annotate mRNA and gDNA seq, Identify 5' and 3' untraslated

[gene26]

Hi, i was given to do these but i never did this before can anyone help how to do these step by step...


Given Mouse Villin protein, mRNA and genomic DNA sequences.

Annotate the mRNA and gDNA sequences to show the start and stop codons, Identify the 5’ and 3’ untranslated regions (UTRs), Identify the transcription start site, Highlight the 3.5kb region upstream of the transcription start site, Identify the binding sites of the Villin F1, R1, F2 and R2 primers

[relaxin]

This seems to be an examination question. We should only give you some hints.

1. Compare the 5'-most cDNA sequence with genomic sequence, you will locate the transcription start site. You have to assume the cDNA sequence is a full-length one.

2. The first ATG in the cDNA sequence is usually the start codon. Then go down the triplet codons until you find one of the three STOP codons. If you have access to a DNA analysis program, it will translate it for you. Compare the translated sequence with the gvien protein sequence to confirm the predicted START and STOP codons.

3. Any sequences on the cDNA sequence that do not encode for protein are UTR.

4. Use the search function of the DNA analysis program (or word processing progress) to locate the primer sequences.

[gene26]

NO THIS IS NOT AN EXAM QUESTION (no marks)

[mchlbrmn]

Genbank RNA sequences are usually annotated to show the translation start and stop.
There are many online tools you can use and insert sequences to analyze them. You can try searches with words such as, "online DNA tool" to start finding them. One is a "BLAT" search. This allows you to input a cDNA sequence and search the genome for matches, thus you can find the exons in the genomic sequence. Here is one link:
http://genome.ucsc.edu/cgi-bin/hgBlat?command=start
At NCBI you can find the more common "BLAST" program that allows you to search Genbank with a sequence. If you have only sequence data, you can find matches in Genbank that may already be annotated, and have links to other resources.
http://blast.ncbi.nlm.nih.gov/Blast.cgi ... =BlastHome