KIR gene promoters for MSP primers design - (Jun/03/2014 )

Hi all, 

Good day, I'm new here and trying to create a simple MSP for my few of my target genes which are KIR (Killer cell immunoglobulin-like receptor) located in chromosome 19. I know most of the researcher using MethPrimer software to design the M and U primers but I met some difficulties to design the primers as there were no CpG island found in the 'promoter sequence'. 

I get the 'promoter' of KIR2DL2 from Ensembl : http://www.ensembl.org/Homo_sapiens/Gene/Sequence?db=core;g=ENSG00000215764;r=GL000209.1:7891-96246 (the sequence before first exon that highlighted in pink) however when I copied and pasted it to MethPrimer, it showed no CpG island found in the input sequence.

Does anyone know how to identify the promoter sequence of a particular gene? I'm totally lost and stuck at this stage.

Thanks. 

Lj Lee on Tue Jun 3 13:23:11 2014 said:

Hi all, 

 

Good day, I'm new here and trying to create a simple MSP for my few of my target genes which are KIR (Killer cell immunoglobulin-like receptor) located in chromosome 19. I know most of the researcher using MethPrimer software to design the M and U primers but I met some difficulties to design the primers as there were no CpG island found in the 'promoter sequence'. 

 

I get the 'promoter' of KIR2DL2 from Ensembl : http://www.ensembl.org/Homo_sapiens/Gene/Sequence?db=core;g=ENSG00000215764;r=GL000209.1:7891-96246 (the sequence before first exon that highlighted in pink) however when I copied and pasted it to MethPrimer, it showed no CpG island found in the input sequence.

 

Does anyone know how to identify the promoter sequence of a particular gene? I'm totally lost and stuck at this stage.

 

Thanks. 

Hi Lj Lee,

It is probably late, but try to use DBTSS (http://dbtss.hgc.jp/) or EPD (http://epd.vital-it.ch/).

rakun on Mon Sep 8 11:03:51 2014 said:

 

Lj Lee on Tue Jun 3 13:23:11 2014 said:

Hi all, 

 

Good day, I'm new here and trying to create a simple MSP for my few of my target genes which are KIR (Killer cell immunoglobulin-like receptor) located in chromosome 19. I know most of the researcher using MethPrimer software to design the M and U primers but I met some difficulties to design the primers as there were no CpG island found in the 'promoter sequence'. 

 

I get the 'promoter' of KIR2DL2 from Ensembl : http://www.ensembl.org/Homo_sapiens/Gene/Sequence?db=core;g=ENSG00000215764;r=GL000209.1:7891-96246 (the sequence before first exon that highlighted in pink) however when I copied and pasted it to MethPrimer, it showed no CpG island found in the input sequence.

 

Does anyone know how to identify the promoter sequence of a particular gene? I'm totally lost and stuck at this stage.

 

Thanks. 

Hi Lj Lee,

 

It is probably late, but try to use DBTSS (http://dbtss.hgc.jp/) or EPD (http://epd.vital-it.ch/).

 

Hi Rakun,

 

Thanks for ur reply, i will try it