Investigation 2: Non-homologous elements: The Sex Determining Region of The Y
chromosome
Let's return to the Y chromosome to explore some non-homologous elements. There are
obviously many more genes on the X chromosome that are not present on the Y chromosome,
but for our exercise, we will investigate a gene found only on the Y chromosome- the gene Sexdetermining Region of the Y chromosome, or SRY.
To conduct a search for the human SRY gene: Navigate back to "Browse your Genome"
http://www.ncbi.nlm.nih.gov/projects/genome/guide/human/index.shtml
Under the chromosomes image is the search field “Find a Gene.” One can search for a specific
gene by name here.
Type in "sex determining region of the Y" or “SRY” in the text field, and select Homo sapiens
in the drop-down menu.
Hit the go button.
In the results, find the record for the human SRY gene on chromosome Y, cytogenetic location
Yp11.3
Click the link for the human SRY gene record.
This gene is also known as TDF and TDY (for testis-determining factor and testis determining
region on Y, respectively).
Click the ‘reference sequence details’ link. This will take you to another section of the report
that links to the Reference Sequences for the SRY gene transcript and the SRY protein.
Scroll down to the “NCBI Reference Sequences (RefSeq)” heading, or click the “Reference
Sequences” option from the Table on contents on the far right of the SRY record page.
Click on the record for the mRNA transcript: NM_003140.2, as shown below. This is the
accession number, or unique identification number, for the nucleotide record for the human SRY
gene.
Clicking the record number will take you to the full GenBank database record for the nucleotide
coding sequence of the human SRY gene. The first line of the record gives the accession number
and length of the sequence. At the end of the record, the full nucleotide sequence is given.
Answer the following question in your laboratory notebook in the “Answers/Conclusions”
section:
Question 2-1: According to the Nucleotide database sequence record, how many base pairs (bp)
is the human SRY transcript?
Now go back to the Entrez Gene record, where you selected the record for the SRY transcript
sequence. This time, select the record for the protein sequence: NP_003131.1
Answer the following questions in your laboratory notebook in the “Answers/Conclusions”
section:
Question 2-2: According to the record, how many amino acids long is the SRY protein?
Question 2-3: Why do you think the amino acid sequence length is NOT the same number that
you would get by simply dividing the number of nucleotides in the SRY nucleotide sequence by
3?
Although having the gene sequence provides a lot of information, just having the sequence is
not enough. Again go back to the Entrez Gene record, where you selected the record for the SRY
transcript and protein sequence. This time, select the link for “CCDS”. This link will take you to
the coding sequence for SRY, which is a sequence that results from consistent annotation by
researchers.
The annotation of genes is a collaborative effort between international partners. The links below
will give you more information about how gene records are annotated by researchers.
http://www.ncbi.nlm.nih.gov/projects/RefSeq/
http://www.ncbi.nlm.nih.gov/projects/CCDS/
Note how the nucleotide sequence of the consensus record is shorter than the Nucleotide
database sequence for SRY that you reported above because the consensus sequence has been
revised/edited by researchers to show only those nucleotide bases that are translated into the
SRY protein.