Hello,

The gene A3GALT2 has been renamed as a pseudogene 
see Entrez Gene
A3GALT2 – alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase) [Homo sapiens]
alpha 1,3-galactosyltransferase 2 (isoglobotriaosylceramide synthase)
Official Symbol: A3GALT2


Chromosome: 1; Location: 1p35.1
This record was replaced with GeneID: 127550
When you blat the probe on UCSC  you can see it is in the 3'part (non coding !) 
of 2 enSembl transcripts


A3GALT2P at chr1:33772367-33777822 - (ENST00000330379)
A3GALT2P at chr1:33772367-33778491 - (ENST00000442999)



Best 

Philippe



Le 15 janv. 2013 à 13:30, Fenton Christopher Graham a écrit :

> Illumina mapping nuId to genome coordinates. 
> 
>> m2<- read.table("processed_data.csv", header=T, row.names=1, sep="\t")
>> probes<- rownames(m2)
>> dd<- probeID2nuID(probes)
>> seqs<- id2seq(dd[,7])
>> test<- cbind(dd, seqs) 
> 
>> test[grep("r33p5EJWUK57ZWL3no", test[,7]),] 
> 
> Search_Key          "XM_940724.1" 
> ILMN_Gene           "A3GALT2" 
> Accession            "NM_001080438.1" 
> Symbol                "A3GALT2" 
> Probe_Id              "ILMN_1668111" 
> Array_Address_Id "0001740066" 
> nuID                    "r33p5EJWUK57ZWL3no" 
> seq                      "TCTTCTGGCTGCACAAGCCCGCCAAGGTGCTGTCGCCCGAGTTCTGCTGG"
> 
> Now if I BLAT the sequence against GRCh37/hg I get the following.
> QUERY  SCORE START  END QSIZE IDENTITY CHRO STRAND  START    END      SPAN
> YourSeq 50     1    50    50   100.0%     1   -   33772451  33772500  50
> 
> Unfortunately this is not near the CDS.
> If I search UCSC for A3GALT2 I get the following location
> chr1:33,772,365-33,778,183 
> 
> Why are the chromosomal locations for this probe different?
> 
> 
> Chris 
> 
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