Tugas Terstruktur Teknik Analisis Biologi Molekuler Nama : Swaidatul Masluhiya Af.

NIM : 0810913054

Salmonella enterica subsp. enterica serovar Montevideo str. NC_MB1102090054 SEEM054_94, whole genome shotgun sequence
GenBank: AESO01000089.1
FASTA Graphics Go to:

LOCUS DEFINITION ACCESSION VERSION DBLINK KEYWORDS SOURCE ORGANISM

AESO01000089

956 bp

DNA

linear

BCT 07-MAR-2011

Salmonella enterica subsp. enterica serovar Montevideo str. NC_MB110209-0054 SEEM054_94, whole genome shotgun sequence. AESO01000089 AESO01000000 AESO01000089.1 Project: 46903 WGS. Salmonella enterica subsp. enterica serovar Montevideo str. NC_MB110209-0054 Salmonella enterica subsp. enterica serovar Montevideo str. NC_MB110209-0054 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacteriales; Enterobacteriaceae; Salmonella. GI:322643559

REFERENCE AUTHORS

(bases 1 to 956)

Lienau,E.K., Strain,E., Wang,C., Zheng,J., Ottesen,A.R., Keys,C.E., Hammack,T.S., Musser,S.M., Brown,E.W., Allard,M.W., Cao,G., Meng,J. and Stones,R.

TITLE JOURNAL PUBMED REMARK REFERENCE AUTHORS TITLE JOURNAL

Identification of a Salmonellosis Outbreak by Means of Molecular Sequencing N. Engl. J. Med. (2011) In press 21345093 Publication Status: Available-Online prior to print 2 (bases 1 to 956) Strain,E.A., Brown,E. and Allard,M.W. Direct Submission Submitted (18-JAN-2011) Center for Food Safety and Nutrition, United States Food and Drug Administration, 5100 Paint Branch Parkway, College Park, MD 20740, USA

COMMENT

Annotation was added by the NCBI Prokaryotic Genomes Automatic Annotation Pipeline Group. Information about the Pipeline can be found here: http://www.ncbi.nlm.nih.gov/genomes/static/Pipeline.html. Please be aware that the annotation is done automatically with little or no manual curation. ##Genome-Assembly-Data-START## Assembly Method Genome Coverage :: Newbler v. 2.3 :: 20x

Sequencing Technology :: 454 Titanium

##Genome-Assembly-Data-END## FEATURES source Location/Qualifiers 1..956 /organism="Salmonella enterica subsp. enterica serovar Montevideo str. NC_MB110209-0054" /mol_type="genomic DNA" /strain="NC_MB110209-0054" /serovar="Montevideo" /isolate="FDA_2010_155_Clinical-NC-5" /isolation_source="stool" /host="Homo sapiens" /sub_species="enterica" /db_xref="taxon:749949" /collection_date="2009" /note="clinical isolate" gene CDS complement(12..845) /locus_tag="SEEM054_22214" complement(12..845) /locus_tag="SEEM054_22214" /codon_start=1 /transl_table=11 /product="putative inner membrane protein" /protein_id="EFY40117.1" /db_xref="GI:322643560" /translation="MFEETIKKQFELLDISNFNVDISHRLLFVCGGKVDVRAPIPPSF RDRLLTYTAKHASELHEHFILAETFKDYFKENAYPDLLVFEDDIASISSLIIIFLESP GSLVELGIFCNKSELFKKILIVASAEEVSGEDSFIYLGPLEYIKKKVSSSVVIYPWPD PEVLKYDNDFLDDLCVNIKEKLSSIPKTEQFSKDNSGHIALLITEIISLCAPIQLSEI ESALNSLGFNISTKIINRSIYLLQKVGFIDVLSYSSNKYYFPLKERKWVKFGKLKIIN S" ORIGIN 1 ttgttgatta tctatgagtt tattatcttt agtttaccaa attttaccca tttgcgctct 61 tttaatggaa agtaatattt gtttgagcta tatgataaaa cgtctataaa accaactttc 121 tgaagtaaat aaattgatct gttaataatt tttgttgaaa tattaaaccc taatgagttt 181 agggctgatt ctatttcact aagttgtatt ggggcgcaaa gagatataat ttcagtaatt 241 agaagtgcta tatgtccaga attatcctta ctgaattgtt ctgtttttgg gattgatgaa 301 agtttttctt ttatatttac acataaatca tcaagaaaat cattatcgta ttttaagact 361 tcaggatccg gccaaggata gattacaaca gaggatgaga ctttcttctt aatatactct 421 agtgggccta aataaatgaa tgagtcctca ccggatactt cttccgctga agcaacaatc 481 agtatttttt taaatagttc tgatttgttg caaaatatac ctaactcaac taatgatcct 541 ggactttcta aaaaaatgat aataagagat gaaatactgg ctatatcatc ttcaaacacc 601 agaaggtccg gataggcatt ctctttaaaa taatccttga atgtctcagc tagaatgaaa 661 tgttcgtgaa gctcagaggc atgttttgct gtgtaagtga gtagtctatc cctaaaactg 721 gggggaattg gtgcacgtac atcgactttg ccaccacaca cgaaaaggag acgatgagat 781 atatcaacat tgaagttact tatgtctaac aattcaaatt gttttttaat agtttcttca 841 aacattgatt taaacgttat gtatttttga tttgtcttcc gttgatgaaa aaaacgagca 901 atgttttttt gctcgttttt tactctttac tagaggaggc gctagaaaag tttctt

Primer Forward : 5 tgagtcctca ccggatactt 3 GC% = (10/20)*100% =50% TM =(2*(A+T)+(4*(G+C)) =(2*10)+(4*10) =20+40 =60C TA
=(60-5)C =55C

Primer Reverse : 5ttactagagg aggcgctaga 3 Anti-sense GC% : 3 tctagcgcct cctctagtaa 5

= (10/20)*100% =50%

TM

=(2*(A+T)+(4*(G+C)) =(2*10)+(4*10) =20+40 =60C

TA

=(60-5)C =55C

Tugas Terstruktur Teknik Analisis Biologi Molekuler Nama : Atika Yuan Silvia NIM : 0810910004

Gallus gallus thyroid hormone responsive (SPOT14 homolog, rat) (THRSP), mRNA
NCBI Reference Sequence: NM_213577.1

FASTA Graphics
LOCUS DEFINITION NM_213577 797 bp mRNA linear VRT 31-OCT-2010 Gallus gallus thyroid hormone responsive (SPOT14 homolog, rat) (THRSP), mRNA. ACCESSION NM_213577 VERSION NM_213577.1 GI:47087182 KEYWORDS . SOURCE Gallus gallus (chicken) ORGANISM Gallus gallus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Galliformes; Phasianidae; Phasianinae; Gallus. REFERENCE 1 (bases 1 to 797) AUTHORS d'Andre Hirwa,C., Yan,W., Wallace,P., Nie,Q., Luo,C., Li,H., Shen,X., Sun,L., Tang,J., Li,W., Zhu,X., Yang,G. and Zhang,X. TITLE Effects of the thyroid hormone responsive spot 14alpha gene on chicken growth and fat traits JOURNAL Poult. Sci. 89 (9), 1981-1991 (2010) PUBMED 20709985 REMARK GeneRIF: Variations in THRSPalpha in growth an fat traits, and its effects on lipid profile and lipoprotein and glucose and triiodothyronine effects on the THRSPalpha expression in liver and fat cells are reported. REFERENCE 2 (bases 1 to 797) AUTHORS Wang,X., Carre,W., Zhou,H., Lamont,S.J. and Cogburn,L.A. TITLE Duplicated Spot 14 genes in the chicken: characterization and identification of polymorphisms associated with abdominal fat traits JOURNAL Gene 332, 79-88 (2004) PUBMED 15145057 REMARK GeneRIF: THRSPalpha locus is associated with abdominal fat traits in a broiler x Leghorn resource population. COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence was derived from AY568628.1. FEATURES Location/Qualifiers source 1..797 /organism="Gallus gallus" /mol_type="mRNA" /db_xref="taxon:9031" /chromosome="1" /map="1"

gene

CDS

1..797 /gene="THRSP" /gene_synonym="THRSPA" /note="thyroid hormone responsive (SPOT14 homolog, rat)" /db_xref="CGNC:12971" /db_xref="GeneID:404755" 24..422 /gene="THRSP" /gene_synonym="THRSPA" /note="thyroid hormone responsive spot 14 alpha" /codon_start=1 /product="thyroid hormone responsive (SPOT14 homolog, rat)" /protein_id="NP_998742.1" /db_xref="GI:47087183" /db_xref="CGNC:12971" /db_xref="GeneID:404755" /translation="MEQYFSATQKMEQEVMFPSLLRGVFPQDGADPATGGPADLYEHY QLLKAIKPVVERGLASVTDQSPTSNADADTAPYDGIDGIDGNLEERLSHHMNGLQQVL TDLTKNTKALTRRYSQILEEINLGEGQSSS" aaggagtggg gttccccagc ccccgcagac aggcctggcc atatgatggc tggcttgcag cagccagatc acggagactc agtcccacca gctgccacat ggattgcctt catctgtaac tttctttgat aatgaaa gccatggagc ctgctgcgag ctctacgagc tccgtcaccg atagatggca caggttctga ctggaggaga caagggtgat aggaatgtct ggccaatcct gcagtaggca cttgaaacaa aatgtcacca agtacttctc gggtcttccc actaccagct atcagagccc tagatgggaa ccgacctcac tcaacctcgg ctgacgtttg tctgcacaga cccggcaaac gggcagaaat tgcttttgtt gttcccaaag ggccacgcag gcaggacggg cctcaaggcc caccagcaat tctggaggag caaaaacacc tgaaggtcag cagcccagcg ccagcacaga ctcactgctt gagcgttcgc ctgcatgtgc tcaatgatct aagatggagc gccgacccag atcaagcccg gccgacgccg cggctgtccc aaagctctca agcagctcat gcagctttat ggcttggctg tgtttcacct tgttattgct ctagaccacc gaaataaaat

ORIGIN 1 gaggagaggc 61 aggaggtgat 121 ccaccggcgg 181 tggtggagcg 241 acacggcccc 301 accacatgaa 361 cccggaggta 421 gagcctgcac 481 tcctgtgcca 541 taccatccaa 601 ccattcccgg 661 tcctagaagg 721 tccccactag 781 gcaataataa

Primer Forward : 5 gccatggagc agtacttctc 3 GC% = (11/20)*100% =55% TM = (2*(A+T)+(4*(G+C)) = (2*9) + (4*11) = 18 + 44 = 62C

TA

= (62-5) C =57 C

Primer Reverse : 5 tctgcacaga ccagcacaga 3 Anti-sense GC% : 3 tctgtgctgg tctgtgcaga 5

= (11/20)*100% =55%

TM

= (2*(A+T)+(4*(G+C)) = (2*9) + (4*11) = 18 + 44 = 62C

TA

= (62-5) C =57 C