transpeptidase Laperche '86 PNAS 83, 937 |
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g |
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a |
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#256 |
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Glutathione-S-transferase
Yb1 subunit Ding '85 JBC 260, 13268 |
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#259 |
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GAPDH, hu
Tso'85 NAR 13, 2485 |
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#265 |
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Human
Growth Hormone De Noto'81 NAR 9, 3719 |
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#271 |
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Heat
shock 70K human Voellmy '85 PNAS 82, 4949 |
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#272 |
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Heat
shock 27K human Hickey '86 NAR 14, 4127 |
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A |
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#274 |
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Heat
shock 70K ch Morimoto '86 JBC 261, 12692 |
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a |
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A |
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Histocompatibility
antigens |
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#288 |
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Class II
(Hu) histocompatibility Antigen Lawrence '85 NAR 11, 7515 |
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c |
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#290 |
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Class I
(Mu): H-2K La Lanne '83 NAR 11, 1567 |
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G |
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#296 |
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Class II
(mu): E(beta2-chain) Braunstein '86 EMBO 5 2469 |
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t |
c |
t |
c |
c |
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A |
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G |
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#327 |
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Ig
L-chain, kappa-III, hu Klobeck '85 NAR 13, 6499 |
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c |
c |
c |
a |
g |
a |
g |
g |
a |
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c |
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A |
T |
G |
g |
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g |
g |
a |
a |
c |
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a |
t |
g |
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H2 |
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#337 |
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alpha
1-antichymotrypsin, hu Chandra '83 Biochem
22, 5055 |
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g |
c |
a |
g |
a |
g |
t |
t |
g |
a |
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a |
A |
T |
G |
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#341 |
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Alpha 1
antiTrypsin, hu liver Cilibarto '85 Cell 41, 531 |
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a |
g |
t |
g |
a |
a |
t |
c |
g |
a |
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A |
T |
G |
c |
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#348
Insulin-like GF I human Rotwein '86 PNAS 83, 77 |
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c |
t |
t |
c |
a |
g |
a |
a |
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A |
T |
G |
g |
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#349
Insulin-like GF II, rat Soares '86 JMB 192, 737 |
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c |
t |
t |
c |
a |
g |
g |
t |
a |
c |
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A |
T |
G |
g |
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a |
g |
g |
t |
a |
c |
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a |
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g |
g |
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H2 |
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#358
Gamma Interferon, rat Dijkema '85 EMBO 4, 761 |
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a |
g |
c |
t |
c |
t |
g |
a |
g |
a |
c |
a |
A |
T |
G |
a |
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#364
Keratin-I 50k, hu Marchuk '85 PNAS 82, 1609 |
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c |
t |
c |
c |
t |
c |
t |
g |
c |
a |
c |
c |
A |
T |
G |
a |
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#365
Keratin, 67k, hu Johnson '85 PNAS 82, 1896 |
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c |
t |
c |
t |
a |
a |
g |
t |
c |
a |
a |
c |
A |
T |
G |
a |
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#366
Keratin-II 56k, hu Tyner '85 PNAS '82
4683 |
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a |
t |
c |
t |
c |
t |
g |
g |
a |
a |
c |
c |
A |
T |
G |
g |
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#367
Keratin-I 47k, mu Knapp '86 NAR 14, 751 |
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c |
c |
t |
c |
t |
c |
g |
c |
a |
g |
c |
c |
A |
T |
G |
a |
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#369 Keratin B2A, sh Powell '83 NAR 11, 5327 |
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a |
c |
t |
c |
c |
t |
g |
a |
c |
a |
c |
c |
A |
T |
G |
g |
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#377
LDH-C, mu Sakai '87 Bioch. J. 242, 619 |
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g |
t |
a |
a |
g |
g |
c |
t |
c |
a |
a |
c |
A |
T |
G |
t |
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#382
Lipase, Rat hepatic Komaromy '87
PNAS 84, 1526 |
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a |
a |
g |
a |
c |
g |
a |
g |
a |
g |
a |
c |
A |
T |
G |
g |
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#394 apo
Lipoprotein C-II hu Wei '85 JBC 260, 15211 |
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t |
c |
t |
c |
t |
g |
g |
a |
c |
a |
c |
t |
A |
T |
G |
g |
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#403
Interleukin-1beta, hu Clark '86 NAR 14, 7897 |
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t |
c |
t |
g |
a |
a |
g |
c |
a |
g |
c |
c |
A |
T |
G |
g |
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#410
alpha2-Macroglobulin, hu Kan '85 PNAS 82 2282 |
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t |
c |
t |
t |
t |
c |
t |
g |
c |
a |
a |
c |
A |
T |
G |
g |
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? |
|||
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#411
alpha2-Macroglobulin, rat |
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|||||||||||
c |
c |
t |
t |
t |
c |
c |
g |
c |
a |
g |
c |
A |
T |
G |
g |
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? |
|||
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#412
Malate dehydrogenase mu Joh '87 Biochem 26, 2515 |
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c |
c |
c |
g |
c |
c |
c |
t |
a |
g |
c |
c |
A |
T |
G |
c |
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#413
Malic enzyme, mu Bacchi '87 JBC 262,
1558 |
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c |
c |
g |
g |
t |
g |
c |
c |
a |
g |
c |
c |
A |
T |
G |
c |
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#417
menadione reductase, rat Robertson '86 JBC 261, 15794 |
|
|
|||||||||||||||||||
a |
c |
t |
t |
c |
t |
g |
g |
a |
g |
c |
c |
A |
T |
G |
g |
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#419
Metallothionein IB, hu Heguy, '86 MCB 6, 2149 |
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c |
t |
t |
g |
g |
c |
t |
c |
c |
a |
c |
a |
A |
T |
G |
g |
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#420
Metallothionein IF, hy Varshney'86 MCB 6 2149 |
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c |
c |
t |
c |
g |
g |
c |
t |
t |
g |
c |
a |
A |
T |
G |
g |
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#421
Metallothionein II hu Karin '82 Nature 299, 797 |
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|
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c |
t |
t |
c |
a |
g |
c |
t |
c |
g |
c |
c |
A |
T |
G |
g |
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#423
alpha microglobulin, hu Traboni '86 NAR 14, 6340 |
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#433
Myoglobin, hu Weller '86 MCB 6, 4539 |
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#434
Myoglobin mu Blanchetot '86 EJB 159, 469 |
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#439
Myosin L-chain 3, mu Robert '84 Cell 39, 129 |
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#440
Myosin L-chain 2, rat skel Nudel '84 NAR 12, 7175 |
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#442
L-chain 3, ch. Skel Nabeshima '82 NAR 10 6099 |
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#445
Neruoleukin, mu Gurney '86 Sci 234, 566 |
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#450
Nerve GF beta Submax. Gland Selbey'87 MCB 7, 3057 |
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Proto
oncogenes |
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#481rho-ras
related Yeramian '87 NAR 15, 1869 |
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#482 C-sis,
hu PDGF2 Rao, '86 PNAS 83, 2392 |
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#489
preproOpiomelanocortin, XP Martens '87 EJB 165, 467 |
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#492
Ornithine decarboxylase Gupta '85 JBC 260, 2941 |
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#494
Ovalbumin, chicken Mc Reynolds '78 Nat
273, 723 |
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#495
Ovoinhibitor, ch Scott'87 JBC 262, 5899 |
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#519
u-Plasminogen activator hu Riccio '85 NAR 13, 2759 |
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#521
Platelet factor 4 rat Doi '87 MCB 7, 898 |
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#527
ptrPlacental lactogen, hu Saunders '83
JBC 258, 3787 |
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#535
Prostatic BP, C2chain, rat Delaey '87 NAR 15, 1627 |
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#547 PDI
(disulphide isomerase ) rat Edman '85 Nature 317, 267 |
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#549
Proteoglycan 19 core protein, hu Krusius '86 PNAS 83, 7683 |
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#550
Proteolipid protein, mu Hudson '87
PNAS 84, 1454 |
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#551
Pulmonary surfactant, hu White '85 Nature 317, 361 |
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#552
Pyruvate kinase, ch Lonberg '83 PNAS 80, 3661 |
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Receptors |
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# 557beta 2 adrenergic, hu Kobilka '87 PNAS
84, 46 |
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H-1 KL |
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#560
receptor for asialo L2 chain, rat McPhaul '87 MCB 7, 1841 |
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a |
g |
g |
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#569
Receptor for LDL, hu Sudhof '85 Science 228, 815 |
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a |
g |
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c |
t |
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#572
Receptor for Progesterone, ra Loosfelt '86 PNAS '83, 9045 |
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t |
t |
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a |
g |
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#575
Preprorenin, hu fukamizu '86 Gene
49,139 |
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a |
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t |
g |
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g |
g |
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A |
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G |
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#584
Ribophorin II, hu Crimaudo '87 EMBO 6, 75 |
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t |
g |
c |
t |
c |
g |
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a |
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a |
A |
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G |
g |
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#608 2-5
Synthetase, Mu Ichii '86 NAR 14, 10117 |
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t |
c |
c |
a |
g |
a |
c |
t |
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a |
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A |
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G |
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#642
Thymosin-beta 4 rat Horecker '84 PNAS 81 2295 |
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c |
t |
t |
c |
c |
a |
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c |
a |
a |
c |
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A |
T |
G |
t |
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#654
dIF2, tranlation factor rat Ernst '87 JBC 262, 1206 |
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a |
t |
a |
c |
a |
c |
t |
t |
c |
a |
g |
a |
A |
T |
G |
c |
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#671
alpha Tubulin III, CHO Elliott '86 MCB 6, 906 |
|
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|
||||||||||||||||
t |
t |
c |
c |
t |
a |
g |
a |
c |
a |
c |
c |
A |
T |
G |
c |
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#679
Tyrosinase, mu Shibahara '86 NAR 14, 2413 |
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#680
Tyrosine aminotransferase, rat Grange '85 JMB 184, 347 |
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#681
tyrosine hydroxylase, hu Grima '87Nature 326, 707 |
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#683
ubiquitin, hu Baker '87 NAR 15, 443 |
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#684
Ubiquitin, ch Bond '86 MCB 6, 4602 |
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#691
urotensin carp Ishida '86 PNAS 83, 308 |
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The two tandem/overlapped sequences were found in roughly 17% of the published 5’UTRs .
At first glance, there does not seem to be any trend as to species or family of proteins that contain these sequences.
The only thing that can be said is that they appear to be similar to other sequences that act as “sticky” sites or “docking” sites such as those of the RSS of Immunoglobulin families and T Cell receptors or some retroviral kissing loops, miRNAs etc.. This does not mean that one set is derived from the other. One simply can only say that one resembles the other..
Another observation is that some of these sequences are at sites involve splicing and ligation (in the DNA world), and of course protein binding.
Just a note. When a BLAST search for these sequences was done, the results were for cDNAs and not a UTRs, and many of the cDNAs were of unknown genes. It seemed easier to look at sequences from published papers that could be obtained from Pub Med Central to see if there were any very obvious trends.