[BiO BB] Affymetrix probe annotation- anyone need to identifyunknowns?

[Mike Marchywka]

As an example related to my earlier post,  AFFX has this as a class R with 
little info

https://www.affymetrix.com/analysis/netaffx/fullrecord.affx?pk=CANINE%3A1606074_AT
(free,but need to register)

with the reference to this:

http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucest&id=20431335

The  automated scripts found these related things- I also have ORF 
comparisons
but am just looking at gene/transcript alignments for now.

$ cat likely_hits
/cygdrive/e/new/temp/canis/dcm/1606074/temp
AY656737.1-   Canis familiaris isolate 1 breed Basenji mitochondrion, 
complete
AY656738.1-   Canis familiaris isolate 1 breed Jack Russell Terrier
AY656739.1-   Canis familiaris isolate 1 breed Poodle mitochondrion, 
complete
AY656740.1-   Canis familiaris isolate 1 breed Kerry Blue Terrier 
mitochondrion,

AY656741.1-   Canis familiaris isolate 1 breed Irish Setter mitochondrion,
AY656742.1-   Canis familiaris isolate 1 breed Old English Sheepdog
AY656743.1-   Canis familiaris isolate 1 breed Saint Bernard mitochondrion,
AY656744.1-   Canis familiaris isolate 1 breed English Springer Spaniel
AY656745.1-   Canis familiaris isolate 2 breed English Springer Spaniel

Complete sequence is usually a spurious hit but in this case the entry
could mean  something:
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=12700659
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=50301805

And the alignment is quite good ( I haven't checked orf's yet but I now 
generate
these along with clustalw output for putative matches).
( obviously a proportional space font, like most graphics, makes a mess of 
the information...)
CLUSTAL W (1.83) multiple sequence alignment

CANINE_1606074_AT      
--------------------------------------------------------ACGC
AY012152               
AGGTTTGGTCCTAGCCTTCCTATTAGTTTTTAGTAGACTTACACATGCAAGCCTCCACGC
                                                                             
  ****
CANINE_1606074_AT      
CCCAGTGAGAATGCCCTTAAAATCACCAGTGATCTAAAGGAGCAGGTATCAAGCACACTC
AY012152               
CCCAGTGAGAATGCCCTTAAAATCACCAGTGATCTAAAGGAGCAGGTATCAAGCACACTC
                      
************************************************************
CANINE_1606074_AT      
TTAAGTAGCTCATAACACCTTGCTAAGCCACACCCCCACGGGATACAGCAGTGATAAAAA
AY012152               
TTAAGTAGCTCATAACACCTTGCTAAGCCACACCCCCACGGGATACAGCAGTGATAAAAA
                      
************************************************************
CANINE_1606074_AT      
TTAAGCCATAAACGAAAGTTTGACTAAGCCATACTAAATAGGGTTGGTAAATTTCGTGCC
AY012152               
TTAAGCCATAAACGAAAGTTTGACTAAGCCATACTAAATAGGGTTGGTAAATTTCGTGCC
                      
************************************************************
CANINE_1606074_AT      
AGCCACCGCGGTCATACGATTAACCCAAACTAATAGGCCTACGGCGTAAAGCGTGTTCAA
AY012152               
AGCCACCGCGGTCATACGATTAACCCAAACTAATAGGCCTACGGCGTAAAGCGTGTTCAA
                      
************************************************************
CANINE_1606074_AT      
GATACTTTTACACTAAAGTTAAAACTTAACTAAGCCGTAAAAAGCTACAGTTATCATAAA
AY012152               
GATACTTTAACACTAAAGTTAAAACTTAACTAAGCCGTAAAAAGCTACAGTTATCATAAA
                      ******** 
***************************************************
CANINE_1606074_AT      
ATAAACCACGAAAGTGACTTTATAATAATCTGACTACACGATAGCTAAGACCCAAACTGG
AY012152               
ATAAACCACGAAAGTGACTTTATAATAATCTGACTACACGATAGCTAAGACCCAAACTGG
                      
************************************************************
CANINE_1606074_AT      
GATTAGATACCCCACTATGCTTAGCCCTAAACATAGATAATTTTACAACAAAATAATTCG
AY012152               
GATTAGATACCCCACTATGCTTAGCCCTAAACATAGATAATTTTACAACAAAATAATTCG
                      
************************************************************
CANINE_1606074_AT      
CCAGAGGACTACTAGCAATAGCTTAAAACTCAAAGGGACTTGGCGGTGCTTTATATCCCT
AY012152               
CCAGGGGACTACTAGCAATAGCTTAAAACTCAAAGG-ACTTGGCGGTGCTTTATATCCCT
                      **** ******************************* 
***********************
CANINE_1606074_AT      
CTAG--------------------------------------------------------
AY012152               
CTAGAGGAGCCTGTTCTATAATCGATAAACCCCGATAAACCTCACCACCTTTCGCTAATT
                      ****

[ trailer tuncated]

So, if anyone is interested in looking for better id's or could suggest a 
better source for annotations or suggest a reason why these hits are 
irrelevant, please contact me. It does appear that additional information is 
available beyond that posted
on Affx site, at least for the canine array.

Thanks.

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