NCBI Gene: Expression (Part 2): Tissue-Specific Expression

Open NCBI Gene record for SLC25A3

in another browser window to work through this tutorial side by side.

We're now returning to the Gene record for SLC25A3 to address a different question:

This transporter has different splice variants. How can I see whether any of these have tissue-specific expression patterns?

To find tissue-specific expression of splice variants, we will go back to the RNA-seq data, linked from the Gene database record.

In the Table of contents, click "Genomic regions, transcripts and products."

genomic regions link

This is the embedded Graphical Sequence Viewer.

graphical sequence viewer

The display shows the genomic sequence at the top with the aligned mRNA products (transcripts) immediately below:

3 transcripts

The mRNAs align only to the portions of the gene (exons) that are spliced together to make the transcript.

This gene has three different mRNA sequences (transcript variants or splice variants) as shown in the graphic with different patterns of exons.

At the bottom of the viewer, the next-gen RNA data (RNA-seq intron features, aggregate (filtered)) are shown as a histogram chart across the gene.

RNA-seq data

These data highlight the expressed portions of the gene, the exons -- those that are spliced together to make the messenger RNA.

The track that best shows the pattern of exons is the intron-spanning reads track, which provides a negative image of the exons.

You can add an entire set of these tracks for different tissues. This is useful because in some cases particular splice variants have tissue-specific expression.

Click on the "Tracks" menu (the gear icon) in the viewer and select "NCBI Recommended Track Sets," "Expression."


This data is from the expression studies that we looked at in the Expression histogram, earlier.

Once you open the Expression tracks, you will need to re-expand the transcript tracks, to see differences between the splice variants.

Click SLC25A3 (+6) at the very top of the graphical sequence viewer:

slc25a3 +6

Notice that there is a particular exon that appears in one of the splice variants (NM_005888).


Now if you look at the the location of the exon and find the same locations on the expression tracks, below, you can see where different tissues preferentially express the gene.

For example, look at the heart track:

comparing tracks

(Note that, for purposes of illustration, we've removed a number of tracks for this screenshot. You will need to scroll or remove tracks to find the track that reads, "RNA-seq intron-spanning reads, adult, heart...")

You have reached the end of the tutorial for the question: In what tissues and under what conditions is the gene expressed??

NCBI Gene Help Resources

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