Locus Report


Overview

The Locus Report is the core of the Proteome module and an important component of TRANSFAC module. Each Locus Report, presented as a web page, is similarly structured across all species.


Please note: BKL subscribers who have licensed the PROTEOME, TRANSFAC and PGMD modules will see the full complement of information available in a Locus Report. BKL subscribers who have licensed only part of the BKL will see subsets of information, depending on the subscription. The combined Locus Report for subscribers of the complete BIOBASE Knowledge Library is described below.


Locus Reports begin with a descriptive Title Line and comprise information about the gene and the protein, curated as Properties that can be tabulated, and as free-text Annotations. Below the Title Line and list of curated Synonyms the various topics covered in the Locus Report are listed. Specifically, each complete Locus Report has eight Properties blocks: Biomarker Associations, Drug Interactions, Gene Ontology, Expression, Mutant Phenotype, Pathways & Interactions, Transcriptional Regulation, and Protein Features. Each of these Properties blocks contain links to Property Reports that display additional details about the curated information. For example, a subset of Gene Ontology (GO) terms appears in the Gene Ontology block. Clicking the [details] link opens a Property Report that provides the complete list of curated terms, with details about experimental evidence and links to cited references. In addition to the Properties blocks, 3 other sections are included in complete Locus Reports: Identifiers, free-text Annotations, and References cited. Each section is described briefly below.


Please note: Yeast, worm, and mammalian GPCR-related Locus Reports contain Annotation Lines, while Locus Reports for other mammalian entries within the Proteome module or for the TRANSFAC module alone, do not.


Gene and protein symbols mentioned in the Properties and Annotations are hyperlinked to their respective Locus Reports. When a Property or Annotation mentions something for which there exists a BKL Report, a hyperlink connects between Reports.

Locus Reports may be accessed through the BKL Tools or through hyperlinks on BKL reports.


Anatomy of a Locus Report

The structure of a Locus Report is described below. Detailed documentation for the individual BKL components is accessed from links in the menu on the left, at the top of this page.

  • Access help by clicking the help menu  help  and clicking the Locus report help link.

  • Navigate to the desired section of the report by opening the table of contents  toc

Points of navigation within the report are indicated by the following visual cues.

  • Links to additional reports within the BKL are presented as regular text links.

  • Links to external resources are indicated by a blue bubble, such as the PubMedID link shown here:  external link  .

  • Links to display additional text within the page are indicated by a yellow bubble, such as the show abstract link shown here:  expand content  .
  • Links providing an option to download content are indicated by a green bubble, such as the FASTA link shown here:  download content  .
  • Links providing an option to send data to another tool within the BKL are indicated by a gray bubble, such as the Pathfinder link shown here:  download content  .




Introduction Provides a description and synonyms for the gene  
Description
A concise, one-sentence description of the protein, including relevant aspects of a protein's role or function in the cell. Title lines begin with a name phrase, followed by a description of the protein's function and/or the process or pathway in which it is involved, followed by disease information when available for human, mouse, and rat proteins. In the absence of literature-supported functional or disease information, domains and family membership are noted. Subcellular localization, regulation, splicing patterns, and expression patterns are included when pertinent or in the absence of additional information. Title lines that appear on Locus Reports originate from the Proteome Databases and are updated continually to reflect the current literature.
Synonyms
Lists synonyms for the gene and protein, including additional names and abbreviations, separated by semicolons.

Biomarker Associations Displays a tabular summary of literature-derived relationships between human genes, mRNAs, and proteins and human disease processes. The first five entries are shown; click [more ...] to view all entries. Data may be alternately sorted by clicking on the column header. Click on [details] or on the # associations link to view a tabular breakdown of the data supporting the disease-protein associations represented in each section. Click the disease entry listed in the Disease column to open the corresponding Disease View Report. The number of protein-disease relationships represented by each section is shown under each disease, under each relationship heading, and next to each checkmark.  
Type of Association
Categories listed here describe the types of relationship reported between the protein and a disease.
Causal
Indicates a causal relationship between the protein and the disease and can be either confirmed or hypothetical. A tabular breakdown of the data supporting the linkage with each disease (including cited references) is accessible by clicking on [details], which opens a Property Report. The MeSH description of each disease is accessible from the Property Report.
Correlative
Indicates a correlative relationship between the protein and the disease and can be either confirmed or hypothetical. A tabular breakdown of the data supporting the linkage with each disease (including cited references) is accessible by clicking on [details], which opens a Property Report. The MeSH description of each disease is accessible from the Property Report.
Preventative
Indicates a preventative relationship between the protein and the disease and can be either confirmed or hypothetical. A tabular breakdown of the data supporting the linkage with each disease (including cited references) is accessible by clicking on [details], which opens a Property Report. The MeSH description of each disease is accessible from the Property Report.
Negative
Indicates a negative relationship between the protein and the disease, including negative relationships from all categories listed above. A tabular breakdown of the data supporting the linkage with each disease (including cited references) is accessible by clicking on [details], which opens a Property Report. The MeSH description of each disease is accessible from the Property Report.
Indication
Categories listed here describe what the protein/disease association might indicate about the utility of the biomarker.
Disease Mechanism
Indicates that this protein has been reported to provide information on the mechanism behind the disease. A tabular breakdown of the data supporting the linkage with each disease (including cited references) is accessible by clicking on [details], which opens a Property Report.
Prognosis
Indicates that this protein has been reported to provide information on the progression or severity of a disease. A tabular breakdown of the data supporting the linkage with each disease (including cited references) is accessible by clicking on [details], which opens a Property Report.
Therapeutic Target
Indicates that reports on this protein suggest a use as a target for treatment of this disease. A tabular breakdown of the data supporting the linkage with each disease (including cited references) is accessible by clicking on [details], which opens a Property Report.
Inherited Mutations
Provides a link to the Human Gene Mutation Database (HGMD) report for the gene with an overview of the mutation counts contained within. Note that access to HGMD requires a separate subscription.

Pharmacogenomic Variants This section lists the pharmacogenomic variants located within the gene of the page that have been identified as being significantly associated with an altered phenotypic response to a drug.  
Variation
Describes either the amino acid change for the variation, or nucleotide change, conforming to HGVS nomenclature standards. Entries are linked to the corresponding Variant Report.
dbSNP ID
When available, specifies the dbSNP accession.
Phenotype
Describes the impact of genetic variation on drug response.
Study disease
Specifies the disease that was the focus of the study, linked to the corresponding Disease Report.
Study drug
Specifies the drug that was the focus of the study, linked to the corresponding Drug Report.
HGMD
When available, links to a HGMD mutation report that describes the same site of variation.
PMID
PubMed reference number, which specifies the source from which the information is captured.
Named variant
For star (*) alleles, genotypes are represented with gene names followed by allele description e.g. CYP2C9*1/CYP2C9*1.
Sample source
Describes the original source from which sample was genotyped.

Drug Interactions This section lists the drugs that have been recorded in Drugbank as targeting the protein of interest, or are metabolized by the protein of the interest. Drugs are listed in alphabetical order.  
Drugs targeting the protein
Lists Drugbank drugs which target the protein, with links to the corresponding drug report.
Drugs metabolized by the protein
Lists Drugbank drugs which are metabolized by the protein, with links to the corresponding drug report.

Gene Ontology Gene Ontology (GO) is a hierarchical classification system used to describe protein attributes. More than one term indicates that the protein has multiple attributes not adequately described by a single term.  
Molecular function
Describes the biochemical activity of the protein. Additional information about function is accessible by clicking on [details], which opens a detailed Property Report.
Biological process
Describes the biological "objective" to which the protein contributes. Additional information about role is accessible by clicking on [details], which opens a detailed Property Report.
Cellular component
Identifies the place in a cell where the protein is active. Additional information about localization is accessible by clicking on [details], which opens a detailed Property Report.

Expression Spatial patterns of protein or mRNA expression during the development and maintenance of a multicellular organism and regulation of that expression. Expression information is curated for human, mouse, rat, worm, and plant species in the Proteome module.  
Tissue Expression
Organ/Tissue
Describes expression of human, mouse, or rat protein or mRNA in organs and tissues. Additional details, including experimental methods, are accessible by clicking on [details], which opens a detailed Property Report.
Cell Type
Describes expression of human, mouse, or rat protein or mRNA in specific cell types. Additional details, including experimental methods, are accessible by clicking on [details], which opens a detailed Property Report.
Tumor Type
Describes expression of human, mouse, or rat protein or mRNA in specific tumor types. Additional details, including experimental methods, are accessible by clicking on [details], which opens a detailed Property Report.
Location
Describes expression of worm protein or mRNA in specific cell or tissue types. Additional details, including experimental methods, are accessible by clicking on [details], which opens a detailed Property Report.
Organ/Tissue/Cell
Using the Plant Ontology™ (PO), describes expression of a plant protein or mRNA in a particular organ, tissue, or cell type. Additional details, including experimental methods, are accessible by clicking on [details], which opens a detailed Property Report.
Developmental Stage
Using the Plant Ontology™ (PO), describes expression of a plant protein or mRNA during a specific plant developmental stage. Additional details, including experimental methods, are accessible by clicking on [details], which opens a detailed Property Report.
Plant Expression Conditions
Describes expression of a plant protein or mRNA under an experimental condition. Additional details, including experimental methods, are accessible by clicking on [details], which opens a detailed Property Report.
BAR Arabidopsis eFP Browser
Access a view of virtual microarray expression profiles generated by BAR at the University of Toronto via webservice.
BAR eFP Browser
Access a view of virtual cellular localization generated by BAR at the University of Toronto via webservice
Regulation of Gene Expression
Identifies treatments, conditions, physiological changes, proteins, complexes, or pathways that regulate the expression of mRNAs encoded by the gene - either directly or indirectly. Data is organized into the following three topics.
Treatment/Condition
Identifies treatments or conditions that regulate the expression of mRNAs encoded by the gene. Additional details, including the observed changes in expression and the cited references, are accessible by clicking on [details], which opens a detailed Property Report.
Physiological Change
Identifies physiological changes that regulate the expression of mRNAs encoded by the gene. Additional details, including the observed changes in expression and the cited references, are accessible by clicking on [details], which opens a detailed Property Report.
Regulator
Identifies proteins, complexes, or pathways that regulate the expression of mRNAs encoded by the gene, with hyperlinks to the corresponding Reports. Additional details, including the observed changes in expression and the cited references, are accessible by clicking on [details], which opens a detailed Property Report.
Transcription Profile
Hyperlinks to the Transcription Profiling Experiment Index that contains a list of profile categories. Each category expands to a list of profiling experiments available for the gene. Each experiment has a thumbnail that shows the result (fold-change for single-point data sets, or a graph for multipoint data sets) and brings up the Transcription Profile Report. Note that transcription profile data is only available for YPD, PombePD, MycoPathPD, and WormPD.
Commercially available ORF protein expression clones
Provides links, when available, to commercial antibodies for the protein.

Mutant Phenotype For mouse entries, Mutant Phenotype describes gross physiological, behavioral, and cellular phenotypes for mutant mice generated by knockout technology. For yeast and worm entries, Mutant Phenotype describes various phenotypes of null, reduction-of-function, or overproduction mutants. Synthetic lethal interactions are described for yeast genes. For plant entries, this section contains information on mutant or transgenic plants generated by a variety of methods including classical mutation, gene disruption, or ectopic expression. All species will contain information about the phenotypes of closely related homologs when such information has been identified.  
Phenotypic effects of knocking out the mouse gene
Viability effects
Describes the viability of the mutant mouse. When described in the literature, qualifiers are added to describe gender and age. Additional details, including a summary of findings, are accessible by clicking on [details], which opens a detailed Property Report.
Anatomical effects
Describes phenotypes pertaining to specific organs or cells within the mutant mouse. When described in the literature, qualifiers are added to describe gender and changes in degree. Additional details, including a summary of findings are accessible by clicking on [details], which opens a detailed Property Report.
Physiological effects
Describes the overall physiological, behavioral, and/or cellular phenotype of the mutant mouse. When described in the literature, qualifiers are added to describe gender and changes in degree. Additional details, including a summary of findings, are accessible by clicking on [details], which opens a detailed Property Report.
Syntheticly lethal interactions for the yeast gene
Abbreviated list of genes that exhibit synthetic lethality with this gene, with hyperlinks to the corresponding Locus Reports. The full list of synthetic lethal interactions is accessible by clicking on [details], which opens a detailed Property Report.
Phenotypic effects of mutation of the plant gene
Phenotype or affected trait
Using the Trait Ontology™ (TO), describes plant phenotypes or traits affected in a mutant or transgenic plant. Additional details, including a summary of findings are accessible by clicking on [details], which opens a detailed Property Report.
Tissues or stages affected in mutants
Using the Plant Ontology™ (PO), describes plant organs, tissues, cell types, or developmental stages affected in a mutant or transgenic plant. Additional details, including a summary of findings, are accessible by clicking on [details], which opens a detailed Property Report.
Diseases for which the gene is a model
Displays disease models associated with the mutant mouse. Additional details are accessible by clicking on [details], which opens a detailed Property Report.
Mutant phenotype of closely related homologs
Describes mutant phenotypes of model organism homologs, including mouse, worm, and yeast. Displays mutant phenotypes of the closest model organism homolog that possesses mutant phenotype information, including mouse, worm, and yeast. Click the gene name to access the corresponding locus report. Locus reports from organisms not included an a users subscription will not be accessible. Represented homologs are chosen based on the best blast hit possessing phenotype information. If the best blast hit does not have phenotype information, the next best hit is chosen, and so on. Model organism mutant phenotypes on human locus reports include homologs from mouse, worm, and S. cerevisiae. On worm and C. albicans reports, mutant phenotypes from S. cerevisiae homologs are included. For plant reports, this section includes mutant phenotypes from S. cerevisiae, S. pombe, as well as rice and maize homologs. See the descriptions above for details of the model organism mutant phenotypes that are included.
RNAi, Null, Reduction of function, Gain of function, Overproduction
Displays worm phenotypes affected in a mutant or seen using RNAi. Additional details, including reference links, are accessible by clicking on [details], which opens a detailed Property Report.
Null, Reduction of function, Gain of function, Overproduction
Displays yeast phenotypes affected in a mutant. Additional details, including reference links, are accessible by clicking on [details], which opens a detailed Property Report.

Pathways & Interactions Describes pathways and pathways steps (chains) the protein is involved in. Click [hide] to remove curation from view and [show] (not displayed here) to return curation to view. Click here for more details about pathways and pathway steps (chains).  
Pathways
Pathways (Species non-specific)
Describes pathways that the protein is involved in with hyperlinks to the relevant Pathway Report which contains the supporting reactions. All entries can be loaded into the BKL Pathfinder visualizer by clicking the Load in Pathfinder icon. When a hand drawn pathway map is accessible a link is additionally provided in the View Graphic Representation column. Note that "Pathways (Species non-specific)" are constructed from multiple "Pathway Steps (Species non-specific). The first five entries are shown, click [more ...] to view all entries.
Pathway Steps (Species non-specific)
Describes pathways that the protein is involved in with hyperlinks to the relevant Pathway Report which contains the supporting reactions. All entries can be loaded into the BKL Pathfinder visualizer by clicking the Load in Pathfinder icon. Note that "Pathway Steps (Species non-specific)" use "Pathway Steps (Species specific)" as a basis but the literature-based results are summarized to apply generally to all orthologous molecules. The first five entries are shown, click [more ...] to view all entries.
Pathway Steps (Species specific)
Describes pathways that the protein is involved in with hyperlinks to the relevant Pathway Report which contains the supporting reactions. All entries can be loaded into the BKL Pathfinder visualizer by clicking the Load in Pathfinder icon. Note that "Pathway Steps (Species specific)" are derived directly from the literature and represent experimentally demonstrated events that can be specifically attributed to the molecule and species of the page. The first five entries are shown, click [more ...] to view all entries.
Protein-Protein Interactions
Describes regulatory events that affect the protein or its activity. The Species Involved column indicates the source of the observation. When a named species is listed (i.e. Human), it indicates that the regulatory observation was derived directly from the literature and represents an experimentally demonstrated event specific to the species of the page. When a named species is not listed (i.e. ortho summary), it indicates that while the regulatory observation was ultimately derived from the literature and can be traced back to an experimentally demonstrated event, that event is specific to a related species. The Supporting Reaction column indicates the type of the reaction where [se] means semantic reaction, [ps] means pathway step reaction and [me] means molecular evidence reaction. More information about the different reaction types can be found here.
Protein Binding Activity Binds
A tabular display of proteins and complexes the protein interacts with, with hyperlinks to the corresponding Locus Reports for the proteins and Complex Reports for the complexes. Includes a list of related reactions. Clicking on [details] opens the corresponding Reaction Report which provides reaction details and the supporting literature citation. The first five entries are shown, click [more ...] to view all entries.
Events Acting on the Protein
This section presents tabularized lists of events which act on the protein, and includes activation, inhibition, and modification of the protein.
Activated by
A tabular display of regulators that lead to activation of the protein, with hyperlinks to the respective Locus Report or other report. Includes a list of related reactions. Clicking on [details] opens the corresponding Reaction Report which provides reaction details and the supporting literature citation. The first five entries are shown, click [more ...] to view all entries.
Inhibited by
A tabular display of regulators that lead to ihibition of the protein, with hyperlinks to the respective Locus Report or other report. Includes a list of related reactions. Clicking on [details] opens the corresponding Reaction Report which provides reaction details and the supporting literature citation. The first five entries are shown, click [more ...] to view all entries.
Phosphorylated by
A tabular display of regulators that lead to phosphorylation of the protein, with hyperlinks to the respective Locus Report or other report. Includes a list of related reactions. Clicking on [details] opens the corresponding Reaction Report which provides reaction details and the supporting literature citation. The first five entries are shown, click [more ...] to view all entries.
Other regulatory events
A tabular display of regulators that affect the activity of the protein in some manner other than activation, inhibition or phosphorylation, with hyperlinks to the respective Locus Report or other report. Includes a list of related reactions. Clicking on [details] opens the corresponding Reaction Report which provides reaction details and the supporting literature citation. The first five entries are shown, click [more ...] to view all entries.
Events triggered by the protein
This section presents tabularized lists of events triggered by the protein, and includes activation, inhibition, and modification of target proteins by the protein of interest.
Activates
A tabular display of proteins and complexes the protein activates, with hyperlinks to the corresponding Locus Reports for the proteins and Complex Reports for the complexes. Includes a list of related reactions. Clicking on [details] opens the corresponding Reaction Report which provides reaction details and the supporting literature citation. The first five entries are shown, click [more ...] to view all entries.
Inhibits
A tabular display of proteins and complexes the protein inhibits, with hyperlinks to the corresponding Locus Reports for the proteins and TRANSPATH Complex Reports for the complexes. Includes a list of related reactions. Clicking on [details] opens the corresponding Reaction Report which provides reaction details and the supporting literature citation. The first five entries are shown, click [more ...] to view all entries.
Phosphorylates (direct or indirect)
A tabular display of proteins and complexes the protein phosphorylates, with hyperlinks to the corresponding Locus Reports for the proteins and Complex Reports for the complexes. Includes a list of related reactions. Clicking on [details] opens the corresponding Reaction Report which provides reaction details and the supporting literature citation. The first five entries are shown, click [more ...] to view all entries.
Other Regulatory Activities
A tabular display of proteins and complexes the protein regulates in a manner other than activation, inhibition or phosphorylation, with hyperlinks to the corresponding Locus Reports for the proteins and Complex Reports for the complexes. Includes a list of related reactions. Clicking on [details] opens the corresponding Reaction Report which provides reaction details and the supporting literature citation. The first five entries are shown, click [more ...] to view all entries.
Protein-Protein Associations
Provides an abbreviated list of proteins derived from HumanPSD curation that physically interact with the protein. For TRANSPATH subscribers, many of these entries are replicated in the Binds field above. Clicking on [ details] opens a Property Report, which provides the full list of interacting proteins, with experimental details and hyperlinks to the corresponding Locus Reports.

Transcriptional Regulation Describes features of the gene that contribute to its regulation, including the regulatory factors that regulate the gene. Describes the protein binding to DNA and other gene regulation activities attributed to the protein. Clicking the icon loads the gene and its regulators into the BKL Pathfinder.  
Regulation of the gene expression
Chromosome
Cytogenetic location (chromosome number). In the case of mouse entries, this field may also include genetic location (cM). For yeast and worm entries, the number of introns may be indicated (if applicable).
Promoter
Displays hyperlinks to Promoter Reports that correspond to the gene. The provided Match link allows you to directly initiate a Match analysis for predicted transcription factor binding sites within the associated promoter(s). Clicking the Match link opens a dialog box where you are asked to specify whether you wish to analyze all promoters or only the best-supported promoter, the sequence window to be analyzed, and the profile to be used. Results are returned in a new window. For more information about Match or about promoters, please see the Match overview and Promoter Report overview respectively. For IP-only and installed customers, please note that access to the Match feature requires login. If you have not already done so before clicking the link you will be prompted to login before proceeding to the dialog box.
Regulatory Elements
Provides a graphical display of the location of transcription factor binding sites within the gene. Individual transcription factors are color coded for easy location within the Binding Sites and Composite Elements tables where more details are provided. Note that only transcription factors whose binding site coordinates are relative to the TSS (Transcription Start Site) are graphically displayed, while all binding sites are represented in the tabular display.
Transcription factor binding sites
A tabular display of the transcription factor binding sites within the gene, with hyperlinks to the corresponding Site Reports. Also provides the location of the binding site, the name(s) of the transcription factor(s) that bind the sites with hyperlinks to the corresponding Locus Reports, the associated DNA binding reaction, and a summary of the regulatory effect. The first five entries are shown, click [more ...] to view all entries.
Composite element binding sites
A tabular display of the composite elements sites within the gene, with hyperlinks to the corresponding Composite Element Reports. Also provides the location of the composite element, the factors that bind within the composite element with hyperlinks to the corresponding Locus Reports or Complex Reports, and a summary of the regulatory effect. The first five entries are shown, click [more ...] to view all entries.
View in vivo fragments within the vicinity of the gene that are bound by transcription factors
Identifies the regions bound in vivo, as determined by ChIP-Chip assays. Also lists the names of transcription factors that bind the regions, with hyperlinks to the corresponding Locus Reports, the cell source used for the experiment and other supporting details. The first five entries are shown, click [more ...] to view all entries.
Regions with characterized functionality
Describes the regions of a gene, for which functionality was shown under certain conditions, with hyperlinks to the corresponding Functional Region Reports. The first five entries are shown, click [more ...] to view all entries.
Regulation of the mRNA expression
Describes features of the mRNA that contribute to its regulation, including the miRNAs that regulate the mRNA.
miRNA binding sites within the mRNA
A tabular display of the miRNA binding sites, with hyperlinks to the corresponding Site Reports. Also provides the location of the binding site, the name(s) of the miRNA(s) that bind the sites with hyperlinks to the corresponding Locus Reports. The first five entries are shown, click [more ...] to view all entries.
Regulation of the gene expression by the protein
TRANSFAC Factor Classification
Provides the transcription factor classification from the TRANSFAC transcription factor hierarchy. Includes the systematic name of the factor, a link to the systematic transcription factor classification number, a description of the factor type, as well as a link to the classification number for the factor family. Clicking on a classification number takes the user to the transcription factor hierarchy.
Genes bound by the protein
A tabular display of genes the protein interacts with, with hyperlinks to the corresponding Locus Reports for the genes and TRANSFAC Site Reports for the binding sites. Provides information about the location of binding within the gene, as well as the quality score for the interaction. The first five entries are shown, click [more ...] to view all entries.
Binding Region (ChIP-seq or similar experiments)
A tabular list of ChIP experiments that identified binding sites within the region of the gene, with links to the corresponding ChIP experiment report.
Consensus Binding Sequence
ALists the matrix logo for the matrices the protein interacts with, with hyperlinks to the corresponding TRANSFAC Matrix Reports. The first five entries are shown, click [more ...] to view all entries.
Regulation of mRNA expression by the RNA
Describes features of the mRNA that contribute to its regulation, including the miRNAs that regulate the mRNA.
mRNA bound by the RNA
A tabular display of mRNAs the RNA interacts with, with hyperlinks to the corresponding Locus Reports for the genes and TRANSFAC Site Reports for the binding sites. Provides information about the location of binding within the mRNA, as well as the quality score for the interaction. The first five entries are shown, click [more ...] to view all entries.
Transcription factors interacting with the protein
Describes transcription factors that interact with the protein.
Interacting factors
Lists transcription factors that interact with the protein, hyperlinked to the corresponding Locus Reports.

RNA Features Describes the nucleotide sequence of the mRNA, as well as the sequence information origin  
Nucleotide sequence
Provides the leading and trailing nucleotides, along with summary information about the length of the nucleotide sequence
Sequence source
Indicates the public source from which the sequence was derived, with a link to the corresponding report.
Export
FASTA export of the sequence.

Protein Features Displays various protein features as isoform, sequences, domains, modifications and complexes.  
Overview of protein sequence and structure
Family membership
Proteome Gene Family assignment which is based on the presence of an appropriate Gene Ontology term or Pfam domain.
Isoforms
Displays hyperlinks to Protein views of Locus Reports for alternative isoform proteins encoded by this locus.
View associated sequences and their domains
Is displayed only for a protein isogroup entry, which is a group entry for all protein isoforms (e.g. different splice variants) that are encoded by the locus. Lists all protein isoforms belonging to the group.
Sequence Overview
Displays a link to a protein sequence overview report that shows one reference sequence, that has been used for BioKnowledgeTM Transfer and BLAST summary comparison, and the amino acid sequences of the alternative protein isoforms of this locus. Sequence properties such as molecular weight and isoelectric point or protein domains are provided as well. Clicking on [details] opens the Property Report.
Sequence
Displays the seven N-terminal and seven C-terminal amino acids of the initially translated protein product and its length. The full protein sequence and additional details, such as information about protein length, calculated and experimentally-determined molecular weights, isoelectric point (pI), and protein domains, are accessible by clicking on [details], which opens a Property Report.
Sequence Features
Provides a graphical display of the location of features/domains within the protein reference sequence. Graphical displays for the alternative protein isoforms are given in the Property Report with the Protein sequences.
View related proteins
List of significantly related proteins in a number of model organism and mammalian species with the percent identity in parentheses (top matches are shown). These proteins were matched by BLAST similarity and refined with the Smith-Waterman algorithm, and are ordered by e-value. The [details] link at the end of each line brings up a BLAST alignments pop-up window displaying the complete BLAST results and pairwise alignments for the species indicated. Click Reference sequence [details] to open a report with the sequence that has been used for the BLAST calculations.
H. sapiens
List of most related H. sapiens proteins with the percent identity in parentheses.
M. musculus
List of most related M. musculus proteins with the percent identity in parentheses.
R. norvegicus
List of most related R. norvegicus proteins with the percent identity in parentheses.
D. rerio
List of most related D. rerio proteins with the percent identity in parentheses.
D. melanogaster
List of most related D. melanogaster proteins with the percent identity in parentheses.
C. elegans
List of most related C. elegans proteins with the percent identity in parentheses.
S. pombe
List of most related S. pombe proteins with the percent identity in parentheses.
S. cerevisiae
List of most related S. cerevisiae proteins with the percent identity in parentheses.
A. thaliana
List of most related A. thaliana proteins with the percent identity in parentheses.
O. sativa
List of most related O. sativa proteins with the percent identity in parentheses.
Z. mays
List of most related Z. mays proteins with the percent identity in parentheses.
C. albicans
List of most related C. albicans proteins with the percent identity in parentheses.
Others
List of related proteins from human pathogenic fungal species of the MycoPathPD database. Abbreviated species names and the protein symbol are shown, with the percent identity in parenthesis.
BLAST summary
To view a complete list of all organisms for which this is BLASTed against, click on the icon.
View orthologous relationships
Displays BKL Locus (for orthologs and paralogs) and Family Reports associated with the gene or molecule, according to gene and molecule types previously designated for molecules involved in signal transduction. Provides hyperlinks to the individual Reports. Detailed information about the types of genes and molecules described in the BKL can be found here.
View related protein structure
Displays the 3-D structure of the protein with the best PDB BLAST alignment, if available, via webservice.
Post-translational modifications of the protein
Provides information regarding post-translational modification of the protein. Click [hide] to remove curation from view and [show] (not displayed here) to return curation to view.
Modified Forms
Provides a graphical presentation of known residues within the protein that are post-translationally modified.
Acetylated forms
A tabular display of acetylated forms of the protein that includes specification of the site(s) of modification (when known) and a list of related TRANSPATH reactions with links to reaction details and the supporting literature citation. The first five entries are shown, click [more ...] to view all entries.
Phosphorylated forms
A tabular display of phosphorylated forms of the protein that includes specification of the site(s) of modification (when known) and a list of related TRANSPATH reactions with links to reaction details and the supporting literature citation.The first five entries are shown, click [more ...] to view all entries.
Sumoylated forms
A tabular display of sumoylated forms of the protein that includes specification of the site(s) of modification (when known) and a list of related TRANSPATH reactions with links to reaction details and the supporting literature citation.The first five entries are shown, click [more ...] to view all entries.
Ubiquitinated forms
A tabular display of ubiquitinated forms of the protein that includes specification of the site(s) of modification (when known) and a list of related TRANSPATH reactions with links to reaction details and the supporting literature citation.The first five entries are shown, click [more ...] to view all entries.
Other forms
A tabular display of modified forms of the protein other than acetylated, phosphorylated, sumoylated, or ubiquitinated, that includes specification of the site(s) of modification (when known) and a list of related TRANSPATH reactions with links to reaction details and the supporting literature citation.The first five entries are shown, click [more ...] to view all entries.
Modified Forms
Provides an abbreviated list modifications reported for the protein, with a [details] link to a Property Report that provides the complete list and references cited.
View complexes containing the protein
Contains information about precursors and mature forms of the protein, as well as all complexed forms of the protein.
Processed Forms
Lists the precursor or all known processed forms of the protein. Processed forms are posttranslationally processed proteins that have undergone proteolytic cleavage.
Complexes
Lists all complexed forms of the protein. Items in the list are hyperlinked to corresponding Complex Reports. Click here for an explanation of the notation shown for Complexes. Note that for a subset of complexes, the last entry includes an abbreviated list of names of complexes the protein is associated with. The [details] links to a Property Report that provides additional information about other complex members and references cited.

Identifiers Displays internal and external identifiers associated with the gene or protein.  
BKL Accessions
Lists the primary and secondary identifiers for the gene and protein of the page.
External Identifiers
Displays hyperlinks to corresponding entries in external databases.

Annotations Displays free-text annotations manually curated from the scientific literature.  
Annotation Topics
  • Annotations compiled from the literature are presented in this view of the Locus Report for all species.
  • Each bulleted line is an free-text annotation extracted from the published, peer-reviewed scientific literature.
  • For GPCR-PD, some annotations have experimental details that can be hidden or displayed. To show experimental details, click "Show details" in the annotation header. To hide them, click "Hide details." Whichever mode you select will apply to all pages you view until you switch to another mode.
  • Annotations end with hyperlinked PubMed identifiers (in parentheses).
  • Reference numbers correspond to the numbered references in the References view of the Locus Report.
  • All Annotations are categorized and sorted by Annotation Topic, separated by a labeled gray bar as shown above.
  • See detailed documentation for the specific Proteome Database for information about the Annotation topics. Detailed documentation for each Proteome Database is accessible from the menu on the left, at the top of this page.
  • The first five entries are shown for each topic, click [more ...] to view all entries for the topic. Alternatively, click the 'Display all annotations' check box to view all entries for all annotation topics.

References Displays list of references cited in the Locus Report.  
This block gives the full citations, with titles, that correspond to the PubMed identifiers displayed. When a PubMed identifier is not available, the Medline identifier is displayed. When neither a PubMed nor Medline identifier is available, a BIOBASE-specific number is assigned preceded by a "P". Nearly all of the reference numbers are hyperlinked to the Entrez database where the abstracts may be read. All references cited in the annotations and properties section are listed, and other references known to contain information about the protein may also be listed. The first five references are shown, click [more ...] to view all references. View abstracts via webservice by additionally clicking the Show abstract button which appears.

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