Molecular Maps Help

General Comments

Molecular Maps are genomic maps of wild type chromosomes. Each map
represents the data presented in one publication and may contain
information about gene structure, aberration breakpoints, mutations,
regulatory elements, rescue fragments, and sites of transposon
insertions. The coordinate scale used in the publication is preserved.
If known the orientation of the map on the polytene chromosomes is
indicated as positive or negative with respect to the direction of
increasing cytology.

Map data is extracted from graphical maps in figures, from text, and
from DNA sequence (either from the paper itself or from sequence
database entries that cite the paper as a reference). Wherever
possible, exact sizes or positions of entities are used as extracted
from sequence data or author statements. In the absence of sequence
based data, coordinates are estimated from the graphical maps in
figures. An indication of the source of the data is provided in the
comments.

Using the Maps

The maps are presented with the coordinate scale at the top. If no
coordinate system was assigned by the author, maps are displayed with 0
at the left end with coordinates increasing from left to right.  Mapped
features are displayed with other features of a similar nature in
labelled sections beneath the coordinate scale. Thick lines represent
the known extent of a given entity and thin lines represent the range
of uncertainty of the map location (as indicated by the author). For
deficiencies, thick lines represent DNA that is deleted.  Dashed lines
extending off the map indicate that part of the mapped feature is not
contained within the map as drawn. Triangles or diamonds represent
points.

Many of the features are hyperlinked to reports which provide further
details about the mapped entities. All of the aberrations, mutations,
and rescue fragments are linked to the appropriate aberration or allele
reports. Coding sequence (CDS), exon, and regulatory elements are
linked to a gene report. In the near future, the CDS and exon links
will go right to the Protein and Transcript page of the gene. Note that
all of the mapped exons for a gene are indicated but the order in which
they are combined to generate transcripts is not indicated as yet on
the maps.  This information can be found in the transcript reports near
the bottom in the section titled "Transcript composed of exons
numbered:"

The portion of the mapped DNA that has been sequenced and is associated
with a sequence database record is indicated as a GenBank record and
is marked with the Accession number. If a sequence is presented as a
solid line, it represents genomic DNA and indicates that the entire
indicated region has been sequenced. If a seq is drawn with dashed
lines at each end, then some subset of the indicated region has been
sequenced. The latter are most often cDNA sequences which correspond
only to the exonic portions of the map. The sequence entries are
hyperlinked to the appropriate GenBank record.

Below the map, a table lists the actual coordinates in kb of each of
the mapped features. Coordinates listed as X--Y indicate entities that
extend from point X to point Y. Note that for entities that extend off
the map, the table does not give an indication that the entity extends
beyond the map but rather lists the Left-most or Right-most coordinate
of the map.  X~Y indicates the uncertainty in the location of a
particular entity or breakpoint. Coordinates with 4 places after the
decimal point (e.g.  0.1005) represent the locations of entities that
map between bases on the wild type map such as transposon insertions.

We welcome additional information, such as more exact kilobase coordinates, 
from authors. Since each map is based on a specific publication, we 
request more detailed information pertaining only to that publication.

You may send comments, information, and corrections on specific maps to:
flybase-updates@morgan.harvard.edu.



 
Send comments to us at
flybase-help AT morgan.harvard.edu


FlyBase-NG uses Argos: A Replicable Genome infOrmation System