BLAST sequence comparing

[Britta]

A human protein sequence was compared to a human mRNA sequence using TBLASTN. All amino acids of the protein were matched with 100% identity, but the first (5’) and last (3’) parts of the
mRNA were not included in the alignment, is this because of the UTRs?

When the same mRNA was used in a BLASTN search against the human genome all the mRNA was matched but the alignment was split up in several alignments (HSPs).Why is this?

The human mRNA was compared with BLASTN to the orthologous mRNA from mouse, but BLASTN did not produce any alignment. Why?

I am a beginner in the subject and grateful for answers!

[mastal]

When the same mRNA was used in a BLASTN search against the human genome all the mRNA was matched but the alignment was split up in several alignments (HSPs).Why is this?

The genomic DNA has introns, which are spliced out from the mRNA.

The human mRNA was compared with BLASTN to the orthologous mRNA from mouse, but BLASTN did not produce any alignment. Why?

Could be that the score for the alignment did not meet the cutoff values for the parameters used in the blast search, like evalue, or percent identity.

[rhinoceros]

Is this your homework?

A human protein sequence was compared to a human mRNA sequence using TBLASTN. All amino acids of the protein were matched with 100% identity, but the first (5’) and last (3’) parts of the
mRNA were not included in the alignment, is this because of the UTRs?

Could be.

When the same mRNA was used in a BLASTN search against the human genome all the mRNA was matched but the alignment was split up in several alignments (HSPs).Why is this?

Introns?

The human mRNA was compared with BLASTN to the orthologous mRNA from mouse, but BLASTN did not produce any alignment. Why?

The gene has changed extensively in one of the lineages and no homology can be inferred from the nt level? Could be a million other things..

[GenoMax]

The human mRNA was compared with BLASTN to the orthologous mRNA from mouse, but BLASTN did not produce any alignment. Why?

If you are looking at a true ortholog it is surprising that the "functional" bits do not match.

Look at the homologene section from NCBI site (as example here: http://www.ncbi.nlm.nih.gov/homologene/132386). Perhaps NCBI has already done the work for you.

[Britta]

Thanks for the answers!

No, it is not homework, but its tasks from a book and I don´t have anyone to correct me so I wanted to see if I was on the right track.

The last question,
"The human mRNA was compared with BLASTN to the orthologous mRNA from mouse, but BLASTN did not produce any alignment. Why?"

I thought that the nucleotide sequence was not conserved, but if comparing similar protein in BLASTP, they would still be able to show similarities because different nucleotide sequences can give rise to identical / similar amino acid sequences. Is that all wrong?

[mastal]

Thanks for the answers!



I thought that the nucleotide sequence was not conserved, but if comparing similar protein in BLASTP, they would still be able to show similarities because different nucleotide sequences can give rise to identical / similar amino acid sequences. Is that all wrong?

No, you are right.

There are 64 codons but only 20 amino acids, so there is some redundancy in the genetic code.