MSX1 gene

8 posts / 0 new
Last post
Amritha Nair
Amritha Nair's picture
MSX1 gene

Has anyone worked with the MSX1 gene [homo sapiens]. Hoping to work on it and I needed to know if it had any restriction polymorphisms in any of its two exons?

ryan_m
ryan_m's picture
Hi Amritha.

Hi Amritha.
I see that this gene does have a bunch of known SNPs in dbSNP (see this link).

It is pretty likely at least one of these falls within a restriction site. Do you have some enzyme(s) in mind? An easy way to do this would be to do in-silico digestions of the reference transcript sequence and the same sequence with the nonreference allele in place of the reference allele. Does this make sense so far? If you would like, I can supply you with these two sequences. As it happens, I am doing this for the whole genome presently.

Regards,

Ryan

Amritha Nair
Amritha Nair's picture
thanks for the reply... i m

thanks for the reply... i m not quite sure what u mean about in silico digestion... could u elaborate?

ryan_m
ryan_m's picture
Amritha Nair wrote:thanks for

Amritha Nair wrote:

thanks for the reply... i m not quite sure what u mean about in silico digestion... could u elaborate?

Certainly. I apologize for using such jargon. Basically this jut means using a computer program such as this to identify all restriction enzyme target sites in a DNA sequence. These programs will tell you where they all cut and what fragments (and sizes) will result. This will let you know, if you put in both sequences, whether there are any differences in restriction sites between any two alleles.

Does this make more sense?

Ryan

Amritha Nair
Amritha Nair's picture
thanks ryan

thanks ryan
yeah i think i get it.. heard of this neb cutter program before.
basically i need to get the sequences of the reference allele and the one with the SNP.. paste it on the program window.. and see if the SNP is causing a change in the restriction site?
and you said u could provide me with the sequences.. i would appreciate that if that is possible...
also i had another doubt.. what exactly does it mean when one says that an SNP is validated? seen that word a lot in literature..

ryan_m
ryan_m's picture
Hi Amritha.

Hi Amritha.
Yes, that is what I would suggest you do. I have included two sequences below for you. The first one is the cDNA and the second is the cDNA with SNPs replaced.

Ryan
>ENST00000382723
AGGGCCCGGAGCCGGCGAGTGCTCCCGGGAACTCTGCCTGCGCGGCGGCAGCGACCGGAG
GCCAGGCCCAGCACGCCGGAGCTGGCCTGCTGGGGAGGGGCGGGAGGCGCGCGCGGGAGG
GTCCGCCCGGCCAGGGCCCCGGGCGCTCGCAGAGGCCGGCCGCGCTCCCAGCCCGCCCGG
AGCCCATGCCCGGCGGCTGGCCAGTGCTGCGGCAGAAGGGGGGGCCCGGCTCTGCATGGC
CCCGGCTGCTGACATGACTTCTTTGCCACTCGGTGTCAAAGTGGAGGACTCCGCCTTCGG
CAAGCCGGCGGGGGGAGGCGCGGGCCAGGCCCCCAGCGCCGCCGCGGCCACGGCAGCCGC
CATGGGCGCGGACGAGGAGGGGGCCAAGCCCAAAGTGTCCCCTTCGCTCCTGCCCTTCAG
CGTGGAGGCGCTCATGGCCGACCACAGGAAGCCGGGGGCCAAGGAGAGCGCCCTGGCGCC
CTCCGAGGGCGTGCAGGCGGCGGGTGGCTCGGCGCAGCCACTGGGCGTCCCGCCGGGGTC
GCTGGGAGCCCCGGACGCGCCCTCTTCGCCGCGGCCGCTCGGCCATTTCTCGGTGGGGGG
ACTCCTCAAGCTGCCAGAAGATGCGCTCGTCAAAGCCGAGAGCCCCGAGAAGCCCGAGAG
GACCCCGTGGATGCAGAGCCCCCGCTTCTCCCCGCCGCCGGCCAGGCGGCTGAGCCCCCC
AGCCTGCACCCTCCGCAAACACAAGACGAACCGTAAGCCGCGGACGCCCTTCACCACCGC
GCAGCTGCTGGCGCTGGAGCGCAAGTTCCGCCAGAAGCAGTACCTGTCCATCGCCGAGCG
CGCGGAGTTCTCCAGCTCGCTCAGCCTCACTGAGACGCAGGTGAAGATATGGTTCCAGAA
CCGCCGCGCCAAGGCAAAGAGACTACAAGAGGCAGAGCTGGAGAAGCTGAAGATGGCCGC
CAAGCCCATGCTGCCACCGGCTGCCTTCGGCCTCTCCTTCCCTCTCGGCGGCCCCGCAGC
TGTAGCGGCCGCGGCGGGTGCCTCGCTCTACGGTGCCTCTGGCCCCTTCCAGCGCGCCGC
GCTGCCTGTGGCGCCCGTGGGACTCTACACGGCCCATGTGGGCTACAGCATGTACCACCT
GACATAGAGGGTCCCAGGTCGCCCACCTGTGGGCCAGCCGATTCCTCCAGCCCTGGTGCT
GTACCCCCGACGTGCTCCCCTGCTCGGCACCGCCAGCCGCCTTCCCTTTAACCCTCACAC
TGCTCCAGTTTCACCTCTTTGCTCCCTGAGTTCACTCTCCGAAGTCTGATCCCTGCCAAA
AAGTGGCTGGAAGAGTCCCTTAGTACTCTTCTAGCATTTAGATCTACACTCTCGAGTTAA
AGATGGGGAAACTGAGGGCAGAGAGGTTAACAGATTTATCTAAGGTCCCCAGCAGAATTG
ACAGTTGAACAGAGCTAGAGGCCATGTCTCCTGCATAGCTTTTCCCTGTCCTGACACCAG
GCAAGAAAAGCGCAGAGAAATCGGTGTCTGACGATTTTGGAAATGAGAACAATCTCAAAA
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAGAGAAAAAAAAGACTAGCCAGCC
AGGAAGATGAATCCTAGCTTCTTCCATTGGAAAATTTAAGACAAGTTCAACAACAAAACA
TTTGCTCTGGGGGGCAGGGAAAACACAGATGTGTTGCAAAGGTAGGTTGAAGGGACCTCT
CTCTTACCAGTACCAGAAACACAATTGTAAAATTAAAAAAAAAAAAAAACTCTTTCTATT
TAACAGTACATTTGTGTGGCTCTCAAACATCCCTTTGGAAGGGATTGTGTGTACTATGTA
ATATACTGTATATTTGAAATTTTATTATCATTTATATTATAGCTATATTTGTTAAATAAA
TTAATTTTAAGCT
>ENST00000382723 ALTERED
AGGGCCCGGAGCCGGCGAGTGCTCCCGGGAACTCTGCCTGCGCGGCGGCAGCGACC
GGAGGCCAGGCCCAGCACGCCGGAGCTGGCCTGCTGGGGAGGGGCGGGAGGCGCG
CGCGGGAGGGTCCGCCCGGCCAGGGCCCCGGGCGCTCGCAGAGGCCGGCCGCGCTC
CCAGCCCGCCCGGAGCCCATGCCCGGCGGCTGGCCAGTGCTGCGGCAGAAGGGGGG
GCCCGGCTCTGCATGGCCCCGGCTGCTGACATGACTTCTTTGCCACTCGGTGTCAAAG
TGGAGGACTCCGCCTTCGGCAAGCCGGCGGGGGGAGGCGCGGGCCAGGCCCCCAGC
GCCGCCGCGGCCACGGGAGCCGCCATGGGCGCGGACGAGGAGGGGGCCAAGTCCAA
AGTGTCCCCTTCGCTCCTGCCCTTCAGCGTGGAGGCGCTCATGGCCGACCACAGGAAG
CCGGGGGCCAAGGCGAGCGCCCTGGCGCCCTCCGTGGGCGTGCAGGCGGCGGGTGG
CTCGGCGCAGCCACTGCGCGTCCCGCCGGGGTCGCTGGGAGCCCCGGACGCGCCCTC
TTCGCCGCGGCCGCTCGGTCATTTCTCGGTGGGGGAACTCCTCAAGCTGCCAGAAGAT
GCGCTCGTCAAAGCCGAGAGCCCCGAGAAGCCCGAGAGGACCCCGTGGTTGCAGAGC
CCCCGCTTCTCCCCGCCGCCGGCCAGGCGGCTGAGCCCCCCAGCCTGCACCCTCCGCA
AACACAAGACGAACCGTAAGCCGCGGACGCCCTTCACCACCGCGCAGCTGCTGGCGCT
GGAGCGCAAGTTCCGCCAGAAGCAGTACCTGTCCATCGCCGAGCGCGCGGAGTTCTCC
AGCTCGCTCAGCCTCACTGAGACGCAGGTGAAGATATGGTTCCAGAACCGCCGCGCCA
AGGCAAAGAGACTACAAGAGGCAGAGCTGGAGAAGCTGAAGATGGCCGCCAAGCCCA
TGCTGCCACCGGCTGCCTTCGGCCTCTCCTTCCCTCTCGGCGGCCCCGCAGCTGTAGCG
GCCGCGGCGGGTGCCTCGCTCTACGGTGCCTCTGGCCCCTTCCAGCGCGCCGCGCTGC
CTGTGGCGCCCGTGGGACTCTACACGGCCCATGTGGGCTACAGCATGTACCACCTGAC
ATAGAGGGTTCCAGGTCGCCCACCTGTGGGCCAGCCGATTCCTCCAGCCCTGGTGCTG
TACCCCCGACGTGTTTCCCTGCTCGGCACCGCCAGCCGCCTTCCCTTTAACCCTCACAC
TGCTCCAGTTTCACCTTTTTGCTCCCTGAGTTCACTCTCCGAAGTCTGATCCCTGCCAAA
AAGTGGCTGGAAGAGTCCCTTAGTACTCTTCTAGCATTTAGATCTACCCTCTCGAGTTA
AAGATGGGGAAACTGAGGGCAGAGAGGTTAACAGATTTATTTAGGGTCCCCAGCAGA
ATTGACAGTTGAACAGAGCTAGAGGCCATGTCTCCTGCAAAGCTTTTCCCTGTCCTGA
CCCCAGGCAAGAAAAGCGCAAAGAAATCGGTGTTTGACGATTTTGGAAATGAGAACA
ATCTCCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAAAGAGAAAAAAAA
GACTAGCCAGCCAGGAAGATGAATCCTAGCTTCTTCCATTGGAAAATTTAAGACAAG
TTCAACAACAAAACATTTGCTCTGGGGGGCAGGGAAAACACAGATGTGTTGCAAAG
GTAGGTTGAAGGGACCTCTCTCTTACCAGTACCAGAAACACAATTGTAAAATTAAAA
AAAAAAAAACACTTTCTATTTAACAGTACATTTGTGTGGCTCTCAAACATCCCTTTGG
AAGGGATTGTGTGTACTATGTAATATACTGTATATTTGAAATTTTATTATCATTTATAT
TATAGCTATATTTGTTAAATAAATTAATTTTAAGCT

Amritha Nair
Amritha Nair's picture
hi ryan

hi ryan
did what u suggested
but did nt find any restriction sites at the SNPs i was looking at [ the two exons]
thanks for the help though!

ryan_m
ryan_m's picture
Sorry it didn't work out.

Sorry it didn't work out.
Did you try all known enzymes or just a subset?

Ryan