ASSIGNMENT
Submitted To: Dr Faiza Faraz
Submitted By: Mian M Umer
Subject: Bio-Informatics
Class: BS–MLT
Semester: 8th (B)
Roll No: 66
MINHAJ UNIVERSITY LAHORE
Bioinformatics
How to retrieve an article and gene sequence from NCBI?
1st go on the chrome and search for a selective gene.
Then select any one of them, as I select LPL.
After it go on the NCBI website.
I select the nucleotide in database and in gene search bar I write (LPL).
Then check which link has complete info and the article is published on pubmed.
As I select this link and the complete pathway in that is as follows:
Synthetic construct Homo sapiens clone CCSBHm_00005145 LPL (LPL) mRNA, encodes
complete protein
GenBank: KR709683.1
FASTA Graphics
Go to:
LOCUS KR709683 1557 bp DNA linear SYN 01-JUN-2015
DEFINITION Synthetic construct Homo sapiens clone CCSBHm_00005145 LPL (LPL)
mRNA, encodes complete protein.
ACCESSION KR709683
VERSION KR709683.1
KEYWORDS human mutation ORFeome; hmORFeome1.1; Gateway cloning system;
full-length ORF.
SOURCE synthetic construct
ORGANISM synthetic construct
other sequences; artificial sequences.
REFERENCE 1 (bases 1 to 1557)
AUTHORS Sahni,N., Yi,S., Taipale,M., Fuxman Bass,J.I.,
Coulombe-Huntington,J., Yang,F., Peng,J., Weile,J., Karras,G.I.,
Wang,Y., Kovacs,I.A., Kamburov,A., Krykbaeva,I., Lam,M.H.,
Tucker,G., Khurana,V., Sharma,A., Liu,Y.Y., Yachie,N., Zhong,Q.,
Shen,Y., Palagi,A., San-Miguel,A., Fan,C., Balcha,D., Dricot,A.,
Jordan,D.M., Walsh,J.M., Shah,A.A., Yang,X., Stoyanova,A.K.,
Leighton,A., Calderwood,M.A., Jacob,Y., Cusick,M.E.,
Salehi-Ashtiani,K., Whitesell,L.J., Sunyaev,S., Berger,B.,
Barabasi,A.L., Charloteaux,B., Hill,D.E., Hao,T., Roth,F.P.,
Xia,Y., Walhout,A.J., Lindquist,S. and Vidal,M.
TITLE Widespread macromolecular interaction perturbations in human
genetic disorders
JOURNAL Cell 161 (3), 647-660 (2015)
PUBMED 25910212
REFERENCE 2 (bases 1 to 1557)
AUTHORS Sahni,N., Yi,S., Taipale,M., Fuxman Bass,J.I.,
Coulombe-Huntington,J., Yang,F., Peng,J., Weile,J., Karras,G.I.,
Wang,Y., Kovacs,I.A., Kamburov,A., Krykbaeva,I., Lam,M.H.,
Tucker,G., Khurana,V., Sharma,A., Liu,Y.-Y., Yachie,N., Zhong,Q.,
Shen,Y., Palagi,A., San-Miguel,A., Fan,C., Balcha,D., Dricot,A.,
Jordan,D.M., Walsh,J.M., Shah,A.A., Yang,X., Stoyanova,A.K.,
Leighton,A., Calderwood,M.A., Jacob,Y., Cusick,M.E.,
Salehi-Ashtiani,K., Whitesell,L.J., Sunyaev,S., Berger,B.,
Barabasi,A.-L., Charloteaux,B., Hill,D.E., Hao,T., Roth,F.P.,
Xia,Y., Walhout,A.J.M., Lindquist,S. and Vidal,M.
TITLE Direct Submission
JOURNAL Submitted (14-MAY-2015) Center for Cancer Systems Biology (CCSB),
Department of Cancer Biology, Dana-Farber Cancer Institute, 450
Brookline Avenue, Boston, MA 02215, USA
COMMENT For distribution information, please check CCSB website
(http://ccsb.dfci.harvard.edu/ and
http://horfdb.dfci.harvard.edu/).
FEATURES Location/Qualifiers
source 1..1557
/organism="synthetic construct"
/mol_type="other DNA"
/db_xref="taxon:32630"
/clone="CCSBHm_00005145"
/focus
/note="vector:pDONR223; derived from parent clone GenBank
accession: KJ897141"
source 66..1490
/organism="Homo sapiens"
/mol_type="other DNA"
/db_xref="taxon:9606"
gene 66..>1490
/gene="LPL"
/db_xref="GeneID:4023"
CDS 66..>1490
/gene="LPL"
/note="full-length ORF without stop codon"
/codon_start=1
/transl_table=11
/product="LPL"
/protein_id="AKI70065.1"
/db_xref="GeneID:4023"
/translation="MESKALLVLTLAVWLQSLTASRGGVAAADQRRDFIDIESKFALR
TPEDTAEDTCHLIPGVAESVATCHFNHSSKTFMVIHGWTVTGMYESWVPKLVAALYKR
EPDSNVIVVDWLSRAQEHYPVSAGYTKLVGQDVARFINWMEEEFNYPLDNVHLLGYSL
GAHAAGIAGSLTNKKVNRITGLDPAGPNFEYAEAPSRLSPDDADFVDVLHTFTRGSPG
RSIGIQKPVGHVDIYPNGGTFQPGCNIGEAIRVIAERGLGDVDQLVKCSHERSIHLFI
DSLLNEENPSKAYRCSSKEAFEKGLCLSCRKNRCNNLGYEISKVRAKRSSKMYLKTRS
QMPYKVFHYQVKIHFSGTESETHTNQAFEISLYGTVAESENIPFTLPEVSTNKTYSFL
IYTEVDIGELLMLKLKWKSDSYFSWSDWWSSPGFAIQKIRVKAGVTQKKVIFCSREKV
SHLQKGKAPAVFVKCHDKSLNKKSG"
misc_difference 1375
/gene="LPL"
/note="compared to parent clone; results in E to V
substitution"
/replace="a"
ORIGIN
1 gttcgttgca acaaattgat gagcaatgct tttttataat gccaactttg tacaaaaaag
61 ttggcatgga gagcaaagcc ctgctcgtgc tgactctggc cgtgtggctc cagagtctga
121 ccgcctcccg cggaggggtg gccgccgccg accaaagaag agattttatc gacatcgaaa
181 gtaaatttgc cctaaggacc cctgaagaca cagctgagga cacttgccac ctcattcccg
241 gagtagcaga gtccgtggct acctgtcatt tcaatcacag cagcaaaacc ttcatggtga
301 tccatggctg gacggtaaca ggaatgtatg agagttgggt gccaaaactt gtggccgccc
361 tgtacaagag agaaccagac tccaatgtca ttgtggtgga ctggctgtca cgggctcagg
421 agcattaccc agtgtccgcg ggctacacca aactggtggg acaggatgtg gcccggttta
481 tcaactggat ggaggaggag tttaactacc ctctggacaa tgtccatctc ttgggataca
541 gccttggagc ccatgctgct ggcattgcag gaagtctgac caataagaaa gtcaacagaa
601 ttactggcct cgatccagct ggacctaact ttgagtatgc agaagccccg agtcgtcttt
661 ctcctgatga tgcagatttt gtagacgtct tacacacatt caccagaggg tcccctggtc
721 gaagcattgg aatccagaaa ccagttgggc atgttgacat ttacccgaat ggaggtactt
781 ttcagccagg atgtaacatt ggagaagcta tccgcgtgat tgcagagaga ggacttggag
841 atgtggacca gctagtgaag tgctcccacg agcgctccat tcatctcttc atcgactctc
901 tgttgaatga agaaaatcca agtaaggcct acaggtgcag ttccaaggaa gcctttgaga
961 aagggctctg cttgagttgt agaaagaacc gctgcaacaa tctgggctat gagatcagta
1021 aagtcagagc caaaagaagc agcaaaatgt acctgaagac tcgttctcag atgccctaca
1081 aagtcttcca ttaccaagta aagattcatt tttctgggac tgagagtgaa acccatacca
1141 atcaggcctt tgagatttct ctgtatggca ccgtggccga gagtgagaac atcccattca
1201 ctctgcctga agtttccaca aataagacct actccttcct aatttacaca gaggtagata
1261 ttggagaact actcatgttg aagctcaaat ggaagagtga ttcatacttt agctggtcag
1321 actggtggag cagtcccggc ttcgccattc agaagatcag agtaaaagca ggagtgactc
1381 agaaaaaggt gatcttctgt tctagggaga aagtgtctca tttgcagaaa ggaaaggcac
1441 ctgcggtatt tgtgaaatgc catgacaagt ctctgaataa gaagtcaggc tgcccaactt
1501 tcttgtacaa agttggcatt ataagaaagc attgcttatc aatttgttgc aacgaac
After it click on the refernce no of Pubmed artcle and go on it for taking or reading the abstract and
conclusion from there.
Abstract
How disease-associated mutations impair protein activities in the context of biological networks
remains mostly undetermined. Although a few renowned alleles are well characterized, functional
information is missing for over 100,000 disease-associated variants. Here we functionally profile
several thousand missense mutations across a spectrum of Mendelian disorders using various
interaction assays. The majority of disease-associated alleles exhibit wild-type chaperone binding
profiles, suggesting they preserve protein folding or stability. While common variants from healthy
individuals rarely affect interactions, two-thirds of disease-associated alleles perturb protein-protein
interactions, with half corresponding to "edgetic" alleles affecting only a subset of interactions while
leaving most other interactions unperturbed. With transcription factors, many alleles that leave
protein-protein interactions intact affect DNA binding. Different mutations in the same gene leading
to different interaction profiles often result in distinct disease phenotypes. Thus disease-associated
alleles that perturb distinct protein activities rather than grossly affecting folding and stability are
relatively widespread.
Conclusion:
How disease-associated mutations impair protein activities in the context of biological networks
remains mostly undetermined. Although a few renowned alleles are well characterized, functional
information is missing for over 100,000 disease-associated variants. Here we functionally profile
several thousand missense mutations across a spectrum of Mendelian disorders using various
interaction assays. The majority of disease-associated alleles exhibit wild-type chaperone binding
profiles, suggesting they preserve protein folding or stability. While common variants from healthy
individuals rarely affect interactions, two-thirds of disease-associated alleles perturb protein-protein
interactions, with half corresponding to “edgetic” alleles affecting only a subset of interactions while
leaving most other interactions unperturbed. With transcription factors, many alleles that leave
protein-protein interactions intact affect DNA binding. Different mutations in the same gene leading
to different interaction profiles often result in distinct disease phenotypes. Thus disease-associated
alleles that perturb distinct protein activities rather than grossly affecting folding and stability are
relatively widespread.
