SGD Help: Chromosomal Physical Map
Contents
The Chromosomal Physical Map shows the location of ATCC clones as well as all ORFs and other chromosomal features (including tRNA genes, RNA genes, transposons, ribosomal RNAs, small nuclear RNAs, and the LTRs of
transposons) for the entire S. cerevisiae genome. Due to the
large amount of information contained on the Physical Map,
it cannot be displayed on one page in its entirety and is
therefore displayed in regions specified by the user.
Organization of the Physical Map
Note: For reference within this help page, a sample Physical Map for a random region of the genome is included below. To understand the organization and features of the map, you may click on various features
described below and in the next section. As long as you are only one page
removed, you may use the Back option on your browser to return to this
page.
- Whole Chromosome Representation: The top section (above the
thin blue line) of the Physical Map contains an orange bar,
which represents the chromosome in view. The centromere is indicated
by the large black dot. Above the chromosomal bar is a scale in
kilobases and the names of two or more loci along the chromosome. The box outlined in red and overlayed on the orange chromosomal representation indicates which region of the chromosome is currently displayed in the lower section of the graphic. The span of this region and the chromosome number are also specified in the title directly above the Physical Map graphic.
- Displayed Region: The lower section of the Physical Map Display (below the thin blue line) shows the Physical Map for the selected region. The following is a list of
features in this section, moving from top to bottom within the
display.
- Zoom buttons: At the top of this section are the "Zoom In" and
"Zoom out" buttons, when appropriate. If you are at the highest
magnification, only the "Zoom out" button
will show. Conversely, only
the "Zoom in" button will show when it is no longer possible to zoom
out. Directly below these buttons is the scale, in kilobases, for the
region of the chromosome in view.
- ATCC clones: ATCC clones are represented by forest green or
dark blue lines directly below the scale in kilobases. Each is
labelled with its corresponding ATCC number.
- ORFs and Other Chromosomal Features: ORFs and other
chromosomal features are represented just below the ATCC clones. The
legend below the Physical Map Graphic explains the chromosomal feature
representation by color. Watson strand ORFs are indicated by red
bars, whereas Crick strand ORFs are indicated by blue bars. Wherever
it is defined, the primary gene name for an ORF is indicated above its
ORF name in a maroon-like color. Each of the bar representations is
clickable (see below). A pair of dashed red vertical lines appears if
the Physical Map was entered through a specific ORF or other
chromosomal feature. These vertical lines make it easy see which
clones encompass the selected ORF.
- Key and Notes: The Key provided below the Physical Map display gives the color key for the various ORFs and
other chromosomal features represented on the map. The Notes provide
hints on how to navigate the Physical Map.
Maneuvering within the Physical Map
- Viewing different regions within the current chromosome or the
genome: You can change the region of the chromosome you would
like to view or even move to a feature on a different chromosome by
one of the following methods:
- To move to a neighboring region of the chromosome, use the "Retrieve Map Left" and "Retrieve Map Right" links located between the Physical Map and the Key and Notes section.
- To move to a different section of the same
chromosome, click on the orange bar representing the whole
chromosome at the location you would like to display. You will then
retrieve the Physical Map centered around the position you
selected.
- To see the Physical Map for a specific
locus or ORF at any spot along the genome, type in the locus or
ORF name in the box provided at the top of the Physical
Map page and hit Submit. If you have entered a name and change your
mind before submitting it, hit the Reset button. The Physical Map centered around the area you selected will appear, even
if it is on a different chromosome.
- Zoom Functions: Use the "Zoom in " and "Zoom out" buttons to
see either a magnified or less magnified view, respectively, of the
displayed area. Wherever possible, the zoom occurs with respect to
the center of the area currently displayed. The "Zoom in" function
disappears when it is no longer possible to magnify and area, and the
"Zoom out" function disappears when it is not possible to zoom out
further without losing display information.
Retrieving Clone, Locus, and Sequence Information
The Physical Map display has several different types of
clickable objects. These are listed below, along with the type of
information one retrieves after clicking on the object (use the sample
graphic above if you would like to see how each of these clickable
objects works):
|
Clickable Feature |
Representation on Physical Map |
Result of clicking on feature |
|
Centromere |
Black dot |
Sequence information for centromere |
|
ATCC clones |
Forest green or dark blue bars |
Clone information |
|
ORFs |
Red and blue bars |
Sequence information for ORF |
Non-ORF Chromosomal Features |
Bars of varied colors |
Sequence information for chromosomal feature |
Locus name (for a named ORF) |
Maroon text |
Locus page for gene |
Clone name or standard ORF name |
Black text |
Sequence information for clone or ORF |
The Physical Map for a sequence or region can be accessed:
- by selecting a sequence in Gene/Sequence
Resources and choosing Physical Map as the display option
.
- by using the "Map Type" pop-up menu to select the Physical Map
display option in the Genomic
View.
- through the menu bar at the bottom of a Combined
Physical and Genetic Map for a given region or sequence.
- through the menu bar at the bottom of a Chromosomal Features
Map page for a given region (scroll to the bottom of this Chromosomal
Features Map example in order to see the menu bar with the Physical Map option). The Chromosomal Features Map
for a given region may be accessed through Gene/Sequence
Resources or Genomic
View
Go to Gene/Sequence
Resources
Return to Saccharomyces Genome Database