ФЭНДОМ


   LOCUS       NC_008255            4433218 bp    DNA     circular BCT 25-JUL-2006
   DEFINITION  Cytophaga hutchinsonii ATCC 33406, complete genome.
   ACCESSION   NC_008255
   VERSION     NC_008255.1  GI:110636427
   KEYWORDS    .
   SOURCE      Cytophaga hutchinsonii ATCC 33406
     ORGANISM  Cytophaga hutchinsonii ATCC 33406
               Bacteria; Bacteroidetes; Sphingobacteria; Sphingobacteriales;
               Flexibacteraceae; Cytophaga.
   REFERENCE   1  (bases 1 to 4433218)
     AUTHORS   Copeland,A., Lucas,S., Lapidus,A., Barry,K., Detter,J.C., Glavina
               del Rio,T., Hammon,N., Israni,S., Dalin,E., Tice,H., Pitluck,S.,
               Brettin,T., Bruce,D., Challacombe,J.F., Chertkov,O., Han,S.,
               Tapia,R., McBride,M.J., Misra,M., Myers,G.L., Thayer,N.N.,
               Thompson,L.S., Xie,G., Gilna,P., Schmutz,J., Larimer,F., Land,M.,
               Hauser,L., Kyrpides,N., Lykidis,A., Ivanova,N., Mavrommatis,K.,
               Rubin,E. and Richardson,P.
     CONSRTM   US DOE Joint Genome Institute
     TITLE     Complete sequence of Cytophaga hutchinsonii ATCC 33406
     JOURNAL   Unpublished
   REFERENCE   2  (bases 1 to 4433218)
     AUTHORS   .
     CONSRTM   NCBI Genome Project
     TITLE     Direct Submission
     JOURNAL   Submitted (24-JUL-2006) National Center for Biotechnology
               Information, NIH, Bethesda, MD 20894, USA
   REFERENCE   3  (bases 1 to 4433218)
     AUTHORS   Copeland,A., Lucas,S., Lapidus,A., Barry,K., Detter,J.C., Glavina
               del Rio,T., Hammon,N., Israni,S., Dalin,E., Tice,H., Pitluck,S.,
               Brettin,T., Bruce,D., Challacombe,J.F., Chertkov,O., Han,S.,
               Tapia,R., McBride,M.J., Misra,M., Myers,G.L., Thayer,N.N.,
               Thompson,L.S., Xie,G., Gilna,P., Schmutz,J., Larimer,F., Land,M.,
               Hauser,L., Kyrpides,N., Lykidis,A., Ivanova,N., Mavrommatis,K.,
               Rubin,E. and Richardson,P.
     CONSRTM   US DOE Joint Genome Institute
     TITLE     Direct Submission
     JOURNAL   Submitted (02-JUN-2006) US DOE Joint Genome Institute, 2800
               Mitchell Drive B100, Walnut Creek, CA 94598-1698, USA
   COMMENT     PROVISIONAL REFSEQ: This record has not yet been subject to final
               NCBI review. The reference sequence was derived from CP000383.
               URL -- http://www.jgi.doe.gov
                      JGI Project ID: 2351473
                      Source DNA and bacteria available from Mark McBride
                      Contacts: Mark McBride (mcbride@uwm.edu)
                                Paul Richardson (microbes@cuba.jgi-psf.org)
               Plasmid and fosmid libraries were prepared at the Joint Genome
               Institute (JGI) Production Genomics Facility (JGI-PGF) in Walnut
               Creek, CA. Shotgun sequencing was performed at the JGI-PGF to a
               coverage of 15x. Large (40 kb), medium (8 kb) and small (3 kb)
               insert random libraries were partially sequenced with average
               success rate of 90% and average high-quality read lengths of 634
               nucleotides. Finishing was performed at JGI-LANL starting with 29
               contigs and 2 scaffolds. Repetitive regions were identified,
               assembled and finished by manually checking paired reads close to
               each repeat in the assembly with consed and then making a
               subassembly for each repetitive region. 27 gaps were closed with
               primer walks and 2 by PCR. Gene predictions were obtained using
               Glimmer and tRNAs were identified using tRNAScan-SE. Basic analysis
               of the gene predictions was performed by comparing coding sequences
               against the PFam, BLOCKS and Prodom databases. Gene definitions and
               functional classes were added manually by a team of annotators at
               JGI-LANL, using BLAST results in addition to information from the
               basic analysis. A total of 3793 features have been annotated on the
               sequence record.
                The JGI and collaborators endorse the principles for the
               distribution and use of large scale sequencing data adopted by the
               larger genome sequencing community and urge users of this data to
               follow them. it is our intention to publish the work of this
               project in a timely fashion and we welcome collaborative
               interaction on the project and analysis.
               (http://www.genome.gov/page.cfm?pageID=10506376).
               COMPLETENESS: full length.


Расположение РНК Править

Начало Конец Направление Длина PID Ген COG Комментарий
63356 63435 - 80 110636427 CHU_tAsn01 - 07</sub> Asn tRNA
69568 69647 - 80 110636427 CHU_tAla01 - 02</sub> Ala tRNA
120118 121499 + 1382 110636427 CHU_r16S01 - 16S ribosomal RNA
121927 124436 + 2510 110636427 CHU_r23S01 - 23S ribosomal RNA
124780 124816 + 37 110636427 CHU_r5S01 - 5S ribosomal RNA
145782 145857 - 76 110636427 CHU_tPhe01 - 17</sub> Phe tRNA
178917 178992 + 76 110636427 CHU_tGly01 - 01</sub> Gly tRNA
179045 179136 + 92 110636427 CHU_tLeu01 - 15</sub> Leu tRNA
183235 184616 + 1382 110636427 CHU_r16S02 - 16S ribosomal RNA
184777 184853 + 77 110636427 CHU_tIle01 - 14</sub> Ile tRNA
184945 185021 + 77 110636427 CHU_tAla02 - 02</sub> Ala tRNA
185312 187821 + 2510 110636427 CHU_r23S02 - 23S ribosomal RNA
188165 188201 + 37 110636427 CHU_r5S02 - 5S ribosomal RNA
256242 256322 + 81 110636427 CHU_tVal01 - 13</sub> Val tRNA
724579 724658 + 80 110636427 CHU_tArg01 - 11</sub> Arg tRNA
1040456 1040532 - 77 110636427 CHU_tMet01 - 16</sub> Met tRNA
1157965 1158044 + 80 110636427 CHU_tHis01 - 09</sub> His tRNA
1210249 1210336 + 88 110636427 CHU_tSer01 - 08</sub> Ser tRNA
1751703 1751779 - 77 110636427 CHU_tAsp01 - 06</sub> Asp tRNA
1932378 1932457 - 80 110636427 CHU_tMet02 - 16</sub> Met tRNA
1973455 1973533 + 79 110636427 CHU_tThr01 - 12</sub> Thr tRNA
1973775 1973850 + 76 110636427 CHU_tThr02 - 12</sub> Thr tRNA
1993798 1993834 - 37 110636427 CHU_r5S03 - 5S ribosomal RNA
1994178 1996687 - 2510 110636427 CHU_r23S03 - 23S ribosomal RNA
1997115 1998496 - 1382 110636427 CHU_r16S03 - 16S ribosomal RNA
2005947 2006031 + 85 110636427 CHU_tLeu02 - 15</sub> Leu tRNA
2239147 2239224 - 78 110636427 CHU_tPro01 - 03</sub> Pro tRNA
2239296 2239372 - 77 110636427 CHU_tArg02 - 11</sub> Arg tRNA
2239455 2239532 - 78 110636427 CHU_tPro02 - 03</sub> Pro tRNA
2239626 2239717 - 92 110636427 CHU_tSer02 - 08</sub> Ser tRNA
2278047 2278120 - 74 110636427 CHU_tCys01 - 19</sub> Cys tRNA
2526598 2526690 - 93 110636427 CHU_tSer03 - 08</sub> Ser tRNA
2611557 2611631 + 75 110636427 CHU_tArg03 - 11</sub> Arg tRNA
3008953 3009031 - 79 110636427 CHU_tGln01 - 05</sub> Gln tRNA
3197420 3197506 - 87 110636427 CHU_tLeu03 - 15</sub> Leu tRNA
3198774 3198849 - 76 110636427 CHU_tLys01 - 10</sub> Lys tRNA
3199734 3199809 - 76 110636427 CHU_tLys02 - 10</sub> Lys tRNA
3325653 3325731 - 79 110636427 CHU_tPhe02 - 17</sub> Phe tRNA
3325763 3325851 - 89 110636427 CHU_tPseudo01 - Xaa tRNA
3400034 3400118 - 85 110636427 CHU_tLeu04 - 15</sub> Leu tRNA
3422770 3422847 - 78 110636427 CHU_tGlu01 - 04</sub> Glu tRNA
3422949 3423026 - 78 110636427 CHU_tGlu02 - 04</sub> Glu tRNA
3614058 3614131 - 74 110636427 CHU_tTrp01 - 20</sub> Trp tRNA
3615488 3615566 - 79 110636427 CHU_tThr03 - 12</sub> Thr tRNA
3615577 3615655 - 79 110636427 CHU_tGly02 - 01</sub> Gly tRNA
3615732 3615820 - 89 110636427 CHU_tTyr01 - 18</sub> Tyr tRNA
3836007 3836085 - 79 110636427 CHU_tMet03 - 16</sub> Met tRNA
4426462 4426539 - 78 110636427 CHU_tArg04 - 11</sub> Arg tRNA