A simple question on cDNA and protein sequence

cheng

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Join Date: Oct 2010

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A simple question on cDNA and protein sequence

10-06-2010, 12:09 PM

I downloaded cDNA sequence file and protein sequence files, see below:
>ENST00000400890 cdna:known supercontig::GL000195.1:44724:86646:-1 gene:ENSG00000215781
GTCTCCTCTTTCGCCTCCTCCGCTTTGGGAGCCCCGGGCTACTCTTTCACAGCCCCTGTT
GCCCTGTGATCTGTAGGTCCTTGGGGACGCACAGTTAAGATGACAGGACATCCTGGAAGC
TGGGAAATGATATGTATTCATTTCCTACCACCGTAGTGGAAGAGATACTATCCCTATCTT
TACAACTGATAGCATTTCCAACAGTAAGCTGTGAGATTCTGCTTGAAATCACCTCTCAAA
CAAATAAAAAACAGACCTGGGAGACATGCTACGCTCATTCTGCTGAAGAAATAGGCATCA
TAGCTGGGAAACGGATTCACAAGACCCAGGCTGTTCCCTACATATGTTTCCTCCTCCGAC
ATCAGTTCATCAGTCAATCAAGCCATGTGAGAGTGGAGGCCTTGTATTCCCTATTATTCT
TGGGCACTCTACTCCAAGTAGGAAAAGGCCAGGAGGTCCTGTTAAAGGATGCACTCAGAG
CCCGGGCTCCCTAA

-------------------
>ENSP00000383683 pep:known supercontig::GL000195.1:44724:86646:-1 gene:ENSG00000215781 transcript:ENST00000400890
MYSFPTTVVEEILSLSLQLIAFPTVSCEILLEITSQTNKKQTWETCYAHSAEEIGIIAGK
RIHKTQAVPYICFLLRHQFISQSSHVRVEALYSLLFLGTLLQVGKGQEVLLKDALRARAP

They are not matched for the same gene and transciption, why? I'm a newcomer.
Thanks.
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malachig

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Join Date: Aug 2010

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#2

10-06-2010, 08:36 PM

Not sure if this answers your question but... are you sure they are not matching?

It seems like the 3rd frame of that cDNA sequence contains the ORF that results in the protein sequence you have. The ORF opens at position 132 of the cDNA sequence and goes to the end. This was determined by BLAST 2 Sequences online at NCBI.

Click that link, open the 'blastx' tab, paste the cDNA sequence in the first box and the protein sequence in the second box. Then hit the 'BLAST' button.

Result:
Attached Files

cDNA_vs_Protein.txt (1.2 KB, 3 views)
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A simple question on cDNA and protein sequence

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