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Order documents on this page through Loansome Doc Burger J, et al. [See Related Articles] Metal Concentrations in the Eggs of Endangered Florida Scrub-Jays from Central Florida. Arch Environ Contam Toxicol. 1999 Oct;37(3):385-388. [Record as supplied by publisher] PMID: 10473796. Clayton NS, et al. Motivational control of caching behaviour in the scrub jay, Aphelocoma coerulescens. Anim Behav. 1999 Feb;57(2):435-444. [Record as supplied by publisher] PMID: 10049484. Maney DL, et al. [See Related Articles] Effects of vasoactive intestinal peptide on plasma prolactin in passerines. Gen Comp Endocrinol. 1999 Mar;113(3):323-30. PMID: 10068494; UI: 99169111. Schoech SJ, et al. [See Related Articles] Corticosterone, reproductive status, and body mass in a cooperative breeder, the Florida scrub-jay (Aphelocoma coerulescens). Physiol Zool. 1997 Jan-Feb;70(1):68-73. PMID: 9231378; UI: 97375003. Hirsh DC, et al. [See Related Articles] R plasmid-mediated gentamicin resistance in salmonellae isolated from turkeys and their environment. Avian Dis. 1983 Jul-Sep;27(3):766-72. PMID: 6357185; UI: 84052352.

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Other Formats: Links: Arch Environ Contam Toxicol 1999 Oct;37(3):385-388

Metal Concentrations in the Eggs of Endangered Florida Scrub-Jays from Central Florida.
Burger J, Woolfenden GE, Gochfeld M Division of Life Sciences, Rutgers University, Piscataway, New Jersey 08854-8082, USA [Record supplied by publisher] We analyzed metal levels in the eggs of the endangered Florida scrub-jay (Aphelocoma coerulescens), an extremely sedentary and modestly long-lived passerine bird. Eggs were obtained as part of the long-term study of this species at the Archbold Biological Station, located in south central Florida. Following a brief and usually short dispersal, Florida scrub-jays remain in a permanent territory in their scrub oak habitat, where they feed mainly on insects and acorns. As they are low on the food chain and sedentary, we expected levels of contaminants to be comparatively low and to reflect the local environment. No significant yearly differences existed for any metal between eggs collected in 1997 (n = 11) and 1998 (n = 5). Arithmetic mean metal concentrations (whole egg, dry weight) were low for arsenic (34 ppb), cadmium (25 ppb), mercury (74 ppb), and lead (66 ppb), intermediate for chromium (226 ppb), and higher for selenium (1,470 ppb) and manganese (2,230 ppb). Except for the low mercury value, all these means were within the range of mean values reported for a wide range of nonpasserine species, including those at high trophic levels, but are lower than concentrations associated with abnormalities in birds. The three essential elements (chromium, selenium, and manganese) were approximately normally distributed, whereas arsenic, cadmium, lead, and mercury were highly skewed (arithmetic mean much higher than geometric mean).http://link.springer-ny.com/link/service/journals/00244/bibs/37n3p385.html PMID: 10473796 Save the above report in Macintosh Text format

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U77335 Aphelocoma coerulescens cytochrome-b gene, mitochondrial gene encoding mitochondrial protein, complete cds gi|1841724|gb|U77335.1|ACU77335 [1841724] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 1 protein link , or 5731 nucleotide neighbors ) U23975 Aphelocoma coerulescens isolate 2.1 MHC class II B mRNA, partial cds gi|801934|gb|U23975.1|ACU23975 [801934] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 1 MEDLINE link , 1 protein link , or 893 nucleotide neighbors ) U23973 Aphelocoma coerulescens isolate 1.2 MHC class II B mRNA, partial cds gi|801930|gb|U23973.1|ACU23973 [801930] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 1 MEDLINE link , 1 protein link , or 847 nucleotide neighbors ) U23972 Aphelocoma coerulescens isolate 1.1 MHC class II B mRNA, partial cds gi|801928|gb|U23972.1|ACU23972 [801928] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 1 MEDLINE link , 1 protein link , or 574 nucleotide neighbors ) U23966 Aphelocoma coerulescens isolate 3.6 MHC class II B mRNA, partial cds gi|801916|gb|U23966.1|ACU23966 [801916] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 1 MEDLINE link , 1 protein link , or 786 nucleotide neighbors ) U23965 Aphelocoma coerulescens isolate 3.5 MHC class II B mRNA, partial cds gi|801914|gb|U23965.1|ACU23965 [801914] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 1 MEDLINE link , 1 protein link , or 652 nucleotide neighbors ) U23964 Aphelocoma coerulescens isolate 3.4 MHC class II B mRNA, partial cds gi|801912|gb|U23964.1|ACU23964 [801912] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 1 MEDLINE link , 1 protein link , or 535 nucleotide neighbors ) U23963 Aphelocoma coerulescens isolate 3.3 MHC class II B mRNA, partial cds gi|801910|gb|U23963.1|ACU23963 [801910] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 1 MEDLINE link , 1 protein link , or 898 nucleotide neighbors ) U23962 Aphelocoma coerulescens isolate 3.2 MHC class II B mRNA, partial cds gi|801908|gb|U23962.1|ACU23962 [801908]
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GenBank Report
Other Formats: Links: LOCUS ACU23972 599 bp mRNA VRT 27-JUN-1996 DEFINITION Aphelocoma coerulescens isolate 1.1 MHC class II B mRNA, partial cds. ACCESSION U23972 NID g801928 VERSION U23972.1 GI:801928 KEYWORDS . SOURCE scrub jay. ORGANISM Aphelocoma coerulescens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Archosauria; Aves; Neognathae; Passeriformes; Corvidae; Aphelocoma. REFERENCE 1 (sites) AUTHORS Edwards,S.V., Wakeland,E.K. and Potts,W.K. TITLE Contrasting histories of avian and mammalian Mhc genes revealed by class II B sequences from songbirds JOURNAL Proc. Natl. Acad. Sci. U.S.A. 92 (26), 12200-12204 (1995) MEDLINE 96109233 REFERENCE 2 (bases 1 to 599) AUTHORS Edwards,S.V. TITLE Direct Submission JOURNAL Submitted (03-APR-1995) Scott V. Edwards, Zoology, University of Washington, 256 Kincaid Hall, Seattle, WA 98195-1800, USA FEATURES Location/Qualifiers source 1..599 /organism="Aphelocoma coerulescens" /isolate="1.1" /strain="California Scrub Jay" /db_xref="taxon:39617" /clone="67.7" /tissue_type="spleen" /dev_stage="adult" gene 1..599 /gene="MHC class II B" exon 1..24 /gene="MHC class II B" /note="encodes leader peptide" /number=1 CDS <1..>599 /gene="MHC class II B" /codon_start=1 /protein_id="AAB02900.1" /db_xref="PID:g801929" /db_xref="GI:801929" /translation="AAGEKLSRVLQLMVKYDCQFINGTEKVRLVQRDFYNRLQYLMYD SDVVHYVGFTPLGEKVARVWNSDPDFMEQRRAEVDTVCRDNYGVYTPFSVERRVLPSV SISLVPSSSQPSPGRLLCSVMDFYPAEIQVRWFQGQQELSGHVVATDIVPNGDWTYQL LVLLEIPPQRGVSYTCQVEHVSLEQPLSLHWEMPPDAGR" exon 25..279 /gene="MHC class II B" /note="encodes beta 1 peptide" /number=2 exon 280..573 /gene="MHC class II B" /note="encodes beta 2 peptide" /number=3 exon 574..599 /gene="MHC class II B" /note="encodes transmembrane domain" /number=4
Monday, October 11, 1999 Page: 1

BASE COUNT 108 a 181 c 204 g 106 t ORIGIN 1 gctgcgggcg agaagctctc gagggtgctc cagttgatgg taaagtacga ctgtcagttc 61 atcaacggca cggagaaggt gaggttggtg cagagggatt tctacaaccg gctgcagtac 121 ctgatgtacg acagcgatgt ggtgcactac gtggggttca cccccttggg ggagaaggtt 181 gccagggtct ggaacagcga cccggatttc atggagcaaa gacgggctga ggtggacacg 241 gtctgccggg acaactacgg ggtgtacacc ccgttcagcg tggagcgccg agtgctcccc 301 agcgtgtcca tctcgctggt gccctcgagc tcccagccca gccccggccg cctgctctgc 361 tccgtgatgg atttctaccc tgccgagatc caggtgaggt ggttccaggg ccagcaggag 421 ctctcgggcc acgtggtggc caccgacatc gtccccaacg gggactggac ctaccagctg 481 ctggtgctgc tggaaattcc cccccagcgc ggggtcagct acacctgcca ggtggagcac 541 gtcagcctgg agcagccgct gagcctgcac tgggagatgc cgccggacgc cggccgcag //

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Aphelocoma coerulescens isolate 1.1 MHC class II B mRNA, partial cds Views: GenBank view FASTA view ASN.1 view Coding Regions Feature table
Organism: Aphelocoma coerulescens Genetic Code: 1 Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Archosauria; Aves; Neognathae; Passeriformes; Corvidae; Aphelocoma. Contrasting histories of avian and mammalian Mhc genes revealed by class II B sequences from songbirds Edwards,S.V., Wakeland,E.K. and Potts,W.K. Proc. Natl. Acad. Sci. U.S.A. 92 (26), 12200-12204 (1995) 96109233 Direct Submission Edwards,S.V. Submitted (03-APR-1995) Scott V. Edwards, Zoology, University of Washington, 256 Kincaid Hall, Seattle, WA 98195-1800, USA Accession: U23972 Total Bases Sequenced: 599 bp Completed: May 9, 1995.

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AF033544 Corvus corax FhU2 microsatellite sequence gi|2642044|gb|AF033544.1|AF033544 [2642044] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 2 MEDLINE links , or 6 nucleotide neighbors ) AF033544 Corvus corax FhU2 microsatellite sequence gi|2642044|gb|AF033544.1|AF033544 [2642044] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 2 MEDLINE links , or 6 nucleotide neighbors ) AF033556 Pyrrhula pyrrhula FhU2 microsatellite sequence gi|2642056|gb|AF033556.1|AF033556 [2642056] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 2 MEDLINE links , or 6 nucleotide neighbors ) AF033552 Cecropis semirufa FhU2 microsatellite sequence gi|2642052|gb|AF033552.1|AF033552 [2642052] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 2 MEDLINE links , or 7 nucleotide neighbors ) AF033555 Fringilla coelebs FhU2 microsatellite sequence gi|2642055|gb|AF033555.1|AF033555 [2642055] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 2 MEDLINE links , or 4 nucleotide neighbors ) AF033553 Acrocephalus arundinaceus FhU2 microsatellite sequence gi|2642053|gb|AF033553.1|AF033553 [2642053] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 2 MEDLINE links , or 2 nucleotide neighbors ) AF033547 Luscinia svecica FhU2 microsatellite sequence gi|2642047|gb|AF033547.1|AF033547 [2642047] (View GenBank report, FASTA report, ASN.1 report, Graphical view , 2 MEDLINE links , or 2 nucleotide neighbors )

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TGAAAACGACTCGTTGATGTTCT ACGCCGAGGTGTTTGGGCTTCC TTCCCCGGAGGTGAAGTGGTTC TGCAACAAGACCCAGCTGGTGG CAGACGGCAGGGTTGTAACGGA GAGAGACGGGGACAGCATCTCC

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BLASTN 2.0.10 [Aug-26-1999] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= gi|1841724|gb|U77335.1|ACU77335 Aphelocoma coerulescens cytochrome-b gene, mitochondrial gene encoding mitochondrial protein, complete cds (1143 letters) Database: Non-redundant GenBank+EMBL+DDBJ+PDB sequences 482,057 sequences; 1,336,120,306 total letters If you have any problems or questions with the results of this search please refer to the BLAST FAQs

Distribution of 118 Blast Hits on the Query Sequence


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Monday, October 11, 1999

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Monday, October 11, 1999

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gb|U15201|CR15201 Cicinnurus regius mitochondrion cytochrom... 860 0.0 emb|X74253|MIEFCYTB E.fastuosus mitochondrion gene for cyto... 854 0.0 gb|U25733|LSU25733 Lophorina superba isolate SP-J 005/SP-J ... 854 0.0 gb|U15203|PRU15203 Paradisaea rudolphi mitochondrion cytoch... 846 0.0 emb|X74254|MIPPCYTBG P.paradiseus mitochondrion gene for cy... 839 0.0 gb|AF081975|AF081975 Vireo cassinii cassinii specimen-vouch... 839 0.0 gb|U86033.1|CMU86033 Corvus monedula cytochrome b gene, mit... 835 0.0 gb|U25732|LSU25732 Lophorina superba isolate SP-J 004 cytoc... 831 0.0 gb|AF081973|AF081973 Vireo cassinii cassinii specimen-vouch... 831 0.0 gb|AF081977|AF081977 Vireo cassinii cassinii specimen-vouch... 831 0.0 gb|AF082006|AF082006 Vireo plumbeus plumbeus specimen-vouch... 823 0.0 gb|AF081961|AF081961 Vireo flavifrons specimen-voucher LSU ... 823 0.0 gb|AF081971|AF081971 Vireo cassinii cassinii specimen-vouch... 823 0.0 gb|AF081974|AF081974 Vireo cassinii cassinii specimen-vouch... 823 0.0 gb|AF081982|AF081982 Vireo cassinii cassinii specimen-vouch... 823 0.0 gb|AF081984|AF081984 Vireo cassinii cassinii specimen-vouch... 823 0.0 gb|AF081959|AF081959 Vireolanius leucotis leucotis cytochro... 821 0.0 gb|AF081972|AF081972 Vireo cassinii cassinii specimen-vouch... 815 0.0 gb|AF081988|AF081988 Vireo cassinii cassinii specimen-vouch... 815 0.0 gb|AF081987|AF081987 Vireo cassinii cassinii specimen-vouch... 815 0.0 gb|U15202|SMU15202 Seleucidis melanoleuca mitochondrion cyt... 807 0.0 gb|AF081967|AF081967 Vireo solitarius alticola country USA,... 807 0.0 gb|AF081976|AF081976 Vireo cassinii cassinii specimen-vouch... 807 0.0 gb|AF081978|AF081978 Vireo cassinii cassinii specimen-vouch... 807 0.0 gb|U15207|MCU15207 Manucodia comrii mitochondrion cytochrom... 805 0.0 gb|U86041.1|NCU86041 Nucifraga caryocatactes cytochrome b g... 803 0.0 gb|AF081964|AF081964 Vireo solitarius solitarius specimen-v... 799 0.0 gb|AF081970|AF081970 Vireo solitarius alticola country USA,... 799 0.0 gb|AF081968|AF081968 Vireo solitarius alticola country USA,... 791 0.0 gb|AF081965|AF081965 Vireo solitarius solitarius specimen-v... 791 0.0 gb|AF081963|AF081963 Vireo solitarius solitarius specimen-v... 783 0.0 emb|X74252|MIMKCYTB M.keraudrenii mitochondrion gene for cy... 777 0.0 gb|U86032.1|CCU86032 Corvus corone cytochrome b gene, mitoc... 763 0.0 gb|U86040.1|PAU86040 Ptilostomus afer cytochrome b gene, mi... 759 0.0 gb|U86043.1|PGU86043 Pyrrhocorax graculus cytochrome b gene... 755 0.0 gb|AF081997|AF081997 Vireo plumbeus plumbeus specimen-vouch... 751 0.0 gb|U86034.1|GGU86034 Garrulus glandarius cytochrome b gene,... 747 0.0 gb|AF082007|AF082007 Vireo plumbeus plumbeus specimen-vouch... 743 0.0 gb|AF082002|AF082002 Vireo plumbeus plumbeus specimen-vouch... 743 0.0 emb|X74260|MIVOCYTB V.olivaceus mitochondrion gene for cyto... 743 0.0 gb|AF082001|AF082001 Vireo plumbeus plumbeus specimen-vouch... 743 0.0 gb|AF081994|AF081994 Vireo plumbeus plumbeus specimen-vouch... 735 0.0 gb|AF081998|AF081998 Vireo plumbeus plumbeus specimen-vouch... 735 0.0 gb|AF082000|AF082000 Vireo plumbeus plumbeus specimen-vouch... 735 0.0 gb|AF081991|AF081991 Vireo plumbeus plumbeus specimen-vouch... 735 0.0 gb|AF081995|AF081995 Vireo plumbeus plumbeus specimen-vouch... 730 0.0 gb|AF081979|AF081979 Vireo cassinii cassinii specimen-vouch... 728 0.0 gb|AF081962|AF081962 Vireo flavifrons specimen-voucher LSU ... 724 0.0 gb|AF011776|AF011776 Piranga olivacea collector number PRS ... 710 0.0 emb|Y10734|PIMY10734 P.inornatus mitochondrial cytb gene, p... 710 0.0 gb|U86042.1|PIU86042 Perisoreus infaustus cytochrome b gene... 708 0.0 gb|AF094613.1|AF094613 Corvus corone cytochrome b gene, par... 706 0.0 emb|Z73493|MTPTICYTB P.trochiloides mitochondrial cytochrom... 706 0.0 gb|U86037.1|CCU86037 Cissa chinensis cytochrome b gene, mit... 704 0.0 gb|AF011773|AF011773 Piranga ludoviciana tissue number OMVP... 702 0.0 gb|AF011774|AF011774 Piranga ludoviciana tissue number B-10... 700 0.0 gb|U86044.1|PPU86044 Pyrrhocorax pyrrhocorax cytochrome b g... 690 0.0 gb|U86035.1|GLU86035 Garrulus lidthi cytochrome b gene, mit... 688 0.0 gb|AF011767|AF011767 Piranga flava tissue number B-5400 cyt... 678 0.0 gb|AF011772|AF011772 Piranga ludoviciana tissue number B-10... 670 0.0 gb|U77336|CFU77336 Calocitta formosa cytochrome-b gene, mit... 662 0.0 gb|U15205|EAU15205 Epimachus albertisi mitochondrion cytoch... 626 e-177 gb|AF136725.1|AF136725 Stiphrornis erythrothorax specimen-v... 519 e-145 emb|X60941|MIEACB33 Epimachus albertisii mitochondrial gene... 517 e-144 emb|Y10733|PPMY10733 P.proregulus mitochondrial cytb gene, ... 515 e-144 gb|AF136724.1|AF136724 Stiphrornis erythrothorax specimen-v... 511 e-142 gb|U86038.1|UEU86038 Urocissa erythrorhyncha cytochrome b g... 504 e-140
Monday, October 11, 1999 Page: 3

PubMed Search PopSet About Entrez

Nucleotide Protein for Streblospio Limits Display Index Summary Add to Clipboard Save History

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Protein, Nucleotide 1 : Karl SA Biogeography and evolution of poecilogony in the polychaete genus Streblospio: Evidence from molecular genetics, reproductive trials, and morphology [5006496]

Revised: August 24, 1999.

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BLAST Alignment Length

PubMed 386 7 [ [ [ [ [ [ [

Nucleotide

Protein

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Unpublished study.
# of Sequences Display Options: Colour Display x Full Sequences >> Variations All Blocks>> By Block : [1..70] [71..140] [141..210] [211..280] [281..350] [351..386] Tools: Align Save Alignment: Text format PHYLIP format FASTA format with gaps FASTA format without gaps [ [ [ [ [ [ [ . 1] AF020893 > 1 2] AF020894 > 1 3] AF020895 > 1 4] AF020896 > 1 5] AF020897 > 1 6] AF020898 > 1 7] AF020899 > 1 | 10 20 30 40 . | . | . | . | . | . | ATGGCCACAA ACTTACGAAA AACCCACCCA CTAATAAAAA TTATTAAT ATGACTACTA ATCTACGAAA AACCCACCCA ATAATTAAAA TCATTAAC ATGGCTACAA ACTTACGAAA AACCCACCCA ATAATCAAAA TCATTAAC ATGGCAACAA ACTTACGAAA AACTCACCCA ATAATTAAAA TTATCAAT ATGGCTACAA ACCTACGAAA AACCCACCCA ATAATTAAAA TTATCAAT ATGGCCACAA ACTTACGAAA AACCCACCCA ATAATTAAAA TTATCAAC ATGGCCACAA ACTTACGAAA AACCCACCCA ATAATTAAAA TTATCAAC 90 100 110 120 130 140 . | . | . | . | . | . | GCCCATCAAA CATCTCAGCC TGATGAAACT TCGGATCACT ACTGGGC GCCCCTCCAA TATCTCTGCC TGATGAAACC TCGGATCGTT ACTAGGC GTCCCTCCAA CATCTCTGCC TGATGAAACT TCGGATCATT ACTAGGCA GCCCCTCCAA YATCTCYGCC TGATGAAACT TCGGATCACT ACTAGGC GCCCCTCCAA TATCTCTGCC TGATGAAACT TCGGATCACT ATTAGGCA GCCCCTCTAA CATCTCTGCC TGATGAAACT TCGGATCATT ACTAGGCA GCCCATCTAA CATCTCTGCC TGATGAAACT TCGGATCACT ACTAGGC

[ [ [ [ [ [ [

80 . | 1] AF020893 > 71 2] AF020894 > 71 3] AF020895 > 71 4] AF020896 > 71 5] AF020897 > 71 6] AF020898 > 71 7] AF020899 > 71

150 160 170 180 190 200 210 . | . | . | . | . | . | . | 1] AF020893 > 141 CACAGGGATC TTCCTAGCAA TACATTACTC ACCAAACATC TCACTGG 2] AF020894 > 141 CACCGGAATA TTTCTAGCCA TGCACTACTC ACCAAACATC TCACTAG 3] AF020895 > 141 CACCGGAATA TTTCTAGCTA TACACTACTC ACCAAACATC TCACTAGC 4] AF020896 > 141 TACTGGAATC TTTCTAGCAA TACACTACTC ACCAGACATC TCACTAGC 5] AF020897 > 141 TACCGGAATC TTTCTAGCAA TACACTACTC ACCAGACATC TCACTAG 6] AF020898 > 141 TACTGGAATT TTTCTGGCAA TACACTACTC ACCAAACATC TCACTAGC 7] AF020899 > 141 TACCGGAATC TTTCTAGCAA TACACTACTC ACCAAACATC TCACTAGC 220 230 240 250 260 270 280 . | . | . | . | . | . | . | 1] AF020893 > 211 ACCCGAGACG TACAGTACGG ATGACTCATC CGTAACATAC ACGCCA 2] AF020894 > 211 ACCCGAGATG TACAATATGG ATGACTTATC CGAAATACAC ATGCTAA 3] AF020895 > 211 ACCCGAGATG TACAATACGG ATGACTTATC CGAAATATAC ATGCTAA 4] AF020896 > 211 ACTCGAGATG TACAGTATGG ATGACTTATC CGAAACTTAC ACGCCAA 5] AF020897 > 211 ACCCGAGACG TACAGTACGG ATGACTTATC CGAAATATAC ATGCTAA 6] AF020898 > 211 ACCCGAGACG TACAGTACGG ATGGCTTATC CGAAATATAC ATGCCAA 7] AF020899 > 211 ACCCGAGACG TACAATATGG ATGACTCATT CGAAACATAC ATGCCAA 290 300 310 320 330 340 350 . | . | . | . | . | . | . | 1] AF020893 > 281 GCATTTATCT TCACATCGGC CGAGGAATTT ATTACGGCTC ATACTTG 2] AF020894 > 281 GCATATACCT CCATATTGGA CGAGGACTTT ATTACGGCTC CTACCTA 3] AF020895 > 281 GCATATACCT CCATATTGGA CGAGGACTTT ACTATGGCTC CTATTTAT 4] AF020896 > 281 GTATCTACCT CCACATCGGC CGAGGACTTT ACTACGGTTC TTATCTC 5] AF020897 > 281 GCATTTACCT CCACATCGGC CGAGGACTTT ACTACGGCTC TTACCTA 6] AF020898 > 281 GTATCTACCT TCACATCGGT CAAGGACTTT ATTACGGCTC TTATCTAT 7] AF020899 > 281 GCATCTACCT CCACATCGGC CGAGGACTTT ACTACGGCTC TTACTTA

[ [ [ [ [ [ [

[ [ [ [ [ [ [

Monday, October 11, 1999

Page: 1

<

The NCBI Taxonomy Homepage


The taxonomy browser

The NCBI taxonomy database contains the names of all organisms that are represented in the genetic databases with at least one nucleotide or protein sequence. Click on the tree if you want to browse the taxonomic structure or retrieve sequence data for a particular group of organisms.

Taxonomic resources

Do you want to know how many species are currently represented in the genetic databases? Are you interested in the names of the outside experts that have helped the NCBI scientists to build the taxonomy database? Would you like to know what books, journals and databases we draw upon to maintain the taxonomy database? For answers to these and other taxonomy related question click on the book .

FAQs
Frequently asked questions about the taxonomy database. Created December 6, 1995 Comments and questions to info@ncbi.nlm.nih.gov Credits: Detlef Leipe, Vladimir Soussov

Monday, October 11, 1999

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NCBI taxonomy browser


This is the top level of the taxonomy database maintained by NCBI/GenBank. You can explore any of the taxa listed below by clicking it.
Archaea Eubacteria Eukaryota Viroids Viruses Other Unclassified

This is a searchable index. You can enter the name ofsuperspecific taxa (e.g., Porifera) or the name of a particular organism (e.g., Thalarctos maritimus for the polar bear or polar bear itself). Query: Use query string as : complete match Start Search wild card search Reset

set of tokens

The "Set of tokens" option returns longer names that include the search terms, e.g., hybrid taxa. See what happens if you query "Bos taurus" using the "Complete match" option versus the "Set of tokens" option. See examples

These are direct links to some of the organisms commonly used in molecular research projects:
Arabidopsis thaliana Dictyostelium discoideum Fugu rubripes Mus musculus Caenorhabditis elegans Drosophila Hepatitis C virus Mycoplasma Danio rerio (zebrafish) Escherichia coli Homo sapiens Oryza sativa

Plasmodium falciparum Pneumocystis carinii Rattus Saccharomyces cerevisiae Schizosaccharomyces pombe Xenopus laevis Comments and questions to info@ncbi.nlm.nih.gov Credits: Scott Federhen, Carol Hotton, Detlef Leipe, Vladimir Soussov.

Monday, October 11, 1999

Page: 1

Corvidae
Parents: Levels: 3 Passeriformes Display number of nucleotides proteins GoTo Parent structures Accept

Corvidae [ 104 93 ] Click here to get information on this taxon. Aphelocoma [ 29 23 ] Aphelocoma coerulescens(scrub jay) [ 23 23 ] Aphelocoma ultramarina(Mexican jay) [ 6 ] Calocitta [ 1 1 ] Calocitta formosa [ 1 1 ] Cissa [ 1 1 ] Cissa chinensis [ 1 1 ] Corvus [ 40 42 ] Corvus albus(pied crow) [ 1 2 ] Corvus brachyrhynchos [ 2 3 ] Corvus corax [ 16 1 ] Corvus corone [ 4 4 ] Corvus frugilegus [ 4 28 ] Corvus kubaryi(Mariana crow) [ 10 ] Corvus macrorhynchos(jungle crow) [ 2 1 ] Corvus monedula(jackdaw) [ 1 3 ] Cyanocitta [ 1 1 ] Cyanocitta cristata [ 1 1 ] Cyanocorax [ 2 2 ] Cyanocorax chrysops [ 2 2 ] Cyanolyca [ 1 1 ] Cyanolyca viridicyana(white-collared jay) [ 1 1 ] Elminia [ 2 4 ] Elminia longicauda [ 2 4 ] Garrulus [ 2 2 ] Garrulus glandarius [ 1 1 ] Garrulus lidthi [ 1 1 ] Gymnorhinus [ 1 1 ] Gymnorhinus cyanocephala [ 1 1 ] Malaconotinae [ 1 2 ] Dryoscopus [ 1 2 ] Dryoscopus gambensis [ 1 2 ] Nucifraga [ 1 1 ] Nucifraga caryocatactes [ 1 1 ] Oriolus [ 2 1 ] Oriolus xanthornus(dark-throated oriole) [ 2 1 ] Perisoreus [ 2 2 ] Perisoreus canadensis [ 1 1 ] Perisoreus infaustus [ 1 1 ] Pica [ 2 3 ] Pica pica(black-billed magpie) [ 2 3 ] Ptilostomus [ 1 1 ] Ptilostomus afer [ 1 1 ] Pyrrhocorax [ 4 2 ] Pyrrhocorax graculus [ 2 1 ] Pyrrhocorax pyrrhocorax [ 2 1 ] Schetba [ 6 ] Schetba rufa [ 6 ] Terpsiphone [ 2 1 ] Terpsiphone viridis(African paradise-flycatcher) [ 2 1 ] Urocissa [ 1 1 ] Urocissa erythrorhyncha [ 1 1 ]
Monday, October 11, 1999 Page: 1

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The Human Genome

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Web Resources BLAST. Compare your sequence to the genome or its gene products. Cytogenetics. A cytogenetic resource of FISH-mapped, sequence-tagged clones. dbSNP. Database of SNPs and other genetic variations. e-PCR. Check your sequence for STSs and view in genomic context. GEO. Gene Expression Omnibus, a public repository for expression data. HomoloGene. Putative homologies among human, mouse, rat, and zebrafish. Homology Map. Blocks of conserved synteny between mouse and human. LocusLink . Focal point for genes and associated information. OMIM . Guide to genes and inherited disorders maintained by JHU and collaborators. RefSeq . Reference sequences of genomic contigs, mRNAs, and proteins. SAGEmap. Gene expression results from SAGE tags mapped to sequences. Sequencing. Summary of human genome sequencing progress. MapViewer . Interactive viewer for genome maps,sequence, and genes. UniGene . Organization of transcribed sequences into gene-based clusters. UniSTS. A non- redundant collection of STSs with links to maps and sequence.
http://www.ncbi.nlm.nih.gov/genome/guide/human/

Building an information infrastructure A challenge facing researchers today is the ability to piece together and analyze the multitudes of data currently being generated through the Human Genome Project. NCBI's Web site serves an an integrated, one-stop, genomic information infrastructure for biomedical researchers from around the world so that they may use this data in their research efforts. More... Working Draft Analysis Published

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MapViewer tips and tricks When browsing the genome using the new MapViewer, click on Display Settings to choose from several types of maps and . Below are three views of the BRCA2 locus using different display options. Click the image to see the full MapViewer display.

RB1. Complex of retinoblastoma (RB) protein with E7, a viral oncoprotein that frequently binds RB and blocks its function.

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Chromosome: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X [ Y ] Master Map: Genes On Sequence Maps & Options Total Genes On Chromosome: 330 [3 not localized] Region Displayed: 0-59M bp Download/View Sequence/Evidence Genes Labeled: 20 Total Genes in Region: 327 symbol orient. links evidence cyto. SRY RPS4Y Go PCDH22 TBL1Y TSPY TTY8 USP9Y DBY XKRY LOC86614 TTY9 TTY14 TTY10 EIF1AY sv ev - seq mm sv ev - seq mm sv ev hm seq mm sv ev - seq mm sv ev - seq mm sv ev hm seq mm sv ev - seq mm sv ev - seq mm sv ev - seq mm sv ev - seq mm sv ev - seq mm sv ev hm seq mm sv ev - seq mm sv ev - seq mm sv ev - seq mm sv ev - seq mm sv ev - seq mm sv ev - seq mm C C C C C C C C C C C C C C C C C C Yp11.2 Yp11.2 Yp11.2 Yp11.2 Yq11.2 Yq11 sv ev hm seq mm sv ev - seq mm C C Yp11.3 Yp11.3

full name sex determining region Y ribosomal protein S4, Y-linked protocadherin 22 transducin beta-like 1 protein testis specific protein, Y-linked testis transcript Y 8 ubiquitin specific protease 9, Y chromosome (fat facets-like Drosophila) DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide, Y chromosome

Yq11.221 Testis-specific XK-related protein on Y Yq11.221 heat shock transcription factor 2-like Yq11.221 testis transcript Y 9 Yq11.221 testis transcript Y 14

Yq11.221 eukaryotic translation initiation factor 1A, Y chromosome

ideogram master

FLJ22714 TTTY6 PRY DAZ4 LOC84664 DAZ

Yq11.221 testis-specific transcript, Y-linked 6 Yq11.221 PTPN13-like, Y-linked Yq11 deleted in azoospermia 4

Yq11.222 melanoma-associated chondroitin sulfate proteoglycan-like Yq11 deleted in azoospermia

http://www.ncbi.nlm.nih.gov/cgi-bin/Entrez/maps.cgi?ORG=hum&MAPS=ideogr,est,loc&LINKS=ON&VERBOSE=ON&CHR=Y

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Map Viewer Help Human Maps Help FTP Chr. X Resource Data As Table View

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Chromosome: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 [ X ] Y Master Map: Genes On Sequence Maps & Options Total Genes On Chromosome: 2062 [27 not localized] Region Displayed: 0-151M bp Download/View Sequence/Evidence Genes Labeled: 20 Total Genes in Region: 2035 evidence cyto. symbol orient. links SHOX DXF68S1E Go CA5B PRO0386 TM4SF2 UBE1 CLCN5 GAGEB1 KLF8 IL2RG ATP7A TM4SF6 LOC51186 KCNE1L sv ev hm seq mm sv ev - seq mm sv ev hm seq mm sv ev hm seq mm sv ev hm seq mm sv ev - seq mm sv ev - seq mm sv ev hm seq mm sv ev hm seq mm sv ev hm seq mm sv ev - seq mm sv ev hm seq mm sv ev hm seq mm sv ev - seq mm sv ev hm seq mm sv ev - seq mm sv ev hm seq mm sv ev - seq mm C C C C C C C C C C C C C C C C C C Xp21.1 Xp22.13 Xq11 Xp11.23 sv ev - seq mm sv ev - seq mm C C Yp11.3 Xp22.32

full name short stature homeobox DNA segment, numerous copies, expressed probes (GS1 gene) carbonic anhydrase VB, mitochondrial hypothetical protein PRO0386 transmembrane 4 superfamily member 2 ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)

Xp11.23-p11.22 chloride channel 5 (nephrolithiasis 2, X-linked, Dent disease) Xp11.23 Xp11.21 Xq13.1 Xq13.2-q13.3 Xq22 Xq22.1 Xq22.3 Xq24 Xq26.1 Xq26.1-q27.2 Xq28 Xq28 Xq28 G antigen, family B, 1 (prostate associated) Kruppel-like factor 8 interleukin 2 receptor, gamma (severe combined immunodeficiency) ATPase, Cu++ transporting, alpha polypeptide (Menkes syndrome) transmembrane 4 superfamily member 6 pp21 homolog potassium voltage-gated channel, Isk-related family, member 1-like NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 1 (7.5kD, MWFE) CGI-79 protein HIV TAT specific factor 1 hypothetical protein DKFZp761H2024 serine/threonine kinase 23 ubiquitin-like 4

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NDUFA1 LOC51634 HTATSF1 DKFZP761H2024 STK23 UBL4


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Wednesday, April 24, 2002

PDB Molecule of the Month: Thrombin

Page: 1

Thrombin
Molecule of the Month by David S. Goodsell

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index of installments

Anticoagulants
Blood clots are not always wanted. For instance, many people take small doses of aspirin, under the direction of their doctors, to reduce the chance of the blood clots that cause heart attacks. Aspirin acts on the protein cyclooxygenase, which is important in another aspect of clot formation that uses small cell fragments called platelets. The rat poison warfarin, not commonly used these days, blocks the formation of the modified glutamate amino acids that hold calcium ions, shown on the last page. The unfortunate rats then die because of uncontrolled blood clotting. Leeches, as you might expect, also detest blood clots, because it means the end to their meal. They make special proteins that block thrombin (or other enzymes), stopping the formation of the clot. One example, a protein called hirudin, is shown here on the left (from PDB entry 2hgt). The leech protein is shown in blue-- notice how it blocks the active site of thrombin perfectly. Next: Exploring the Structure Previous: In the Right Place at the Right Time
RCSB

http://www.rcsb.org/pdb/molecules/pdb25_3.html