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Sequence
position: This section lists the position or positions of the genomic element
in the NCBI sequence assembly. The numbers
indicate the starting (pterminal-most) and ending (qterminal-most) base
pair positions of the sequence stretch that the element comprises. The
chromosome assignment is also listed, in the form "from Npter", with N
replaced by the specific chromosome assignment. In parentheses is the
group from which the sequence assembly was derived, and this links directly
to a custom view of the surrounding sequence tract in the group's sequence
viewer.
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. If no position was found, the message "No sequence position identifiable"
is shown, and this message links to this help section. SNP draft sequence positions are not calculated
but instead are reported directly from dbSNP.
Occasionally,
more than one position is identified for an element, in which case all
positions are listed. Reasons for this occurring include targeting non-unique
sequence during primer design, genome duplications, and sequence tract
duplications during the sequencing or sequence assembly processes. In
addition, the sequence-based chromosomal position or chromosome assignment
may differ from other mapping information; this is usually indicative
of raw data generation or data handling errors by a data providing group.
Users should be aware that such problems do occur, that use of such discrepant
data should be made with extreme caution, and that a prudent approach
is to closely examine the raw data and perhaps even independently confirm
the localization assignment.
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RH
map position: The first line refers to the marker or two flanking
markers relative to which the element has been localized, with
likelihood
odds >1,000:1. In the example, the element D1S2845 localizes between
the
RH framework markers D1S468 and
D1S2145, which is known as an interval. These framework marker
names are linked to their own element records. Some elements are themselves
RH framework markers, in which case only this specific element is listed
(such as D1S483). Certain markers are not framework markers but have
been assigned
to the same position as a framework marker; in these cases, the marker
position is listed as "Near marker X," with marker X being the actual
framework marker at that position. The second line also refers to
the
map position of the element, but measured instead in centiRays from the p terminus of the
chromosome. In the example, D1S2845 localizes to the interval between
0
and 98.5 cR from 1pter. The third line indicates the RH position or positions
in terms of the RH framework. For example, in the case above, D1S2845
localizes
between RH framework positions 1 to 9
because it lies between where the 1st and 9th markers down from the
p terminus on the RH framework are located.
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Genetic
linkage map positions: Shown only when a marker is a characterized
polymorphism. The data shown here
is divided into two sections. The first section reports the position of the element on the RH framework map, and the second section reports the element’s position relative to the expanded GL framework.
For each section, the three lines of information are very similar to those
shown for the RH map position (section just above): The first line lists
the 1,000:1 likelihood odds placement in terms of flanking markers or
a framework marker; the second line shows the same information with the
defining map positions calculated in centiMorgans from the p terminus;
the third line indicates the localization in terms of the framework position.
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Cytogenetic
position: Lists the cytogenetic band or band range that has been calculated
by eGenome for the given element's cytogenetic position. See the Methods section for
information about how the cytolocations are calculated. In
general, eGenome cytolocations are more accurate but may be less precise
than locations determined by individual groups. Listed as a single band
or as a band range.
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Other
cytogenetic assignments: Lists the cytogenetic band or band ranges
that have been reported by other groups for the given element's cytogenetic
position. Each reported position is listed on a separate line, with the
group (source) performing the cytogenetic localization listed first, followed
by the large-insert clone used for the localization, and then the localization
itself. These localizations are taken directly from the source's data
and are thus reported "as is".
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RH
score: Shown only for RH markers. Displays the raw scoring data which
was used to localize this element. The RH panel used for the mapping, either
GB4 (Genebridge4) or G3 (Stanford G3), is listed on the first line, and
the panel name is linked to a further description of RH panel construction.
The RH vector information is shown on the subsequent two lines. This vector
represents the raw data used for RH-based localization.
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RHdb
entry: Shown
only for elements which have RH localizations List of one or more RH entries listed in RHdb which are associated with the element.
These entry names are clickable and retrieve the corresponding RHdb records.
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Primer
sequences: Shown only for elements which are PCR-formatted. The DNA
sequence for the primers used for amplification is shown.
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Neighboring
elements: This section lists all elements and SNP's in eGenome that localize within a certain
specified distance of the element currently being viewed. The default
distances are 50 kb for elements and 2 kb for SNP's; that is, elements
within 50 kb on either side of the displayed element are listed. To change
this window size, replace the number 50 (or 2 for SNP's) with the desired
value and click on the GO button. This will refresh the page but will
show the new set of elements or SNP's If there are no elements and/or
SNP's within the designated window size, the message “None”
is displayed along with the window size control setting.
The neighboring elements are displayed in the table, sorted by proximity
to the element. The most pterminal element relative to the element of
record is displayed first, and the most pterminal element is displayed
last. Elements which are either partially or completely within the sequence
stretch assigned to the displayed element are indicated as overlapping
or within, respectively. A gap in the spacing between
lines indicates the transition between elements pterminal and qterminal to the displayed element
The first column displays the eGenome name for the element or SNP, with
the name linked to the eGenome individual record for that element. The
second column lists the distance in base pairs from the original element
of interest. The third column lists the orientation on the chromosome
relative to the element of interest, displayed relative to the pterminus
and qterminus of the chromosome. Non-SNP elements are shown in the first
table, with SNP's displayed in the subsequent table.
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Description
tab
The
description tab lists all informational data for a genomic element, including
the type of element, the expression status, associated EST clusters, and
alternative names/database IDs. Note that SNP's have a different
format which includes variation status, relationship to genes, validation
status, and alternative names/database IDs.
Element
type: Elements can be RH framework markers, Markers, Polymorphisms, or SNP's. For the example above, the record
for an RH marker is shown. Each element type has a record format
with a slightly
different set of information that presented.
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Expression
status: Indicates whether the genomic element represents a sequence
feature that generates an RNA transcript. The status options are transcribed,
not transcribed, and unknown.
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UniGene
EST cluster: Lists a UniGene EST cluster if one is associated
with the element. Cluster names are clickable and linked externally to
the corresponding cluster record in the UniGene database. If the element
is not associated with a cluster, then "None" is displayed.
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Alternate
names and database IDs: This is a listing of all names and assigned
database identifiers (such as an ID given to an element by the group from which the element was derived) for the displayed element. For
RH elements which consist of more than one RHdb entry, all names and IDs associated
with all of the entries representing the element are listed. The only
exclusions to the list of IDs are assigned sequence accession numbers,
UniGene cluster IDs, and RHdb IDs, each of which appear in their own categories
elsewhere within the element record. Note that the ID list shown is not
exhaustive. The IDs are written in the format Source: ID. In the example
above, Sanger_STS represents the source
of the ID and stSG50695 is the Sanger Institute's
identifier for that particular element. Note that the underlined Sanger_STS
links to eGenome's definition of this group, while the underlined stSG50695
represents a clickable link to the record
for this marker at the Sanger Institute itself. External databases not
containing specific information about individual elements only have a
generic link to their eGenome definition, while their IDs are not clickable. This
is evident for the dbSNP entry in the example above.
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Description tab: SNP's
The
SNP's description tab lists all informational data for a SNP, including
variation status, relationship to genes, validation status, and alternative
names/database IDs. Note that other types of eGenome elements have a different
format, which includes the type of element, the expression status,
associated EST clusters, and alternative names/database IDs. All of the
information displayed in this tab is from dbSNP.
Element
type: Elements can be RH framework markers, RH markers, polymorphic markers, or SNP's. For the example above, the record for
a SNP is shown. Each element type has a record format with a slightly
different set of information that presented.
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Variation
status:
Lists up to four parameters relating to variation for the listed SNP.
Base pair change details the base pair change invoked
in the DNA by the variation. For example, a display of A/C indicates that
either an adenine or cytosine base is present at the indicated base position
for this SNP. Heterozygosity reports the average estimated
heterozygosity score for this variation, which is based mostly upon the
number of samples assayed and the genetic makeup of the samples. Assay
sample size indicates the number of independent chromosomes (the
genotype of a diploid individual contains two chromosomes) that were originally
assayed to identify this SNP. Population data sample size
indicates the total number of independent chromosomes (the genotype of
a diploid individual contains two chromosomes) that were assayed to precisely
determine the frequency of each variant in one or more human sub-populations.
Some of these genotypes may have been generated subsequent to the original
SNP detection assay.
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Genic
status: This section indicates whether the SNP is associated with
any transcripts and, if so, what the physical relationship between the
SNP and the transcript(s) is, if known. If the SNP is not known to be
in proximity to a gene (as defined by the NCBI's current gene model),
this section does not appear. If there is
a known association, a table is shown, with one row for each gene
associated with the SNP. The table has up to 4 columns. The first column
lists Associated gene(s). This lists one or more genes in close proximity
to the transcript. The official gene symbol is displayed. The second column displays the Entrez Gene identifier associated with the gene. This ID is linked to the corresponding NCBI Entrez Gene record.
The third column lists the Relationship between the SNP and the gene,
in terms of the gene's known or predicted genomic structure. The
relationship options are coding (if the SNP is within the protein-encoding
region of the gene), mRNA-UTR (if the SNP is transcribed but
not encoded into protein), intron, splice site, locus-region (if the SNP is within 2 kb 5' or 500 bp 3' to a gene, but not within the transcript of the gene)
or unknown. More detail regarding how dbSNP categorizes SNP/gene relationships can be found here. If the SNP is within the coding region of the gene, a final column, Coding status, is shown. The options here are synonymous (if the base pair variation
does not affect the amino acid sequence of the protein), non-synonymous
(the variation does affect the amino acid sequence of the protein), or
undetermined. Note that information listed in the Genic status table is
constantly evolving and in certain cases is based upon predictive models
with some degree of inaccuracy.
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Validation
status: Lists whether the SNP has been experimentally validated to
be a viable SNP. The status options are validated, not validated, or unknown.
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Alternate
names and database IDs: This is a listing of names and
assigned database identifiers (such as an ID given to an SNP by
the group from
which the SNP was identified) for the displayed SNP. The ID list shown
is not exhaustive. For SNP's, these are grouped into ID sets for
each independent dbSNP
submission representing the SNP. The IDs are written in the format Source:ID.
In the first example above, CGAP-GAI represents the source of the ID
and 48278 is the identifier used by that source for that particular SNP.
When this
was submitted to dbSNP, dbSNP then assigned an ssID to this submission,
corresponding in this case to ss8522. Thus, all SNP's have two
source:ID pairs, one from
dbSNP and one from the original submitter. The dbSNP identifiers and
the submitter identifiers are both linked to the dbSNP reference SNP
record containing the
identifier. Each source name is linked to a description of the source,
provided either by eGenome or dbSNP.
In this way, all
individual submissions to dbSNP are grouped with their corresponding
dbSNP ssID in eGenome (there are three for this record). For those familiar
with dbSNP,
eGenome represents reference
SNP's but links also to individual submitter
SNP's comprising the refSNP.
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Clones & Sequences tab
The
Clones & Sequences tab lists all data relating to DNA clones and DNA
sequence information for a genomic element, including the element's source
DNA sequence, the position in the draft genome sequence, the sequence
of and base pair position in large-insert clones known to contain the element, homology
searches and graphical viewing of DNA sequences, and a listing of large-insert
clones known to contain the element.
Flanking
sequence (SNP's only): Shows the DNA sequence immediately 5' and 3'
to the variant base. The 5' sequence, labeled"5' Assay", is shown
first. The last base listed in the 5' sequence is the base immediately
5'
to the variant base. This is followed by the variant base itself, which
is shown in red. All observed base variants are listed between the brackets.
For example, [C/T] indicates
that at this base position, either a C or a T has been detected. The following
"3' Assay" displays the sequence immediately 3' to the variant base.
Source sequence: Lists one or more sequence accession numbers identifying
DNA sequence that has been associated with this genomic element. In many
cases, the sequence ID listed is what was used to either design oligonucleotides
specific to the element and used for its localization. Sequence IDs listed
for SNP's were commonly the source sequence used to identify the SNP. Each accession
number is linked to the DNA sequence record in GenBank.
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Genome
sequence: This section lists the position or positions of the genomic
element in the NCBI sequence
assembly. The numbers indicate the starting (pterminal-most) and ending
(qterminal-most) base pair positions of the sequence stretch that the
element comprises. The chromosome assignment is also listed, in the form
"from Npter", with N replaced by the specific chromosome assignment. In
parentheses is the group from which the sequence assembly was derived,
and this links directly to a custom view of the surrounding sequence tract
in the group's sequence viewer.
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. If no position was found,
the message "No sequence position identifiable" is shown, and this message
links to this help section. SNP
draft sequence positions are not calculated but instead are reported directly
from dbSNP.
Occasionally,
more than one position is identified for an element, in which case all
positions are listed. Reasons for this occurring include targeting non-unique
sequence during primer design, genome duplications, and sequence tract
duplications during the sequencing or sequence assembly processes. In
addition, the sequence-based chromosomal position or chromosome assignment
may differ from other mapping information; this is usually indicative
of raw data generation or data handling errors by a data providing group.
Users should be aware that such problems do occur, that use of such discrepant
data should be made with extreme caution, and that a prudent approach
is to closely examine the raw data and perhaps even independently confirm
the localization assignment.
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Large-insert
clone sequence: This section lists the position or positions of the genomic
element within large-insert clones whose sequences have been determined
at least in part. The numbers indicate the starting and ending base pair
positions of the sequence stretch that the element comprises. The GenBank accession number for the clone's
sequence, which is linked to its GenBank record, is listed next. Also listed
is the large-insert clone itself. Clicking on the clone name will perform
a name lookup search in the NCBI Clone Registry. Clone names
usually have a prefix that designates the source library, followed by
a specific clone address within the library.
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Sequence
tools: In this section, two sequence analysis tools are available. Please also refer to the help pages of the respective external websites providing these tools for additional information about these utilities.
The
first utility is a method for performing homology searches of any DNA
sequence listed on the page using BLAST. At left, under "BLAST sequence", is a selection menu listing
all DNA sequences listed on the page; select the one you wish to search
with. In the middle, under "in GenBank database", is a selection menu
listing all of the sequence databases that can be searched; select the
database of interest. To find out more information about which GenBank
database is appropriate, click on the word database above the menu,
which provides a description of each database. At the right, under "in",
is a selection menu providing phylogenetic restriction of the search.
Using the default "all species" will perform a search of all entries in
the chosen GenBank database. Selecting a phylogenetic group from the list
will instead restrict the search to sequence records within the group
for the database selected. After making the three menu selections, click
on the GO button to perform the search at GenBank. Please note that BLAST
searches with long sequences may take considerable time or could timeout,
depending upon the current NCBI server load. Note also that this function
is provided courtesy of GenBank, and any results, functionality, and performance
issues are solely within the domain of the NCBI. Further information and
more sophisticated homology searches are available at the BLAST website.
The second
utility allows users to view any DNA sequence listed on the page in several
external sequence/genome viewers. At left, under "View sequence", is a
selection menu listing all DNA sequences listed on the page; select the
one you wish to view. At right, under "in" is a selection menu listing
the genome viewers; select the one you wish to view the sequence in. After
making the two menu selections, click on the GO button to view the sequence.
Currently, the UCSC, Ensembl, and NCBI MapViewer viewers can be utilized.
The utility performs a search at the selected website using the DNA sequence
accession number, provided that the external site's database contains
the accession number (see here for more information regarding External
links). Successful use of these viewers requires familiarization
with the viewer's capabilities and configuration, and documentation for
these can be found at each site.
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Large-insert
clones: Lists all large-insert clones that have been reported or calculated
to contain the genomic element being viewed. This information is displayed
in a table, with the column titles linked to the specific help section
for that column. The large-insert clones table has four columns: Clone
name, Type, Sequence
ID, and Identified by, each of which
is explained in detail directly below.
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Clone name: This column lists the name of each
clone reported to contain the genomic element being viewed. Clone names
are linked to specific clone records at WICGR (for YAC's) or the NCBI Clone Registry (all other clone
types). Clone names usually have a prefix that designates the source library,
followed by a specific clone address within the library.
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Type: This column lists the type of
large-insert clone being listed. Types include BAC's, PAC's, YAC's, P1s, cosmids, and fosmids). Each type links to a definition
of what the clone type is.
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Sequence ID: This column lists the GenBank DNA accession number for any clone whose sequence has been determined and deposited in GenBank. Each sequence ID links to the corresponding record for that sequence at GenBank. No YAC clones have associated sequences.
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Identified by: This column lists the group or source
that reported or determined that the genomic element being viewed is contained
within the large-insert clone listed. Group names link to a description
about the group, from which direct links to group websites can be found.
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