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KIR gene promoters for MSP primers design

promoter msp methylation

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#1 Lj Lee

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Posted 03 June 2014 - 05:23 AM

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.o...09.1:7891-96246 (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. smile.png


Edited by Lj Lee, 03 June 2014 - 05:24 AM.


#2 rakun

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Posted 08 September 2014 - 03:03 AM

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.o...09.1:7891-96246 (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. smile.png

Hi Lj Lee,

 

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



#3 Lj Lee

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Posted 08 September 2014 - 05:17 PM

 

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.o...09.1:7891-96246 (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. smile.png

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 

 







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