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RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

AlaskaDenise

AlaskaDenise

In Memoriam
http://mammalia.gsc.riken.jp/swine_influenza/

The new deposits include the first test in Mexico City:
(this is the site Toaster2 posted about)

LOCUS GQ292941 558 bp cRNA linear VRL 23-JUN-2009
DEFINITION Influenza A virus (A/Mexico City/1/2009(H1N1)) segment 4
hemagglutinin (HA) gene, partial cds.
ACCESSION GQ292941
VERSION GQ292941.1 GI:241872078
DBLINK Project:37813
KEYWORDS .
SOURCE Influenza A virus (A/Mexico City/1/2009(H1N1))
ORGANISM Influenza A virus (A/Mexico City/1/2009(H1N1))
Viruses; ssRNA negative-strand viruses; Orthomyxoviridae;
Influenzavirus A.
REFERENCE 1 (bases 1 to 558)
AUTHORS Zepeda-Lopez,H.M., Perea-Araujo,L.L., Zarate-Segura,P.B.,
Vazquez-Perez,J.A., Miliar-Garcia,A., Garibay-Orijel,C.,
Dominguez-Lopez,A., Badillo-Corona,J.A., Garcia-Gonzalez,O.P.,
Aguilar-Faisan,L. and Bravo-Madrigal,J.
TITLE Influenza A (H1N1) in Mexico City during critical outbreak
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 558)
AUTHORS Zepeda-Lopez,H.M., Perea-Araujo,L.L., Zarate-Segura,P.B.,
Vazquez-Perez,J.A., Miliar-Garcia,A., Garibay-Orijel,C.,
Dominguez-Lopez,A., Badillo-Corona,J.A., Garcia-Gonzalez,O.P.,
Aguilar-Faisan,L. and Bravo-Madrigal,J.
TITLE Direct Submission
JOURNAL Submitted (23-JUN-2009) Laboratorio de Medicina de la Conservacion,
Escuela Superior de Medicina/Instituto Politecnico Nacional,
Salvador Diaz Miron esq. Plan de San luis S/N, Mexico City 11340,
Mexico
COMMENT Swine influenza A (H1N1) virus isolated during human swine flu
outbreak of 2009.
FEATURES Location/Qualifiers
source 1..558
/organism="Influenza A virus (A/Mexico City/1/2009(H1N1))"
/mol_type="viral cRNA"
/strain="A/Mexico City/1/2009"
/serotype="H1N1"
/host="Homo sapiens; age 18 years"
/db_xref="taxon:654705"
/segment="4"
/country="Mexico"
/collection_date="01-May-2009"
/note="lineage: swl"
gene <1..>558
/gene="HA"
CDS <1..>558
/gene="HA"
/codon_start=1
/product="hemagglutinin"
/protein_id="ACS68848.1"
/db_xref="GI:241872079"
/translation="HQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKE
FNHLEKRIENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLK
NNAKEIGNGCFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQ
ILAIYSTVASSLVLVVSLGAISFWMC"
ORIGIN
1 catcaaaatg agcaggggtc aggatatgca gccgacctga agagcacaca gaatgccatt
61 gacgagatta ctaacaaagt aaattctgtt attgaaaaga tgaatacaca gttcacagca
121 gtaggtaaag agttcaacca cctggaaaaa agaatagaga atttaaataa aaaagttgat
181 gatggtttcc tggacatttg gacttacaat gccgaactgt tggttctatt ggaaaatgaa
241 agaactttgg actaccacga ttcaaatgtg aagaacttat atgaaaaggt aagaagccag
301 ctaaaaaaca atgccaagga aattggaaac ggctgctttg aattttacca caaatgcgat
361 aacacgtgca tggaaagtgt caaaaatggg acttatgact acccaaaata ctcagaggaa
421 gcaaaattaa acagagaaga aatagatggg gtaaagctgg aatcaacaag gatttaccag
481 attttggcga tctattcaac tgtcgccagt tcattggtac tggtagtctc cctgggggca
541 atcagtttct ggatgtgc

.
 
Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

At least the one above is not yet in the NCBI data base.

.
 
Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

only 3 PB2s are shown and they are all an "E". :)

.
 
Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

I believe I'm see a "Y" in the NA of GQ293078! :(

Influenza A virus (A/Zhejiang/2/2009(H1N1))


Would someone more knowledgeable please check my work?

.
 
Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

genbank has them on the swine-flu page,
although some of the records don't load.

It's not yet available at the search page.


Does riken allow to download them all into one file ?



http://mammalia.gsc.riken.jp/swine_influenza/
 
Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

AlaskaDenise said:
I believe I'm see a "Y" in the NA of GQ293078! :(

Influenza A virus (A/Zhejiang/2/2009(H1N1))


Would someone more knowledgeable please check my work?

.
Click to expand...


I see a H : ...APNYHY...
position 275
 
Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

I left out the position I was referencing (obviously), I meant 274.

Their "[NA of A/Zhejiang/2/2009(H1N1) : GQ293078] Mutation information"
scroll down window on the lower right clearly reads " 274Y".

If the mutation line format is confusing, it helps to read the "help" link on the 1st page - upper right top line.

I await Mamabird's reading.

.
 
Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

Thanks to both of you for examining the sequences and sharing with us what you found. :tiphat: The more eyes, the better.
 
Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

gsgs said:
genbank has them on the swine-flu page,
although some of the records don't load.

It's not yet available at the search page.........
Click to expand...

I have problems on the main NCBI page also. It doesn't appear to know about the same data that the Riken database is clearly extracting from NCBI. I'm assuming they have different permissions.

I haven't learned how to use the other databases yet, so can't answer your questions on that.

.
 
Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

it's 275, not 274.
274 is counting by another system, presumably N2
 
Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

Dr. Niman just explained that we need to see a YYY in the area, not a YHY.

So our tami meds still work (for now).

Pheeew. :)

.
 
Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

AlaskaDenise said:
I have problems on the main NCBI page also. It doesn't appear to know about the same data that the Riken database is clearly extracting from NCBI. I'm assuming they have different permissions.

I haven't learned how to use the other databases yet, so can't answer your questions on that.

.
Click to expand...
All sequences at NBCI that can be viewed by the public, are public - no permission required.
 
Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

niman said:
All sequences at NBCI that can be viewed by the public, are public - no permission required.
Click to expand...

So why would a sequence segment in the Riken site not show up in a search through the front-door to the NCBI site?

A few days ago, it seemed to be a timing issue, i.e., that Riken had a more current update.

.
 
Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

AlaskaDenise said:
Dr. Niman just explained that we need to see a YYY in the area, not a YHY.

So our tami meds still work (for now).

Pheeew. :)

.
Click to expand...

Thank you very much Alaska Denise. I really do appreciate the analysis. I don't understand it, and I really like the "bottom line". :applause:
 
Re: RIKEN FAMSBASE - 164 new sequences deposited : 164 Mexico, 6 China, 12 Japan, & 12 Spain

AlaskaDenise said:
I believe I'm see a "Y" in the NA of GQ293078! :(

Influenza A virus (A/Zhejiang/2/2009(H1N1))


Would someone more knowledgeable please check my work?

.
Click to expand...

What would that mean?
 
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