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EBI DbfetchID AACZ02115232; SV 1; linear; genomic DNA; WGS; MAM; 2824 BP. XX AC AACZ02115232; AACZ02000000; AACZ00000000; XX DT 19-MAR-2006 (Rel. 87, Created) DT 04-DEC-2008 (Rel. 98, Last updated, Version 2) XX DE Pan troglodytes chromosome 10 bld2_Cont125.85, whole genome shotgun DE sequence. XX KW WGS. XX OS Pan troglodytes (chimpanzee) OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; OC Pan. XX RN [1] RP 1-2824 RX DOI; 10.1038/nature04072 RX PUBMED; 16136131. RG Chimpanzee Sequencing and Analysis Consortium RA ; RT "Initial sequence of the chimpanzee genome and comparison with the human RT genome"; RL Nature 437(7055):69-87(2005). XX RN [2] RP 1-2824 RX DOI; 10.1038/nature04101 RX PUBMED; 16136134. RA Hughes J.F., Skaletsky H., Pyntikova T., Minx P.J., Graves T., Rozen S., RA Wilson R.K., Page D.C.; RT "Conservation of Y-linked genes during human evolution revealed by RT comparative sequencing in chimpanzee"; RL Nature 437(7055):100-103(2005). XX RN [3] RP 1-2824 RA Yang S.P., Hillier L.W., Chinwalla A.T., Fulton L.A., Huang X., RA Wilson R.K.; RT ; RL Submitted (26-NOV-2003) to the EMBL/GenBank/DDBJ databases. RL Genome Sequencing Center, Washington University School of Medicine, 4444 RL Forest Park, St. Louis, MO 63108, USA XX RN [4] RP 1-2824 RA Yang S.P., Hillier L.W., Chinwalla A.T., Fulton L.A., Glasscock J., RA Wallis J.W., Huang X., Mardis E.R., Wilson R.K.; RT ; RL Submitted (17-FEB-2006) to the EMBL/GenBank/DDBJ databases. RL Genome Sequencing Center, Washington University School of Medicine, 4444 RL Forest Park Parkway, St. Louis, MO 63108, USA XX DR EMBL-CON; CM000324. DR GOA; P0C594. DR InterPro; IPR000340; Dual-sp_phosphatase_cat-dom. DR InterPro; IPR000387; Dual-sp/Tyr_phosphatase. DR InterPro; IPR016130; Tyr_Pase_AS. DR InterPro; IPR020405; Dual-sp_phosphatase_famA. DR InterPro; IPR020417; Dual-sp_phosphatase. DR InterPro; IPR020422; Dual-sp_phosphatase_subgr_cat. DR UniProtKB/Swiss-Prot; P0C594; DUPD1_PANTR. XX CC Sequencing/Assembly: The whole genome shotgun sequence data were CC assembled and organized by the Washington University Genome CC Sequencing Center. The underlying whole genome shotgun data were CC generated at the Washington University School of Medicine and the CC Broad Institute. A 5 megabase region of chromosome 7 was finished CC at the Washington University Genome Sequencing Center CC (chr7:84674857-89461887). The chromosome Y sequence was finished at CC the Washington University Genome Sequencing Center with detailed CC mapping and extensive collaboration with David Page's group at the CC Whitehead Institute (The DNA Sequence of Chimpanzee Chromosome Y, CC unpublished; Hughes et al., Conservation of Y-linked genes during CC human evolution revealed by comparative sequencing in chimpanzee. CC Nature, 2005 437:100-3; PMID:16136134). The chromosome 21 sequence CC data was kindly provided by Todd Taylor and the Riken Genome CC Sciences Center (Watanabe et al., DNA sequence and comparative CC analysis of chimpanzee chromosome 22. Nature. 2004 May CC 27;429(6990):382-8. PMID: 15164055). CC This assembly covers about 97 percent of the genome and is based on CC 6X sequence coverage. It is composed of 246,375 contigs with an N50 CC length of 29 kb, and 44,454 supercontigs with an N50 length of 9.7 CC Mb. The total contig length, not including estimated gap sizes, is CC 2.97 Gb. Of that total, 2.82 Gb has been ordered and oriented CC along specific chimpanzee chromomes, 107Mb has been linked to CC chromosomes but is unplaced, and 50Mb remains unlinked (chrUn). CC The whole genome shotgun data from primary donor-derived reads CC (Clint, a captive-born male chimpanzee from the Yerkes Primate CC Research Center (Atlanta, USA)) were assembled using PCAP (Huang CC 2006) using stringent parameters derived by eliminating detectable CC global mis-assemblies (interchromosomal cross-overs determined by CC alignment of the chimpanzee genome against the human genome) larger CC than 50kb. CC The assembly data were aligned against the human genome at UCSC (B. CC Raney) utilizing BLASTZ (Schwartz 2003) to align and score CC non-repetitive chimpanzee regions against repeat-masked human CC sequence. Alignment chains differentiated between orthologous and CC paralogous alignments (Kent 2003) and only 'reciprocal best' CC alignments were retained in the alignment set. The chimpanzee AGP CC files were generated from these alignments in a manner similar to CC that already described (The Chimpanzee Genome Sequencing Consortium CC 2005). Centromeres were introduced into the chimp sequence at the CC positions of the centromeres in the human chromosomes. Ten CC documented/known human inversions (Yunis 1982) supported by the CC assembly were introduced into the ordering as was the separation of CC alignments to human chromosome 2 into chimpanzee chromosomes 2A and CC 2B. We removed the contigs from the WGS project that corresponded CC to the finished chromosome 21 and chromosome Y sequences and a 5 Mb CC finished region from chimpanzee chromosome 7 because they are CC represented by the corresponding finished sequences. The CC chromosome 21 sequence is GenBank Accession Number BA000046 and the CC chromosome Y sequence is GenBank Accession Numbers CC DP000054-DP000056 and AC163716.2. XX FH Key Location/Qualifiers FH FT source 1..2824 FT /organism="Pan troglodytes" FT /chromosome="10" FT /isolate="Yerkes chimp pedigree #C0471 (Clint)" FT /mol_type="genomic DNA" FT /sex="male" FT /db_xref="taxon:9598" XX SQ Sequence 2824 BP; 762 A; 639 C; 742 G; 680 T; 1 other; aaaaaaaaaa aaaaaattag ctgggcgtgg tagtgcatgc ctgtaatccc agctactcag 60 gaggctgagg caagagaatt gcttaaaccc aggaggtgga ggttgcagtg agtcaagatg 120 gtgccactgc actccagcct gggtgacaga aggagactcc atctcaaaaa aaaaaaaagt 180 aaacccttta tatgtgtgta tatgtttcct tatgttggca atagcccaca caaggtagta 240 gaagtatgca agtaaattta acactggtta gtcaggggta gaattaagag gagacaaagg 300 gagattatgc agtttgtctt tataaccctc tacctcattt aacctagtat aattaagcat 360 gtcatatttg taactttttc aattaaaaaa aagaaagacg aaaggcaagg gatgcttaac 420 ctggatcttc ctatggctag acgattatct ctaggtatta agcagcaaga tgtgtattaa 480 aatcacatat aggccgggca cggtggctca tacctttaat cccggcactt tgggaggctg 540 atgtgggcag atcaactgag gtcaggagtt ggagaccagc ctggccaaca tggtgaaacc 600 ctgcttctac taaaaataaa aaattagcca ggtgtggagg caggtgcctg taatcccagc 660 tacttgggaa gctgagacag aggattgctt gaacccagga ggcagaggtt gcagtgagcc 720 gaggtcaaac cactccaacc tgcacttcaa cgcgggtgac agggtgagac tgtctcgcaa 780 aaaaaaagaa aagaaaaaga aaataaatac aataatatat ggaggggtcc tacagcatct 840 gctccttggt gagatggaac atggctggag tccgggagag tggagggagg agcagttaag 900 aacaagcctc tgggttgggc agagctgcat tttaatccca gctctctgcc accgactgag 960 ctgtgggact tgggccagtt atttaactgc tctgtgcctc agtttcccta tctttataat 1020 gggagtaatt agcttctatc actgggttat caggagagaa aaatgagatc aagcatgcag 1080 gatgcttagc acagtgcctg gcatacagtg ttcaagaaag gatagtcgtt atcattatta 1140 atattattta cagtaggtgc atctcagttg tgtagggagt ggggaatggt ggttataaaa 1200 atctaaagga ggtgacagtg acctaaattt aggctcccat acttccaggc atatattgat 1260 gtgttcctgc accatcaacc taagaaatga ttttattctt gagggtatta tagctagcta 1320 aaataaaaga ctacatttcc caagctccct tgcagctagg ggcaggggaa gtctgggatg 1380 ggactttgct ttcagaagat gcccttctgc tctttctttc cctccaccct cctgctgtct 1440 gggtcctaga gttgatggct ggggtcctgg cggcaatctg ggaccctgca gcacctggag 1500 ggaagaagcc acgtccccag gacagtggcg cagaaacaca ggagtctgag tccctgatga 1560 ccctgcagtg gccgtgccag ccccagccca cctccctctg cacttatatg tgagagagaa 1620 ataaacctct atcttgccta agactttgtt taggttttct gtaatgtgaa ggtaagccca 1680 gccctaacta attgagttct cacagaacta caaattccaa agcccacggc taggaggtgg 1740 cacagggcgt ggcctgggga ggggctgctg cctgctccca agcgagcctg ggcctgagca 1800 cttactcatc accaatgtag agcttgggcc agacctcgtt gacgtgggtg tactggggac 1860 tgcccttcca gaagagccgc tccagctcaa aggctccagg ggtgcagtag tcctcctcct 1920 ccccttcctc ctccatcttc agcgacagcc tcttggcaga tgagtaggca ttcttgaggc 1980 ttgtcttcac ttctccagat gtcattttag agccaaggga ttttctctcc tttctgcagc 2040 tggttatgag agagaagcag gatgggggtt agcaggggac actgaggcag ggaataagct 2100 ttacaaaaag aggtgggaat aagcttatct taaaatttgg caagagtttc cccaacctgc 2160 tatgccccgg cttcctcttc ccaggccaca caggtaaaca aggaaggcca tgatggcagt 2220 taaatgacac ttccccaatg ttccaatctt tctagagaag gagagctggg gtcctcggac 2280 gtgggccaag gcgggctctg gagctaagaa atcctgcaag cagccagttc cttcccacct 2340 ttctttagac tttactcctt tggttcctac tttttccttt atctgactga aacctactgg 2400 tttgggccat ttgggaccca aaataggaag gcccagaaga tccctgacat tccaggcctg 2460 tggccctctc agtgtctgca gggagccatc agccagtgga aagagtacat cgccaaggcc 2520 atacctgccc gggcctgggt ctgggccaca cgcacatcag caggacttca gaagccttga 2580 gaggggagga aaccggctgc atgagggtta acctgtcaga agagctgaag gcaacgctca 2640 cgctctcaca ctgggagcct ggccatcact gtgttaactt accaagggaa ttggaagaga 2700 tgccccaaga tagaaagctg tgcctcgaga ctgaaatgtg catttggaga gcttgttagg 2760 ctctgccagt ggaatgtggg agaggacttt ccattgtccc caaggagagg aattgncagg 2820 gaat 2824 // |
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