Protein Lab
Abinezer Abebe
STEAM
Program
Conserved
domain found in cupin and related proteins
A diverse protein domains
superfamily which includes both metal-dependent and metal-independent enzymes,
as well as catalytically inactive seed storage proteins
My protein is UniprotiP09923
ALPL(1x) also known as Intestinal-type alkaline phosphatase one of
the most used database. No considered domain for this specific protein so I used
the default.
My first result was Homo Sapiens
Chromosomes 2 and I choose that data because it was most relevant.
LOCUS NC_000002 242193529 bp DNA
linear CON 17-AUG-2020
DEFINITION Homo sapiens chromosome 2, GRCh38.p13 Primary
Assembly.
ACCESSION NC_000002
VERSION NC_000002.12
DBLINK BioProject: PRJNA168
Assembly: GCF_000001405.39
KEYWORDS RefSeq.
SOURCE Homo sapiens (human)
ORGANISM
Homo sapiens
Eukaryota; Metazoa; Chordata;
Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria;
Euarchontoglires; Primates; Haplorrhini;
Catarrhini; Hominidae; Homo.
REFERENCE 1
(bases 1 to 242193529)
AUTHORS
Hillier,L.W., Graves,T.A., Fulton,R.S., Fulton,L.A., Pepin,K.H.,
Minx,P., Wagner-McPherson,C.,
Layman,D., Wylie,K., Sekhon,M.,
Becker,M.C., Fewell,G.A., Delehaunty,K.D.,
Miner,T.L., Nash,W.E.,
Kremitzki,C., Oddy,L., Du,H.,
Sun,H., Bradshaw-Cordum,H., Ali,J.,
Carter,J., Cordes,M., Harris,A.,
Isak,A., van Brunt,A., Nguyen,C.,
Du,F., Courtney,L., Kalicki,J.,
Ozersky,P., Abbott,S.,
Armstrong,J., Belter,E.A.,
Caruso,L., Cedroni,M., Cotton,M.,
Davidson,T., Desai,A., Elliott,G.,
Erb,T., Fronick,C., Gaige,T.,
Haakenson,W., Haglund,K.,
Holmes,A., Harkins,R., Kim,K.,
Kruchowski,S.S., Strong,C.M.,
Grewal,N., Goyea,E., Hou,S., Levy,A.,
Martinka,S., Mead,K.,
McLellan,M.D., Meyer,R., Randall-Maher,J.,
Tomlinson,C., Dauphin-Kohlberg,S.,
Kozlowicz-Reilly,A., Shah,N.,
Swearengen-Shahid,S., Snider,J.,
Strong,J.T., Thompson,J.,
Yoakum,M., Leonard,S., Pearman,C.,
Trani,L., Radionenko,M.,
Waligorski,J.E., Wang,C.,
Rock,S.M., Tin-Wollam,A.M., Maupin,R.,
Latreille,P., Wendl,M.C.,
Yang,S.P., Pohl,C., Wallis,J.W.,
Spieth,J., Bieri,T.A.,
Berkowicz,N., Nelson,J.O., Osborne,J.,
Ding,L., Meyer,R., Sabo,A.,
Shotland,Y., Sinha,P., Wohldmann,P.E.,
Cook,L.L., Hickenbotham,M.T.,
Eldred,J., Williams,D., Jones,T.A.,
She,X., Ciccarelli,F.D., Izaurralde,E.,
Taylor,J., Schmutz,J.,
Myers,R.M., Cox,D.R., Huang,X.,
McPherson,J.D., Mardis,E.R.,
Clifton,S.W., Warren,W.C.,
Chinwalla,A.T., Eddy,S.R., Marra,M.A.,
Ovcharenko,I., Furey,T.S.,
Miller,W., Eichler,E.E., Bork,P.,
Suyama,M., Torrents,D.,
Waterston,R.H. and Wilson,R.K.
TITLE
Generation and annotation of the DNA sequences of human chromosomes
2 and 4
JOURNAL
Nature 434 (7034), 724-731 (2005)
PUBMED
15815621
REFERENCE 2
(bases 1 to 242193529)
CONSRTM
International Human Genome Sequencing Consortium
TITLE
Finishing the euchromatic sequence of the human genome
JOURNAL
Nature 431 (7011), 931-945 (2004)
PUBMED
15496913
REFERENCE 3
(bases 1 to 242193529)
AUTHORS
Lander,E.S., Linton,L.M., Birren,B., Nusbaum,C., Zody,M.C.,
Baldwin,J., Devon,K., Dewar,K.,
Doyle,M., FitzHugh,W., Funke,R.,
Gage,D., Harris,K., Heaford,A.,
Howland,J., Kann,L., Lehoczky,J.,
LeVine,R., McEwan,P., McKernan,K.,
Meldrim,J., Mesirov,J.P.,
Miranda,C., Morris,W., Naylor,J.,
Raymond,C., Rosetti,M.,
Santos,R., Sheridan,A., Sougnez,C.,
Stange-Thomann,N.,
Stojanovic,N., Subramanian,A.,
Wyman,D., Rogers,J., Sulston,J.,
Ainscough,R., Beck,S., Bentley,D.,
Burton,J., Clee,C., Carter,N.,
Coulson,A., Deadman,R.,
Deloukas,P., Dunham,A., Dunham,I.,
Durbin,R., French,L., Grafham,D.,
Gregory,S., Hubbard,T.,
Humphray,S., Hunt,A., Jones,M.,
Lloyd,C., McMurray,A., Matthews,L.,
Mercer,S., Milne,S., Mullikin,J.C.,
Mungall,A., Plumb,R., Ross,M.,
Shownkeen,R., Sims,S.,
Waterston,R.H., Wilson,R.K., Hillier,L.W.,
McPherson,J.D., Marra,M.A.,
Mardis,E.R., Fulton,L.A.,
Chinwalla,A.T., Pepin,K.H.,
Gish,W.R., Chissoe,S.L., Wendl,M.C.,
Delehaunty,K.D., Miner,T.L.,
Delehaunty,A., Kramer,J.B., Cook,L.L.,
Fulton,R.S., Johnson,D.L.,
Minx,P.J., Clifton,S.W., Hawkins,T.,
Branscomb,E., Predki,P.,
Richardson,P., Wenning,S., Slezak,T.,
Doggett,N., Cheng,J.F., Olsen,A., Lucas,S.,
Elkin,C.,
Uberbacher,E., Frazier,M.,
Gibbs,R.A., Muzny,D.M., Scherer,S.E.,
Bouck,J.B., Sodergren,E.J.,
Worley,K.C., Rives,C.M., Gorrell,J.H.,
Metzker,M.L., Naylor,S.L.,
Kucherlapati,R.S., Nelson,D.L.,
Weinstock,G.M., Sakaki,Y.,
Fujiyama,A., Hattori,M., Yada,T.,
Toyoda,A., Itoh,T., Kawagoe,C.,
Watanabe,H., Totoki,Y., Taylor,T.,
Weissenbach,J., Heilig,R., Saurin,W.,
Artiguenave,F., Brottier,P.,
Bruls,T., Pelletier,E., Robert,C.,
Wincker,P., Smith,D.R.,
Doucette-Stamm,L., Rubenfield,M.,
Weinstock,K., Lee,H.M.,
Dubois,J., Rosenthal,A.,
Platzer,M., Nyakatura,G., Taudien,S.,
Rump,A., Yang,H., Yu,J., Wang,J.,
Huang,G., Gu,J., Hood,L.,
Rowen,L., Madan,A., Qin,S.,
Davis,R.W., Federspiel,N.A.,
Abola,A.P., Proctor,M.J.,
Myers,R.M., Schmutz,J., Dickson,M.,
Grimwood,J., Cox,D.R., Olson,M.V., Kaul,R.,
Raymond,C., Shimizu,N.,
Kawasaki,K., Minoshima,S.,
Evans,G.A., Athanasiou,M., Schultz,R.,
Roe,B.A., Chen,F., Pan,H.,
Ramser,J., Lehrach,H., Reinhardt,R.,
McCombie,W.R., de la Bastide,M.,
Dedhia,N., Blocker,H.,
Hornischer,K., Nordsiek,G., Agarwala,R., Aravind,L., Bailey,J.A.,
Bateman,A., Batzoglou,S.,
Birney,E., Bork,P., Brown,D.G.,
Burge,C.B., Cerutti,L., Chen,H.C.,
Church,D., Clamp,M.,
Copley,R.R., Doerks,T., Eddy,S.R.,
Eichler,E.E., Furey,T.S.,
Galagan,J., Gilbert,J.G.,
Harmon,C., Hayashizaki,Y., Haussler,D.,
Hermjakob,H., Hokamp,K., Jang,W.,
Johnson,L.S., Jones,T.A.,
Kasif,S., Kaspryzk,A., Kennedy,S.,
Kent,W.J., Kitts,P.,
Koonin,E.V., Korf,I., Kulp,D., Lancet,D.,
Lowe,T.M., McLysaght,A.,
Mikkelsen,T., Moran,J.V.,
Mulder,N., Pollara,V.J., Ponting,C.P.,
Schuler,G., Schultz,J., Slater,G.,
Smit,A.F., Stupka,E.,
Szustakowski,J., Thierry-Mieg,D.,
Thierry-Mieg,J., Wagner,L.,
Wallis,J., Wheeler,R., Williams,A.,
Wolf,Y.I., Wolfe,K.H.,
Yang,S.P., Yeh,R.F., Collins,F.,
Guyer,M.S., Peterson,J.,
Felsenfeld,A., Wetterstrand,K.A.,
Patrinos,A., Morgan,M.J., de
Jong,P., Catanese,J.J.,
Osoegawa,K., Shizuya,H., Choi,S. and
Chen,Y.J.
CONSRTM
International Human Genome Sequencing Consortium
TITLE
Initial sequencing and analysis of the human genome
JOURNAL
Nature 409 (6822), 860-921 (2001)
PUBMED
11237011
REMARK
Erratum:[Nature 2001 Aug 2;412(6846):565]
COMMENT REFSEQ
INFORMATION: The reference sequence is identical to
On Feb 3, 2014 this sequence
version replaced NC_000002.11.
Assembly Name: GRCh38.p13 Primary
Assembly
The DNA sequence is composed of
genomic sequence, primarily
finished clones that were sequenced
as part of the Human Genome
Project. PCR products and WGS shotgun
sequence have been added
where necessary to fill gaps or
correct errors. All such additions
are manually curated by GRC staff.
For more information see:
##Genome-Annotation-Data-START##
Annotation Provider :: NCBI
Annotation Status :: Updated annotation
Annotation Name :: Homo sapiens Updated Annotation
Annotation Version :: 109.20200815
Annotation Pipeline :: NCBI eukaryotic genome annotation
pipeline
Annotation Software Version :: 8.5
Annotation Method :: Best-placed RefSeq; propagated
RefSeq model
Features Annotated :: Gene; mRNA; CDS; ncRNA
##Genome-Annotation-Data-END##
source
1..242193529
/organism="Homo
sapiens"
/mol_type="genomic
DNA"
/db_xref="taxon:9606"
/chromosome="2"
CONTIG
join(gap(10000),NT_005334.17:1..16135119,gap(1000),
NT_022184.16:1..73184560,gap(200000),NT_187177.1:1..871832,
gap(1000000),NT_034508.3:1..735634,gap(50000),
NT_187178.1:1..1902412,gap(50000),NT_187179.1:1..152458,
gap(203000),NT_005403.18:1..147687514,gap(10000))
1.
Between the two database I searched for there was massive difference
in how the data was displayed and gathered. The second resource had way better modules
to help display and project the data of my protein.
After adjusting my parameters for a blast I couldn’t find
the “graphic summary” button.
My result after running default primers.
Hello,
ReplyDeleteIt looks as if you couldn't make any primers form the blast results?
-Chad