identification of agilent micro array non coding RNA id

Question

[Dr. Pradeep]

Dear all, I tried various methods to identify the ensembl id or gene id for non-coding micro array agilent id-ASHGV40053163.but i couldnt . It will be very useful for my research work. ncbi geo dataset-GSE124352 Please help me identify this non coding RNA. Thank you. Dr. Pradeep Kumar, MDS

Answer 1

[GenoMax]

If you look at the platform https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL21827 table that ID has the following sequence from hg19 build. It is denoted as non-coding.

CCTCAAGTGCAAAATGTATAAACTCATCATAGCAATAAATTCCCGCATCATGCATTTCAA

If you blat with the sequence at UCSC you get the following hits.

   ACTIONS      QUERY   SCORE START   END QSIZE IDENTITY  CHROM  STRAND  START       END   SPAN
-----------------------------------------------------------------------------------------------
browser details YourSeq    60     1    60    60   100.0%  chr9   +    98257598  98257657     60
browser details YourSeq    21    18    38    60   100.0%  chr5   -    21130605  21130625     21
browser details YourSeq    20    11    30    60   100.0%  chr3   +    63194722  63194741     20

First one appears to be full size and that would be your best bet. It seems to be in the intron of PTCH1 gene.