Hello,
By reviewing the data in the UCSC Gene track, the two sequences that you
refer to by RefSeq ID (NM_007294 and NM_007295) are revealed to be
isoforms of the same Human Gene BRCA1. UnitProt lists 5 isoforms:
http://www.uniprot.org/uniprot/P38398. Other tracks in the UCSC Browser
(such as CCDS) list 3 associated RefSeq sequences.
Each data track has specific rules for grouping together mRNA sequence
data into translated protein groups "representing" an individual
protein. Read the track's Description and Methods to determine how to
interpret the corresponding data. Each is different, whether from
internal or external sources, and designed to answer a range of
scientific inquiries. Only you can determine which data grouping
criteria meet your research needs.
Once reviewing the available protein tracks, you can use the Table
Browser to extract the mRNA and/or protein sequence. Select the
clade/genome/assembly along with group and track of interest. The
default table is usually the one you will want to use ("View table
schema" to see contents). Filter by genomic region or by using gene name
identifiers. Output as sequence will result in a fasta formatted data
file (name the file to download). Choices for Gene Prediction tracks
often include mRNA, Protein, and Genomic.
All data is mapped to the genomic - this is how you will locate where
features (such as SNPs) intersect with protein/mRNA sequence.
Output the UCSC Gene track data as fields from table (all or linked) to
gain genomic coordinate information.
To find any SNPs, change the track/table to a SNP track, filter by
genomic region or identifier, and select an output format that includes
genomic coordinates. Or, use the intersection function to filter the SNP
table using a custom track containing only your genes of interest. It is
very useful to view this information within the assembly browser window
when investigating a particular protein. Start bu setting the Base
Position, Gene prediction track(s), and SNP track to display = full and
setting extraneous tracks to hide. Zoom down to base level to examine
the most detailed level of information. Add additional tracks for more
information. Comparative Genomic tracks (such as Conservation) and may
be very interesting to include as well as data from the ENCODE groups
(when coverage is available).
Some FAQ/Help documentation about included tracks/custom tracks:
http://genome.ucsc.edu/FAQ/FAQtracks
http://genome.ucsc.edu/FAQ/FAQcustom
Table Browser help:
http://genome.ucsc.edu/cgi-bin/hgTables?command=start#Help
http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html
Thank you,
Jennifer Jackson
UCSC Genome Bioinformatics Group
[email protected] wrote:
> Hi There,
>
> Where can I get gene's sequence and their corresponding translated protein's
> sequence?
>
> I am wondering how people know where the snp site is. If they find the
> snp site in gene sequence, how to decide which the corresponding site
> of translated protein. If they find the snp site in protein sequence,
> how they know which site it is in the corresponding gene sequence.
>
>
> For the two mRNA of gene brca1,
>
> NM_007294
> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_007295.2
> (CDS:201..5792)
>
> and
> NM_007294
> http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?val=NM_007294.2
> (CDS:398..5989)
>
> why they are translated to the different protein sequences
> but same swiss-prot id P38398?
>
> Thank you.
>
> Van
>
>
>
>
> _______________________________________________
> Genome maillist - [email protected]
> http://www.soe.ucsc.edu/mailman/listinfo/genome
>
_______________________________________________
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http://www.soe.ucsc.edu/mailman/listinfo/genome
