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Doitsujin -> RE: Major major frustration (Jul. 6 2006 17:29:51)
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At first, very very sorry for this off Topic!!
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Start OFF TOPIC:
But I was forced to do it.. Its like you throw a wood..the dog cant resist..it HAS to bring it back. So I study this mess,.. I cant resist to find the origin of Deniz DNA-Sequence.... sorry..But Im helpless....
By the way the DNA alphabet has more than ATG and C It has a minimum of 15 letters maybe some more which I dont know at the moment.
Ok Deniz you wanted it you get it..hehe ^^
I searched it with BLAST//-Genbank which is in the USA. But EMBL from England and DDBJ from Japan would give the same results.
If you can tell me why they would give me exact the same results, I will pay for one packet of strings for you. (^_-) But the answere is not: Coz the sequence is the same.
I found a full match in the cDNA clone of Oryza sativa. (=CDNA clone:J033028O18, full insert sequence Oryza sativa, 49 sequence(s))
Its nearely 100% shure that its from the genome of the Oryza sativa (japonica cultivar-group)
The more common name is Japanese rice!!
Hey where did you get this sequence?? Is that a joke with the japanese rice coz of my name?? WUHAHA ^^ Thats cool Deniz!!
With 60% its from a chromosome maybe the 18th of Mus musculus. But I dont think so.
But nothing is 100% shure in biology-science..so it could be wrong. But I think Im right..hmmm[>:]
Here is a picture and some details of the rice:
Here I show you the searchresult:
GenBank
LOCUS AK101172 1857 bp mRNA linear PLN 24-JUL-2003
DEFINITION Oryza sativa (japonica cultivar-group) cDNA clone:J033028O18, full
insert sequence.
ACCESSION AK101172
VERSION AK101172.1 GI:32986381
KEYWORDS FLI_CDNA; CAP trapper.
SOURCE Oryza sativa (japonica cultivar-group)
ORGANISM Oryza sativa (japonica cultivar-group)
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
REFERENCE 1
AUTHORS The Rice Full-Length cDNA Consortium, National Institute of
Agrobiological Sciences Rice Full-Length cDNA Project Team:,
Kikuchi,S., Satoh,K., Nagata,T., Kawagashira,N., Doi,K.,
Kishimoto,N., Yazaki,J., Ishikawa,M., Yamada,H., Ooka,H., Hotta,I.,
Kojima,K., Namiki,T., Ohneda,E., Yahagi,W., Suzuki,K., Li,C.,
Ohtsuki,K., Shishiki,T., Foundation of Advancement of International
Science Genome Sequencing & Analysis Group:, Otomo,Y., Murakami,K.,
Iida,Y., Sugano,S., Fujimura,T., Suzuki,Y., Tsunoda,Y.,
Kurosaki,T., Kodama,T., Masuda,H., Kobayashi,M., Xie,Q., Lu,M.,
Narikawa,R., Sugiyama,A., Mizuno,K., Yokomizo,S., Niikura,J.,
Ikeda,R., Ishibiki,J., Kawamata,M., Yoshimura,A., Miura,J.,
Kusumegi,T., Oka,M., Ryu,R., Ueda,M., Matsubara,K., RIKEN:,
Kawai,J., Carninci,P., Adachi,J., Aizawa,K., Arakawa,T., Fukuda,S.,
Hara,A., Hashidume,W., Hayatsu,N., Imotani,K., Ishii,Y., Itoh,M.,
Kagawa,I., Kondo,S., Konno,H., Miyazaki,A., Osato,N., Ota,Y.,
Saito,R., Sasaki,D., Sato,K., Shibata,K., Shinagawa,A., Shiraki,T.,
Yoshino,M. and Hayashizaki,Y.
TITLE Collection, mapping, and annotation of over 28,000 cDNA clones from
japonica rice
JOURNAL Science 301 (5631), 376-379 (2003)
PUBMED 12869764
REFERENCE 2 (bases 1 to 1857)
AUTHORS Adachi,J., Aizawa,K., Akimura,T., Arakawa,T., Carninci,P., Doi,K.,
Fujimura,T., Fukuda,S., Hanagaki,T., Hara,A., Hashizume,W.,
Hayashida,K., Hayashizaki,Y., Hayatsu,N., Hiramoto,K., Hiraoka,T.,
Hori,F., Hotta,I., Iida,J., Iida,Y., Ikeda,R., Imamura,K.,
Imotani,K., Ishibiki,J., Ishii,Y., Ishikawa,M., Itoh,M., Kagawa,I.,
Kanagawa,S., Katoh,H., Kawagashira,N., Kawai,J., Kawamata,M.,
Kikuchi,S., Kishikawa-Hirozane,T., Kishimoto,N., Kobayashi,M.,
Kodama,T., Kojima,K., Kojima,Y., Kondo,S., Konno,H., Kouda,M.,
Koya,S., Kurihara,C., Kurosaki,T., Kusumegi,T., Li,C., Lu,M.,
Masuda,H., Matsubara,K., Matsuyama,T., Miura,J., Miyazaki,A.,
Mizuno,K., Murakami,K., Murata,M., Nagata,T., Nakamura,M.,
Namiki,T., Narikawa,R., Niikura,J., Nishi,K., Nomura,K.,
Numasaki,R., Ohneda,E., Ohno,M., Ohtsuki,K., Oka,M., Ooka,H.,
Osato,N., Ota,Y., Otomo,Y., Ryu,R., Saitoh,H., Sakai,C., Sakai,K.,
Sakazume,N., Sano,H., Sasaki,D., Sato,K., Satoh,K., Shibata,K.,
Shinagawa,A., Shiraki,T., Shishiki,T., Sogabe,Y., Sugano,S.,
Sugiyama,A., Suzuki,K., Suzuki,Y., Tagami,M., Tagami-Takeda,Y.,
Tagawa,A., Takahashi,F., Takaku-Akahira,S., Tanaka,T., Tomaru,A.,
Toya,T., Tsunoda,Y., Ueda,M., Waki,K., Xie,Q., Yahagi,W.,
Yamada,H., Yamamoto,M., Yasunishi,A., Yazaki,J., Yokomizo,S. and
Yoshimura,A.
TITLE Direct Submission
JOURNAL Submitted (27-AUG-2002) Shoshi Kikuchi, National Institute of
Agrobiological Sciences, Department of Molecular Genetics, Head of
Laboratory of Gene Expression; 2-1-2 Kannondai, Tsukuba, Ibaraki
305-8602, Japan (E-mail:skikuchi@nias.affrc.go.jp,
Tel:81-29-838-7007, Fax:81-29-838-7007)
COMMENT This clone is one of the 28K full-length cDNA clones from japonica
rice.
URL : http://cdna01.dna.affrc.go.jp/cDNA/
NIAS Rice Full-Length cDNA Project Team: Kikuchi,S., Satoh,K.,
Nagata,T., Kawagashira,N., Doi,K., Kishimoto,N., Yazaki,J.,
Ishikawa,M., Yamada,H., Ooka,H., Hotta,I., Kojima,K., Namiki,T.,
Ohneda,E., Yahagi,W., Suzuki,K., Li,C., Ohtsuki,K., Shishiki,T. and
Yamamoto,M.
FAIS Genome Sequencing & Analysis Group: Otomo,Y., Iida,Y.,
Fujimura,T., Ikeda,R., Ishibiki,J., Kawamata,M., Kobayashi,M.,
Kodama,T., Kurosaki,T., Kusumegi,T., Lu,M., Masuda,H., Miura,J.,
Mizuno,K., Narikawa,R., Niikura,J., Oka,M., Ryu,R., Sugano,S.,
Sugiyama,A., Suzuki,Y., Tsunoda,Y., Ueda,M., Xie,Q., Yokomizo,S.,
Yoshimura,A., Matsubara,K. and Murakami,K.
Genome Exploration Research Group in Riken Genomic Sciences Center
and Genome Science Laboratory in Riken: Adachi,J., Aizawa,K.,
Akimura,T., Arakawa,T., Carninci,P., Fukuda,S., Hanagaki,T.,
Hara,A., Hashizume,W., Hayashida,K., Hayatsu,N., Hiramoto,K.,
Hiraoka,T., Hori,F., Iida,J., Imamura,K., Imotani,K., Ishii,Y.,
Itoh,M., Kagawa,I., Kanagawa,S., Katoh,H., Kawai,J.,
Kishikawa-Hirozane,T., Kojima,Y., Kondo,S., Konno,H., Kouda,M.,
Koya,S., Kurihara,C., Matsuyama,T., Miyazaki,A., Murata,M.,
Nakamura,M., Nishi,K., Nomura,K., Numasaki,R., Ohno,M., Osato,N.,
Ota,Y., Saitoh,H., Sakai,C., Sakai,K., Sakazume,N., Sano,H.,
Sasaki,D., Sato,K., Shibata,K., Shinagawa,A., Shiraki,T.,
Sogabe,Y., Tagami,M., Tagami-Takeda,Y., Tagawa,A., Takahashi,F.,
Takaku-Akahira,S., Tanaka,T., Tomaru,A., Toya,T., Waki,K.,
Yasunishi,A. and Hayashizaki,Y.
FEATURES Location/Qualifiers
source 1..1857
/organism="Oryza sativa (japonica cultivar-group)"
/mol_type="mRNA"
/cultivar="Nipponbare"
/db_xref="taxon:39947"
/clone="J033028O18"
ORIGIN
1 ggttagtta-->a gctttcccct cccaattaat taagtttagc tcttatcaga gcgagagaga
61 gagagagaga gggaagaaga agaagtggaa gtggtatgta tgtgcccatg tccattgccg
121 cagaaacaaa ctgtagcagc agcagcagca gctagtgaag tactacagta cagtagtgag
181 gacttaatca aacggggcgc gcggggtgcc ccctagctct cctcattcca ccaccatgcc
241 caccccgcca tcgccatgcc tcttcttcct cttcctcctc ttcttcatgt ggtcgtctca
301 ctctcacctt ggcgccgcct ccgacgcgga cgcgctgctc gccctcaagt ccgccctcga
361 ccgctccgac cgcctcccct ggcgccgcga caccgccccc gccttgtgct cctcctggct
421 cggcgtgcgc cagtgctccc aacctccccg ggacaggagg gtcaccaagc tcgtcctcga
481 gaacctcaac ctcaccggcg tcctcaccgc caccctcctc gccccgctct ccgagctgcg
541 cgtcctcagc ctcaagtcca acgccctcac cggccccatc cccgacgccc tccccgccgc
601 cctccctaac ctcaagctgc tctacctctc cgccaaccgc ctccagggcc gcatcccgcc
661 caccctcgcc ctcctccacc gcgccaccgt cctcgtcctc tcctccaacc tcctccatgg
721 cgctgagggc ctacttccag gccaaggagg agcgactcct cgtctacgat tactacccca
781 atggcagcct cttctccctc ctccacgggt ccagcagccg gacgtcgagc aaggggaagc
841 ccctgcactg gacgtcgtgc atgaagatcg cggaggatgt cgccgccggg ctggtgcacc
901 tgcaccagtc gccgccggct ggcatcgtgc acggcaacct caagccctcc aacgtcctcc
961 tcggccccga cttcgaatcg tgcctcaccg attacggtct ggtgcccacg ctgctcccct
1021 cccacgccga tctcgcctcc tccacgtccg tcctataccg agcgccggaa actcgcaccg
1081 cccatgcctt cacgccggcg tccgacgtgt acagcttcgg cgtgctcctc ctggagctgc
1141 tcaccgggaa ggcgccgttc caggacctga tggagatgca cagcgatgac atcccgagct
1201 gggtgcgggc agtgcgtgag gaagagacgg agtccggcgg ggagtccgcg tccgctggcg
1261 gcacggagga gaagctcggt gcgctgatca gcattgcggc ggcctgcgtg gtggcggacc
1321 cggcgaggcg gccaaccaca ccggaggtgc tacggatggt gagggaggca agggcggagg
1381 caatgtcgtc gtcgaacagc agcgaccggt caccagcgcg gtggtcagac gccgtgcagg
1441 tgcagatggg catgggggtg ccgcgagatc agggagagct aggaggactc acctgatcga
1501 tcgatcagca gctgatctca tcctgatcag cagctgatca tcgcctggct ggccggcttg
1561 ttgttacttt acttcatgta ccgtagcagc aaaaaaagtg tagttaccac tcaatttgtc
1621 ttggctcaaa gaatgactca ttcttcaggc aacacttttt aaataccagg ggtctttgat
1681 ttgggacttg tgtaggtttt tagcagggaa gggtggggca ttgggagata ctcctagctt
1741 agataggttc agagatgaag attctctggg ctggatctgt ctgtaaatct tttttggatt
1801 gttgtaaact tgtccttttt attttttccg gagtggagct aaactggttt atgtgtc
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Above is the mached sequence. But listen, its not a 100% identical match. Coz of that there are some tiny mismatches like the end.. But to 1561 are the main matches.
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Here some screenshots from the results to proove it. (Only the link, not the pic, coz we talk about flamenco here..it would be too much I think)
http://img172.imageshack.us/img172/2544/blast45tt.jpg
http://img172.imageshack.us/img172/8468/blast21mw.jpg
http://img172.imageshack.us/img172/5030/blast38cf.jpg
By the way,..many scientists made a collection (Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.) It was published in Science. 2004 Jan 9;303(5655):168; author reply 168.
You can get it here Deniz. (^_-)
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&query_hl=1&list_uids=12869764
Any more sequence questions??[:)][:)][8|][8|][8D]
Off Topic end.
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Images are resized automatically to a maximum width of 800px
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