|
The
data table consists of the symbols legend and four sections: the Markers section,
the Polymorphisms section, the SNP's section and
the Bundles section. Each section displays a different subset of information
about the genomic elements of interest. Only one section is displayed
in the browser window at a given time. The RH markers section is shown by default when the individual record is first displayed.
Other sections can be accessed by clicking on the section tabs for polymorphism
and bundle that appear directly above the specific element data. To move
from one section to another, click on the appropriate tab, as seen here:
The tab for the active (currently viewed) section is colored dark blue,
while tabs for other sections containing data are light blue. Sections
containing no data have grayed tabs. Each section has a list of one or
more elements matching the query parameter, headed by a dark blue stripe
that lists the column categories.
Back
to Data Table / Back to top
Polymorphism
& SNP symbol:
This triangle-shaped symbol will appear directly after any element name
in the Name column of the summary
table that represents both a SNP and a polymorphism somewhere within the sequence that the element
spans.
Back
to Data Table / Back to top
Contains SNP
symbol: This square-shaped symbol
will appear directly after any element name in the Name column
of the summary table
that contains an identified SNP somewhere within the sequence that the
element spans.
Back
to Data Table / Back to top
Marker
& Polymorphism symbol:
This star-shaped symbol will appear directly after any element name in
the Name column
of the summary table that represents both a marker and a polymorphism somewhere within the sequence
that the element spans.
Back
to Data Table / Back to top
Bold text:
A statement "Bold text - RH/GL framework element" will appear
in the symbols legend whenever one or more elements in the summary table
are members of the framework maps used to construct the overall RH and
genetic linkage maps (click here
for details of this process). Any such elements have their entire entries
displayed in bold text.
Back
to Data Table / Back to top
Help button: This help button links to
the summary table help page that you are
now viewing.
Back
to Data Table / Back to top
Markers
tab
The
Markers tab lists all DNA
markers that have a chromosomal position. These elements are sorted
by chromosomal location (p terminus to q terminus), or for keyword searches,
by name. For each element, a summary of the chromosomal localization(s)
and transcriptional status is listed. Elements with text in bold print
indicate that they are on either the RH
framework, GL
framework, or both.
Name column: Displays
the name of each element matching the query parameters. This displays
the official element name selected by eGenome. The element name is selected to be most
appropriate from all of names and aliases that the eGenome database has
identified. Click here for an explanation of how names
are selected. The element names are clickable and link to their corresponding
individual records. For example, clicking on "D1S2830" in the first entry
shown above would give more complete information about that element. In
some cases, clicking on the Name leads to a list of multiple elements
with that name rather than a single element record. This occurs for elements
which have been named identically by multiple groups, but whose sequence
positions (i.e. primer pair sequences) have been reported differently.
However, elements sharing the same name and same sequence position but
which have been independently localized are grouped into a bundle (reflected in the bundle column). Definitions
of the symbols following certain element Names can be found here.
Back
to Markers / Back to top
Bundle column: Lists the assigned name of the
bundle to which each element has been placed. These names link
to the corresponding bundle records.
Back
to Markers / Back to top
Status
column: Indicates whether the genomic element represents a sequence
feature that generates an RNA transcript. The status options are transcribed,
not transcribed, unknown, and transcribed?. Transcribed? indicates that
there are multiple elements, likely derived from independent groups, which
have identical names and sequence positions but have a conflicting transcriptional
status recorded.
Back
to Markers / Back to top
Sequence position column: Lists
the position of the genomic element in the public sequence assembly. The numbers indicate the base pair position of
the sequence stretch that the element comprises, rounded to the nearest
kilobase. If a position could not be determined, the entry reads "Unknown". If there
are multiple sequence positions, the entry reads "Multiple", and all of
the identified positions can be viewed in the element record(s) by clicking
on the element name. More information about why multiple or discrepant
sequence positions may occur can be found here. The
base pair positions are calculated beginning at the pterminus of the chromosome
(bp position 1 is the pterminal-most base that has been determined for
that chromosome). These sequence positions have been determined using e-PCR, and a sequence position is reported only if both primer sequences
for the genomic element exactly match the genomic sequence with the proper
distance and orientation between each primer. See the Methods
section for information about how the sequence positions are calculated.
Back
to Markers / Back to top
RH position column: Lists
the RH framework position or interval of each element, usually defined by two flanking RH framework markers.
If an element is or localizes near a single RH framework marker, only
that single framework marker is shown. See the Methods section
for information about how the RH positions are calculated. Each framework marker name is linked to the corresponding
individual record for that marker.
Back
to Markers / Back to top
Cytolocation column: Lists
the cytogenetic band or band range that has been calculated for the given
element's cytogenetic position. See the Methods section for information about how the
cytolocations are calculated.
Back
to Markers/ Back to top
Polymorphisms tab
The
Polymorphisms tab lists all elements that are polymorphic in nature, except
for SNP's, which are listed in their own tab.
Polymorphic elements are sorted by chromosomal location (p terminus to
q terminus). For each element, a summary of the chromosomal localization(s)
and transcriptional status is listed. Elements with text in bold
print indicate that they are on either the RH
framework, GL
framework, or both.
Name column: Lists
the name of each element matching the query parameters. This displays
the official element name selected for display by eGenome. The element name is selected
to be most appropriate from all of names and aliases that the eGenome
database has identified. Click here for an explanation of how names are
selected. The element names are clickable and link to their corresponding
individual records. For example, clicking on "D1S2890" in the first entry
shown above would give more complete information about that element.
In some cases, clicking on the Name leads to a list of multiple elements
with that name rather than a single element record. This occurs for elements
which have been named identically by multiple groups, but whose sequence
positions (i.e. primer pair sequences) have been reported differently.
However, elements sharing the same name and same sequence position but
which have been independently localized are grouped into a bundle (reflected in the bundle column). Definitions
of the symbols following certain element Names can be found here.
Back
to Polymorphisms / Back to top
Bundle column:
Lists the assigned name of the bundle to which each element has been placed. These names link
to the corresponding bundle records.
Back
to Polymorphisms / Back to top
Status column: Indicates
whether the genomic element represents a sequence feature that generates
an RNA transcript. The status options are transcribed, not transcribed,
unknown, and transcribed?. Transcribed? indicates that there are multiple
elements, likely derived from independent groups, which have identical
names and sequence positions but have a conflicting transcriptional status
recorded.
Back
to Polymorphisms / Back to top
Sequence position column: Lists
the position of the genomic element in the public sequence assembly. The numbers indicate the base pair position of
the sequence stretch that the element comprises, rounded to the nearest
kilobase. If no position could not be determined, the entry reads "Unknown". If there
are multiple sequence positions, the entry reads "Multiple", and all of
the identified positions can be viewed in the element record(s) by clicking
on the element name. More information about why multiple or discrepant
sequence positions may occur can be found here. The
base pair positions are calculated beginning at the pterminus of the chromosome
(bp position 1 is the pterminal-most base that has been determined for
that chromosome). These sequence positions have been determined using
e-PCR, and a sequence position is reported only if both primer sequences
for the genomic element exactly match the genomic sequence with the proper
distance and orientation between each primer. See the Methods
section for information about how the sequence positions are calculated.
Back
to Polymorphisms / Back to top
cM position column: Lists
the GL framework position or interval of each element, expressed in terms of centiMorgan distance from the
pterminius of the chromosome. If an element is or localizes near a single
GL framework marker, only that single framework marker position is shown. See the
Methods
section for information about how the GL positions are calculated.
Back
to Polymorphisms / Back to top
Cytolocation column: Lists
the cytogenetic band or band range that has been calculated for the given
element's cytogenetic position. See the Methods section for information about how the
cytolocations are calculated.
Back
to Polymorphisms / Back to top
SNP's tab
The
SNP tab lists all elements that have identified variations at a single
base pair. Variations involving more than one base pair and those with
genetic linkage mapping information, are found in the polymorphisms
tab. These elements are sorted by chromosomal location (p terminus
to q terminus). For each element, a summary of the chromosomal localization(s)
and transcriptional status is listed.
Name column: Displays
the name of each SNP matching the query parameters. This displays the
official SNP name selected by eGenome, which is the dbSNP rsID identifier. The SNP names are clickable and link
to their corresponding individual records. For example, clicking on "rs1910292" in the first entry
shown above would give more complete information about that SNP.
Back
to SNP's / Back to top
Status
column: Indicates whether the genomic element represents a sequence
feature that generates an RNA transcript. The status options are transcribed,
not transcribed, unknown, and transcribed?. Transcribed? indicates that
there are multiple elements, likely derived from independent groups, which
have identical names and sequence positions but have a conflicting transcriptional
status recorded.
Back
to SNP's / Back to top
Sequence position column: Lists
the position of the genomic element in the public sequence assembly. The numbers indicate the base pair position of
the sequence stretch that the element comprises, rounded to the nearest
kilobase. If a position could not be determined, the entry reads "Unknown". If there
are multiple sequence positions, the entry reads "Multiple", and all of
the identified positions can be viewed in the element record(s) by clicking
on the element name. More information about why multiple or discrepant
sequence positions may occur can be found here. The
base pair positions are calculated beginning at the pterminus of the chromosome
(bp position 1 is the pterminal-most base that has been determined for
that chromosome). These sequence positions have been determined using
e-PCR, and a sequence position is reported only if both primer sequences
for the genomic element exactly match the genomic sequence with the proper
distance and orientation between each primer. See the Methods
section for information about how the sequence positions are calculated.
Back
to SNP's / Back to top
Cytolocation column: Lists
the cytogenetic band or band range that has been calculated for the given
element's cytogenetic position. See the Methods section for information about how the
cytolocations are calculated.
Back
to SNP's / Back to top
Bundles
tab
The
Bundles tab lists all elements that have been grouped into bundles and which meet the query parameters. Bundles are groups of elements
that share identical molecular definitions (i.e., the same primer sequences) but which have each been individually and independently localized.
Bundles are sorted by chromosomal location (p terminus to q terminus). For each
element, a summary of the chromosomal localization(s) and transcriptional
status is listed. Elements with text in bold print indicate that they are on either the RH framework, GL framework, or both.
Bundle name column: Lists the name of each
bundle matching the query parameters. This displays the official bundle
name
selected
for display by eGenome. The bundle name is selected to be the most appropriate
from all of names and aliases that the eGenome database has identified.
Click here
for an explanation of how names are selected. The element names are clickable
and link to their corresponding bundle records.
For example, clicking on "D1S197" in the first entry shown above
would give more complete information about that bundle. Definitions of
the symbols following certain element Names can be found here.
Back
to Bundles / Back to top
Status column: Indicates whether the bundle
represents a sequence feature that generates an RNA transcript. The status
options are transcribed, not transcribed, unknown, and transcribed?. Transcribed?
indicates that there are multiple elements, likely derived from independent
groups, which have identical names and sequence positions but have a conflicting
transcriptional status recorded.
Back
to Bundles / Back to top
Sequence position column: Lists
the calculated max position of the bundle in the public sequence assembly. The numbers indicate the base pair position of
the sequence stretch that the element comprises, rounded to the nearest
kilobase. If a position could not be determined, the entry reads "Unknown". If there
are multiple sequence positions, the entry reads "Multiple", and all of
the identified positions can be viewed in the element record(s) by clicking
on the element name. More information about why multiple or discrepant
sequence positions may occur can be found here. The
base pair positions are calculated beginning at the pterminus of the chromosome
(bp position 1 is the pterminal-most base that has been determined for
that chromosome). These sequence positions have been determined using
e-PCR, and a sequence position is reported only if both primer sequences
for the genomic element exactly match the genomic sequence with the proper
distance and orientation between each primer. See the Methods
section
for information about how the sequence positions are calculated.
Back
to Bundles / Back to top
Cytolocation column: Lists
the cytogenetic band or band range that has been calculated for the given
bundle's cytogenetic position, which is based upon the calculated max location for the bundle. See the Methods
section for more information about how the cytolocations are calculated.
Back
to Bundles
|
