Difference between revisions of "Essay !10 - By using Drosophlia melanogaster protein sequence, Finding the human orthologue candidates and variants of w, sc, cdk1 Code : KSI0022"

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<p>Genetics Homework # 3 &ndash; Genome browser</p>
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<p style="text-align:center"><span style="font-size:36px">&lt;Genomics&nbsp;Essay&nbsp;#10 &ndash; Genome browser&gt;</span></p>
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p>UNIST BIO - 20141110 Sangin Kim</p>
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<p style="text-align:right"><strong>UNIST BIO - 20141110 Sangin Kim</strong></p>
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p>White (w)</p>
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<p style="text-align:center"><span style="color:#008000"><strong><span style="font-size:28px">White (w)</span></strong></span></p>
  
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<p>Drosophila melanogaster protein sequence of White (w)</p>
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<p><strong>Drosophila melanogaster protein sequence of White (w)</strong></p>
  
 
<p>&gt;sp|P10090|WHITE_DROME Protein white OS=Drosophila melanogaster GN=w PE=2 SV=2</p>
 
<p>&gt;sp|P10090|WHITE_DROME Protein white OS=Drosophila melanogaster GN=w PE=2 SV=2</p>
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<p>YVGLAILIVSFRVLAYLALRLRARRKE</p>
 
<p>YVGLAILIVSFRVLAYLALRLRARRKE</p>
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<p><img alt="그림입니다.
 
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&amp;#xA;원본 그림의 이름: 11.PNG
 
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&amp;#xA;원본 그림의 크기: 가로 1072pixel, 세로 212pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB0000126030ec.PNG" style="height:84pt; width:425pt" /></p>
 
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<p>Human orthologue candidates and comparing (w)</p>
 
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<p><img alt="그림입니다.
 
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&amp;#xA;원본 그림의 이름: 111.PNG
 
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&amp;#xA;원본 그림의 크기: 가로 1110pixel, 세로 463pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB0000126030f2.PNG" style="height:177pt; width:425pt" /></p>
 
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p><img alt="그림입니다.
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<p><img alt="" src="/ckfinder/userfiles/images/noname01.PNG" style="height:212px; width:1072px" /></p>
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&amp;#xA;원본 그림의 이름: 1111111.PNG
 
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&amp;#xA;원본 그림의 크기: 가로 1119pixel, 세로 38pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB0000126030f6.PNG" style="height:14pt; width:425pt" /></p>
 
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
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<p><img alt="그림입니다.
 
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&amp;#xA;원본 그림의 이름: 1 ortholog.PNG
 
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&amp;#xA;원본 그림의 크기: 가로 1138pixel, 세로 642pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB0000126030fa.PNG" style="height:239pt; width:425pt" /></p>
 
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p>Many-to-many ortholog</p>
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<p><strong>Human orthologue candidates and comparing (w)</strong></p>
  
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<p>&nbsp;</p>
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<p><img alt="" src="/ckfinder/userfiles/images/noname02.PNG" style="height:463px; width:1110px" /></p>
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<p>&nbsp;</p>
 
  
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<p>&nbsp;</p>
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<p><img alt="" src="/ckfinder/userfiles/images/noname03.PNG" style="height:38px; width:1119px" /></p>
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p>Selected one of the human orthologue candidate and variants (w)</p>
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<p><img alt="" src="/ckfinder/userfiles/images/noname04.PNG" style="height:642px; width:1138px" /></p>
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p>&nbsp;</p>
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<p>Many-to-many ortholog</p>
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
−
<p><img alt="그림입니다.
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<p><strong>Selected one of the human orthologue candidate and variants (w)</strong></p>
−
&amp;#xA;원본 그림의 이름: 111111111111.PNG
 
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&amp;#xA;원본 그림의 크기: 가로 684pixel, 세로 494pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB000012603102.PNG" style="height:307pt; width:425pt" /></p>
 
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p>&nbsp;</p>
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<p><img alt="" src="/ckfinder/userfiles/images/noname05.PNG" style="height:494px; width:684px" /></p>
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
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<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p>Scalloped (sc)</p>
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<p style="text-align:center"><span style="color:#008000"><strong><span style="font-size:28px">Scalloped (sc)</span></strong></span></p>
  
−
<p>Drosophila melanogaster protein sequence of Scalloped (sc)</p>
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<p><strong>Drosophila melanogaster protein sequence of Scalloped (sc)</strong></p>
  
 
<p>&gt;sp|P30052|SCAL_DROME Protein scalloped OS=Drosophila melanogaster GN=sd PE=1 SV=1</p>
 
<p>&gt;sp|P30052|SCAL_DROME Protein scalloped OS=Drosophila melanogaster GN=sd PE=1 SV=1</p>
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<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p>&nbsp;</p>
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<p><img alt="" src="/ckfinder/userfiles/images/noname06.PNG" style="height:164px; width:1003px" /></p>
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<p><img alt="그림입니다.
 
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&amp;#xA;원본 그림의 이름: 222222.PNG
 
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&amp;#xA;원본 그림의 크기: 가로 1003pixel, 세로 164pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB00001260310a.PNG" style="height:69pt; width:425pt" /></p>
 
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<p>&nbsp;</p>
 
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−
<p>Human orthologue candidates and comparing (sc)</p>
 
−
 
 
−
<p>&nbsp;</p>
 
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p><img alt="그림입니다.
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<p><img alt="" src="/ckfinder/userfiles/images/noname07.PNG" style="height:368px; width:1136px" /></p>
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&amp;#xA;원본 그림의 이름: 222222222.PNG
 
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&amp;#xA;원본 그림의 크기: 가로 1136pixel, 세로 368pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB000012603113.PNG" style="height:137pt; width:425pt" /></p>
 
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
−
<p><img alt="그림입니다.
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<p><strong>Human orthologue candidates and comparing (sc)</strong></p>
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&amp;#xA;원본 그림의 이름: 222.PNG
 
−
&amp;#xA;원본 그림의 크기: 가로 1119pixel, 세로 33pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB00001260311a.PNG" style="height:12pt; width:425pt" /></p>
 
  
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<p>&nbsp;</p>
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<p><img alt="" src="/ckfinder/userfiles/images/noname08.PNG" style="height:33px; width:1119px" /></p>
  
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<p><img alt="그림입니다.
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<p><img alt="" src="/ckfinder/userfiles/images/noname09.PNG" style="height:71px; width:1121px" /></p>
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&amp;#xA;원본 그림의 이름: 22.PNG
 
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&amp;#xA;원본 그림의 크기: 가로 1121pixel, 세로 71pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB00001260311e.PNG" style="height:27pt; width:425pt" /></p>
 
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<p>&nbsp;</p>
 
  
 
<p>1-to-many ortholog</p>
 
<p>1-to-many ortholog</p>
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<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
−
<p>Selected one of the human orthologue candidate and variants (sc)</p>
+
<p><strong>Selected one of the human orthologue candidate and variants (sc)</strong></p>
  
−
<p><img alt="그림입니다.
+
<p><img alt="" src="/ckfinder/userfiles/images/noname10.PNG" style="height:490px; width:685px" /></p>
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&amp;#xA;원본 그림의 이름: 2222222222222222222222222222222222222222222222222222222222222222222222.PNG
 
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&amp;#xA;원본 그림의 크기: 가로 685pixel, 세로 490pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB000012603124.PNG" style="height:304pt; width:425pt" /></p>
 
  
 
<p>(1) Missense variants - 3527</p>
 
<p>(1) Missense variants - 3527</p>
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<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p>Cdk1</p>
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<p style="text-align:center"><span style="color:#008000"><span style="font-size:28px"><strong>Cdk1</strong></span></span></p>
  
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<p>&nbsp;</p>
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<p><strong>Drosophila melanogaster protein sequence of Cdk1</strong></p>
−
 
 
−
<p>Drosophila melanogaster protein sequence of Cdk1</p>
 
−
 
 
−
<p>&nbsp;</p>
 
  
 
<p>&gt;sp|P23572|CDK1_DROME Cyclin-dependent kinase 1 OS=Drosophila melanogaster GN=Cdk1 PE=1 SV=1</p>
 
<p>&gt;sp|P23572|CDK1_DROME Cyclin-dependent kinase 1 OS=Drosophila melanogaster GN=Cdk1 PE=1 SV=1</p>
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<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p>&nbsp;</p>
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<p><img alt="" src="/ckfinder/userfiles/images/noname11.PNG" style="height:163px; width:989px" /></p>
 +
 
 +
<p><strong>Human orthologue candidates and comparing (Cdk1)</strong></p>
  
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<p><img alt="그림입니다.
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<p><img alt="" src="/ckfinder/userfiles/images/noname12.PNG" style="height:374px; width:1128px" /></p>
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&amp;#xA;원본 그림의 이름: 123123.PNG
 
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&amp;#xA;원본 그림의 크기: 가로 989pixel, 세로 163pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB00001260312c.PNG" style="height:70pt; width:425pt" /></p>
 
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
−
<p>Human orthologue candidates and comparing (Cdk1)</p>
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<p><img alt="" src="/ckfinder/userfiles/images/noname13.PNG" style="height:33px; width:1119px" /></p>
  
−
<p><img alt="그림입니다.
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<p><img alt="" src="/ckfinder/userfiles/images/noname14.PNG" style="height:74px; width:1117px" /></p>
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&amp;#xA;원본 그림의 이름: 123123123123.PNG
 
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&amp;#xA;원본 그림의 크기: 가로 1128pixel, 세로 374pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB000012603130.PNG" style="height:141pt; width:425pt" /></p>
 
  
 
<p>&nbsp;</p>
 
<p>&nbsp;</p>
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<p>&nbsp;</p>
 
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<p><img alt="그림입니다.
 
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&amp;#xA;원본 그림의 이름: 123.PNG
 
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&amp;#xA;원본 그림의 크기: 가로 1119pixel, 세로 33pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB000012603134.PNG" style="height:12pt; width:425pt" /></p>
 
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<p><img alt="그림입니다.
 
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&amp;#xA;원본 그림의 이름: 123123123123123123.PNG
 
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&amp;#xA;원본 그림의 크기: 가로 1117pixel, 세로 74pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB000012603135.PNG" style="height:28pt; width:425pt" /></p>
 
  
 
<p>1 &ndash; to &ndash; 1 ortholog</p>
 
<p>1 &ndash; to &ndash; 1 ortholog</p>
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<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p>Selected one of the human orthologue candidate and variants (Cdk1)</p>
+
<p><strong>Selected one of the human orthologue candidate and variants (Cdk1)</strong></p>
  
−
<p>&nbsp;</p>
+
<p><img alt="" src="/ckfinder/userfiles/images/noname15.PNG" style="height:486px; width:680px" /></p>
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<p><img alt="그림입니다.
 
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&amp;#xA;원본 그림의 이름: 12312312312312312312312312.PNG
 
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&amp;#xA;원본 그림의 크기: 가로 680pixel, 세로 486pixel" src="file:///C:\Users\상인\AppData\Local\Temp\Hnc\BinData\EMB00001260313b.PNG" style="height:303pt; width:425pt" /></p>
 
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<p>&nbsp;</p>
 
  
 
<p>(1) Missense variants - 1354</p>
 
<p>(1) Missense variants - 1354</p>
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<p>&nbsp;</p>
 
<p>&nbsp;</p>
  
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<p>2016.10.14.Fri</p>
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<p style="text-align:right">2016.10.14.Fri</p>
  
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<p>UNIST BIO Junior 20141110 Sangin Kim</p>
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<p style="text-align:right">UNIST BIO Junior 20141110 Sangin Kim</p>

Latest revision as of 16:02, 9 November 2016

<Genomics Essay #10 – Genome browser>

 

UNIST BIO - 20141110 Sangin Kim

 

White (w)

Drosophila melanogaster protein sequence of White (w)

>sp|P10090|WHITE_DROME Protein white OS=Drosophila melanogaster GN=w PE=2 SV=2

MGQEDQELLIRGGSKHPSAEHLNNGDSGAASQSCINQGFGQAKNYGTLLPPSPPEDSGSG

SGQLAENLTYAWHNMDIFGAVNQPGSGWRQLVNRTRGLFCNERHIPAPRKHLLKNVCGVA

YPGELLAVMGSSGAGKTTLLNALAFRSPQGIQVSPSGMRLLNGQPVDAKEMQARCAYVQQ

DDLFIGSLTAREHLIFQAMVRMPRHLTYRQRVARVDQVIQELSLSKCQHTIIGVPGRVKG

LSGGERKRLAFASEALTDPPLLICDEPTSGLDSFTAHSVVQVLKKLSQKGKTVILTIHQP

SSELFELFDKILLMAEGRVAFLGTPSEAVDFFSYVGAQCPTNYNPADFYVQVLAVVPGRE

IESRDRIAKICDNFAISKVARDMEQLLATKNLEKPLEQPENGYTYKATWFMQFRAVLWRS

WLSVLKEPLLVKVRLIQTTMVAILIGLIFLGQQLTQVGVMNINGAIFLFLTNMTFQNVFA

TINVFTSELPVFMREARSRLYRCDTYFLGKTIAELPLFLTVPLVFTAIAYPMIGLRAGVL

HFFNCLALVTLVANVSTSFGYLISCASSSTSMALSVGPPVIIPFLLFGGFFLNSGSVPVY

LKWLSYLSWFRYANEGLLINQWADVEPGEISCTSSNTTCPSSGKVILETLNFSAADLPLD

YVGLAILIVSFRVLAYLALRLRARRKE

 

 

 

Human orthologue candidates and comparing (w)

 

 

Many-to-many ortholog

 

Selected one of the human orthologue candidate and variants (w)

 

 

(1) Missense variants - 10718

(2) Synonymous variants - 6883

(3) Intronic variants - 248025

 

 

Scalloped (sc)

Drosophila melanogaster protein sequence of Scalloped (sc)

>sp|P30052|SCAL_DROME Protein scalloped OS=Drosophila melanogaster GN=sd PE=1 SV=1

MKNITSSSTCSTGLLQLQNNLSCSELEVAEKTEQQAVGPGTIPSPWTPVNAGPPGALGSA

DTNGSMVDSKNLDVGDMSDDEKDLSSADAEGVWSPDIEQSFQEALSIYPPCGRRKIILSD

EGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLREIQAKIKVQFWQPGLQPST

SQDFYDYSIKPFPQPPYPAGKTSTAVSGDETGIPPSQLPWEGRAIATHKFRLLEFTAFME

IQRDEIYHRHLFVQLGGKPSFSDPLLETVDIRQIFDKFPEKSGGLKDLYEKGPQNAFYLV

KCWADLNTDLTTGSETGDFYGVTSQYESNENVVLVCSTIVCSFGKQVVEKVESEYSRLEN

NRYVYRIQRSPMCEYMINFIQKLKNLPERYMMNSVLENFTILQVMRARETQETLLCIAYV

FEVAAQNSGTTHHIYRLIKE

 

 

 

Human orthologue candidates and comparing (sc)

1-to-many ortholog

 

 

Selected one of the human orthologue candidate and variants (sc)

(1) Missense variants - 3527

(2) Synonymous variants - 2175

(3) Intronic variants - 145182

 

 

Cdk1

Drosophila melanogaster protein sequence of Cdk1

>sp|P23572|CDK1_DROME Cyclin-dependent kinase 1 OS=Drosophila melanogaster GN=Cdk1 PE=1 SV=1

MEDFEKIEKIGEGTYGVVYKGRNRLTGQIVAMKKIRLESDDEGVPSTAIREISLLKELKH

ENIVCLEDVLMEENRIYLIFEFLSMDLKKYMDSLPVDKHMESELVRSYLYQITSAILFCH

RRRVLHRDLKPQNLLIDKSGLIKVADFGLGRSFGIPVRIYTHEIVTLWYRAPEVLLGSPR

YSCPVDIWSIGCIFAEMATRKPLFQGDSEIDQLFRMFRILKTPTEDIWPGVTSLPDYKNT

FPCWSTNQLTNQLKNLDANGIDLIQKMLIYDPVHRISAKDILEHPYFNGFQSGLVRN

 

Human orthologue candidates and comparing (Cdk1)

 

 

1 – to – 1 ortholog

 

Selected one of the human orthologue candidate and variants (Cdk1)

(1) Missense variants - 1354

(2) Synonymous variants - 958

(3) Intronic variants - 29424

 

 

2016.10.14.Fri

UNIST BIO Junior 20141110 Sangin Kim

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