-> SEQUENCE RETRIEVAL
| Sequence
Retrieval Resources |
|
| NOTE: Databases and tools which perform complex integrated data retrieval are described in the "High-Throughput Data Retrieval" section within the "Data Integration" page ! | |
| Dbfetch (EBI) |
Dbfetch is an
acronym for "database fetch". Dbfetch provides an easy
way to retrieve entries from various databases at the EBI in a
consistent manner. It can be used from any browser as well as well as
within a web-aware scripting tool that uses wget, lynx or similar. |
| Ensembl (EBI+Sanger) including: Ensembl - basic search BioMart |
Ensembl is
a joint project
between EMBL-EBI and
the Sanger Centre to develop a
software system which produces and maintains automatic annotation
on eukaryotic genomes. 1. Ensembl - basic search: 1.1. All Species at once: Using the "Search Ensembl" option at the Ensembl homepage, it is possible to look for genes in all species, using gene names, accession numbers, diseases, protein domain names, ... NOTE that the output of a keyword sequence search here is considerably smaller than via SRS or ENTREZ ! 1.2. Search the human genome: for genes, proteins, diseases, domains, SNPs and many more. 1.3. Search the mouse genome: for genes, proteins, diseases, domains, SNPs and many more. 2. BioMart: BioMart is a powerful data retrieval tool that generates lists of biological objects (e.g. genes, SNPs) from data held in the Ensembl (and other) databases. Please refer to the corresponding section for details ! |
| Entrez (NCBI) |
Entrez
is a very
powerful
search and retrieval system that integrates information from
databases at NCBI. In fact, it is designed to retrieve not
only sequences but data from many different sources. Please refer to the Entrez main section for details. |
| Fetch (EMBnet.ch) |
Fetch is an alternative for NCBI-Entrez; limited mainly to sequence databases, like GenBank, Swissprot, UniGene, RefSeq, but includes also Prosite and Interpro entries. NOTE that the search term is limited to ID or Accession number (no keyword search possible !) |
| SRS - Sequence
Retrieval System (LION) |
SRS is
a very
comprehensive
retrieval system for database entries. SRS was initially developed
at the EBI, and is also available as commercial versions from LION Bioiscience
(Heidelberg, Germany). Note: There is no recent publication on SRS, but there are excellent SRS online documentations. 1. Access to public SRS servers is available at (some selected sites): - SRS6 at EBI - SRS6 at Sanger - SRS6 at DKFZ - SRS6 at EMBnet Austria NOTE that the various public SRS servers contain a different set of searchable libraries ! NOTE: All SRS sites provide extensive Help how to use SRS !! 2. SRS session: You can perform searches using accession numbers, keywords, authors, and many more. The set of databases ranges from sequence libraries (EMBL, PIR, SWISSPROT;...), SeqRelated libraries (Prosite, Prints, Pfam, EPD, UTR, UNIGENE, UNIEST, ...), transcription factor libraries (TFSITE, TFFACTOR, TFMATRIX), literature db (MEDLINE,...), 3D Structures (PDB,...), Genome db (LocusLink,...), Mutation db (OMIM, ...), metabolic pathways (ENZYME,...), and many more ! Datasets can be saved in various formats, like complete database entries, or FASTA sequence files only.
|
| UCSC Table Browser (UCSC) |
The UCSC
Table Browser provides a powerful and flexible graphical
interface for querying and manipulating the UCSC Genome Browser annotation
tables. The Table Browser lets you retrieve the DNA sequence
data or annotation data underlying Genome Browser tracks for
the entire
genome, a specified coordinate range, or a set of accessions. Please refer to the main section of UCSC Table Browser for detailed information ! |
| General
Sequence
Databases |
|
| NOTE: This section is intended to give an overview about some of the most important sequence databases (DNA and protein). Many of these databases are used by other tools and programs described elsewhere on this web portal. | |
| CCDS (EBI, NCBI, UCSC, Sanger) |
The Consensus CDS (CCDS)
database, started in March 2005, is a collaborative effort to identify
a core set of human protein coding regions that are consistently
annotated and of high quality. Annotation of genes on the human genome
is provided by multiple public resources, using different methods, and
resulting in information that is similar but not always identical. The
human genome sequence is now sufficiently stable to start identifying
those gene placements that are identical, and to make those data public
and supported as a core set by the three major public human genome
browsers. The long term goal is to support
convergence towards a standard set of gene annotations on the human
genome. Ways to access CCDS (selection): 1. CCDS membership is indicated on Ensembl, NCBI Map Viewer, UCSC, and Vega genome browser (of WTSI - Wellcome Trust Sanger Institute) and/or browser-associated gene, transcript, or protein reports. 2. Links to the CCDS Database are provided on NCBI Entrez Gene reports and RefSeq transcript and protein sequence records. 3.The CCDS Database can be directly queried by accession identifier, Entrez Gene ID, CCDS ID, or Gene Symbol. The CCDS query interface does not support full text searching and so you may want to use Entrez Gene to retrieve the gene of interest and follow the link provided in the RefSeq section to the CCDS browser. CCDS database structure: The CCDS set includes coding regions that are annotated as full-length (with an initiating ATG and valid stop-codon), can be translated from the genome without frameshifts, and use consensus splice-sites. Therefore, CCDS entries always span only the coding region of a transcript, and not the UTRs ! Typical CCDS accessions: refer to section CCDS IDs. |
| Ensembl Databases (EBI+Sanger) |
Ensembl is
a joint project
between EMBL-EBI and
the Sanger Centre to develop a
software system which produces and maintains automatic annotation
on eukaryotic genomes. The resulting databases contain genomic
sequences with features attached. Of particular importance are gene
features which represent protein coding genes in the genome. Ensembl
copes with rapid updates in data and provides stable identifiers for
genes so researches can track genes of interest across different
versions of the data. The Ensembl system is being applied to genomes of
different origanisms and is being kept up to date with the current
state of genome sequencing. Ways to access Ensembl (selection): 1. The diverse Ensembl Databases are accessible at the Ensembl website. Please refer also to the chapter "Ensembl - basic search". Ensembl Databases: There is a series of individual Ensembl databases, according to different organisms and according to different types of molecules. Examples: ENSEMBL is a virtual database containing genomic sequences and annotations for all organisms currently available. ENSEMBL_CDNA is a virtual database containing all cDNA sequences from all organisms. ENSEMBL_RNA is a virtual database containing all RNA sequences from all organisms. ENSEMBL_PROT is a virtual database containing all protein sequences from all organisms. Typical Ensembl accessions: refer to section Ensembl IDs. |
| GenBank (NCBI) EMBL-Bank (EBI) DDBJ (NIG) including: BankIt Sequin TPA - Third Party Annotation dataset (EBI) NRNUC (NCBI) GENPEPT (NCBI) NRPEP (NCBI) |
GenBank
is the NIH genetic sequence database, an annotated
collection of all publicly available DNA sequences. Since 1992
it has been based at the National Center for
Biotechnology Information (NCBI), a division of the National Library of
Medicine, located on the NIH campus. GenBank
records are annotated using a standard set of biological terms and show
these annotations in a Feature Table. GenBank is part of the International
Nucleotide Sequence Database Collaboration,
which comprises the DNA DataBank of Japan (DDBJ) at the National
Institute of Genetics (NIG), the European Molecular
Biology Laboratory (EMBL-Bank) , and GenBank at
NCBI. Each of
the three groups collects a portion of the total sequence data reported
worldwide, and all new and updated database entries are exchanged
between the groups on a daily basis. These 3 databases are designed to
provide and encourage access within
the scientific community to the most up to date and comprehensive DNA
sequence information. GenBank database organization: GenBank has traditionally been partitioned into "divisions" of taxonomic groups (like BCT for bacteria or PRI for primates). In recent years, divisions have been added corresponding to specific sequencing strategies, like EST (expressed sequence tag), STS (sequence-tagged site), GSS (genome survey sequence), HTG (high throughput genomic), HTC (high throughput cDNA) and environmental sample (ENV) sequence sets. Ways to access GenBank (selection): 1. Text search using the NCBI Entrez system. 2. Sequence search using BLAST. 3. Text search via public SRS servers. Note: The list of databases in SRS shows several entries directing to GenBank, like GENBANKRELEASE (latest full release of GENBANK), GENBANKNEW (recent updates), or GENBANKTPA (the Third Party Annotation dataset). Likewise, the EMBL databases are organized accordingly. 4. Text search via Dbfetch ("simple version of SRS"). Data Submission to GenBank: The data in GenBank are submitted primarily by individual authors to one of the three databases, or by sequencing centers as batches of EST, STS, GSS, HTC, WGS, or HTG sequences. 1. BankIt: is the tool of choice for simple submissions, when only one or a small number of records is to be submitted. Authors enter sequence information directly into a form and add biological annotation. 2. Sequin: is a standalone multi-platform submission program, available for download for Windows, UNIX, and Mac systems. Sequin handles both simple sequences and complex sequence sets, like those generated by population or mutaion studies. Typical GenBank accessions: refer to section GenBank IDs. Related Databases: 1. The Third Party Annotation (TPA) dataset is a complement to the existing DDBJ/EMBL/GenBank comprehensive database of primary nucleotide sequences, which typically result from direct sequencing of cDNA's, EST's, genomic DNA's etc. Primary data are defined to be data for which the submitting group has done the sequencing and annotation, and as 'owner' of these data has privileges to submit updates/corrections etc. In contrast, non-primary sequences are defined as sequences which a) consist exclusively of sequences from one or several already existing entries 'owned' by other groups or b) consist of a mixture of new & already existing sequences. These sequences are submitted to DDBJ/EMBL/GenBank as part of the process of publishing biological experiments that include the annotation of existing nucleotide sequences in the primary sequence database. Thus, a publicly accessible TPA record will be linked to a publication that documents that the data are supported by biological experimentation. 2. NRNUC is the non-redundant nucleotide sequence database from NCBI. It contains sequences from GENBANK, EMBL, DDBJ and PDB without EST, STS, GSS or HTG sequences. This non-redundant database is often selected at BLAST searches, when the user wants to limit the output to "better annotated" transcripts. 3. GENPEPT is a protein database translated from the current release of GENBANK. 4. NRPEP is the non-redundant protein database from NCBI. It contains both GENBANK translations, but also sequences from protein databases like PDB, SWISSPROT and PIR. |
| RefSeq (NCBI) |
The Reference Sequence (RefSeq)
collection aims to provide a
comprehensive, integrated, non-redundant set of sequences, including
genomic DNA, transcript (RNA), and protein products, for major
research
organisms. RefSeq standards serve as the basis for medical, functional,
and diversity studies; they provide a stable reference for gene
identification and characterization, mutation analysis, expression
studies, polymorphism discovery, and comparative analyses. Example: Most genes / mRNAs are characterized by a series of cDNA sequences which have been deposited by different research groups in databases like GenBank. As example, cDNA sequences often miss the extreme 5'-end of the mRNA. RefSeq now tries to pick those sequences as "RefSeqs" which are the most "reliable" ones. Ways to access RefSeq (selection): 1. Text search using the NCBI Entrez system. Note that RefSeq entries are included in the "Entrez Nucleotide" section which covers also the total GenBank database. The output list can be filtered via the "Limits" tab and the selection "only from RefSeq". Note that property restrictions may also be directly entered as part of the query term, see this RefSeq query help section for details. 2. Sequence search using BLAST (nr database). Note: RefSeq records are also included in pre-computed BLAST analyses available at NCBI (BLink). 3. Text search via public SRS servers. Note: The list of databases in SRS shows several entries related to RefSeq, reflecting a partition of RefSeq into distinct subsets (mRNA, genomic, protein, non-coding RNA). 4. RefSeqs for each gene are also listed in gene reports like those available via the Entrez Gene pages, and are also graphically mapped onto genomes like in the UCSC genome browser. RefSeq database structure: There are 2 RefSeq databases, containing either DNA or protein sequences. Similar to GenBank, there are "Release", "Updates" and "ALL" (virtual combined) databases. Typical RefSeq accessions: refer to section RefSeq IDs. Note: Starting in March 2005, the CCDS database is a new collaborative effort to identify a core set of human protein coding regions that are consistently annotated and of high quality. Thereby, the CCDS database also makes use of the RefSeq databases. |
| Swiss-Prot / UniProt (SIB, EBI) TrEMBL / UniProt (EBI) |
The Swiss-Prot Protein
Sequence Database is a database of protein
sequences produced collaboratively by Amos Bairoch (University of
Geneva) and the EMBL Data Library. The data in Swiss-Prot are derived
from translations of DNA sequences from the EMBL Nucleotide Sequence
Database, adapted from the Protein Identification Resource (PIR)
collection, extracted from the literature and directly submitted by
researchers. It contains high-quality annotation,is
non-redundant,
and cross-referenced to several other databases, notably the EMBL
nucleotide sequence database, PROSITE pattern database and PDB.
SWISS-PROT is a curated protein sequence database which strives to
provide a high level of annotation (such as the description of the
function of a protein, its domain structure, post-translational
modifications, variants, etc), a minimal level of redundancy and a
high level of integration with other databases. TrEMBL (also known as SPTREMBL) is a computer-annotated protein sequence database supplementing the SWISSPROT Protein Sequence Data Bank. TrEMBL contains the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database not yet integrated in SWISS-PROT. TrEMBL can be considered as a preliminary section of SWISS-PROT. For all TrEMBL entries which should finally be upgraded to the standard SWISS-PROT quality, SWISS-PROT accession numbers have been assigned. Swiss-Prot and TrEMBL database structure: At public SRS sites, there is a list of Swiss-Prot / TrEMBL databases, like: SWISSPROT (Release); SWISSPROT (Updates); SPTREMBL; SWISSPROT_SPLICEVAR (a database containing splice isoforms of proteins from SWISSPROT); TREMBL_SPLICEVAR (a database containing splice isoforms of proteins from TrEMBL); SWISSPROTALL (a virtual database containing the latest full release of SWISSPROT plus the updates SWISSNEW); SWISSPROTPLUS (a virtual database containing SWISSPROTALL and TrEMBL). UniProt database structure: UniProt databases are listed in SRS database lists as UNIREF100, UNIREF90 and UNIREF50. Please also refer to the UniProt section for details ! Typical Swiss-Prot / TrEMBL / UniProt accessions: see section Swiss-Prot / TrEMBL / UniProt IDs. Note: In 2002, EBI, SIB (Swiss Institute of Bioinformatics), and PIR (Protein Information Resource) joined forces as the UniProt consortium. The primary mission is to support biological research by maintaining a high quality database that serves as a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase. UniProt is essentially built of Swiss-Prot and TrEMBL. Please also refer to the UniProt section for details ! |
| ID Guide |
|
| NOTE: Often, when reading publications or
database entries, accession numbers appear where the user initially has
no idea which database these IDs are derived from. The purpose of this
section is to list typical IDs and accession numbers of important
databases, which may help to identify others of the same type. Please note that the terms "ID" and "accession number"
are used in a quite loose definition here. Most entries are derived
from one example gene/protein: PTGS2 (COX2), in order to demonstrate the wide
range of data available for one gene of interest. NOTE: At the FAQ page, FAQ DAT6 shows tools to convert lists of specific IDs into corresponding other IDs. |
|
| BIND IDs (Blueprint, Toronto, Canada) 217962 |
BIND IDs: BIND (Biomolecular
Interaction Network Database) is hosted by the Blueprint Initiative in Toronto,
Canada. BIND is a database designed to store
full descriptions of interactions, molecular complexes
and pathways. Interactions between any two molecules composed
of proteins, nucleic acids and small molecules are described. Typical BIND accessions: BIND accessions are simple numbers without prefix. - 217962: This BIND entry describes the interaction between the protein TTP (ZFP36) with the example Cox2 mRNA. Please refer also to the BIND main section. |
| BioCyc IDs (SRI International) including: MetaCyc, HumanCyc |
BioCyc IDs:
BioCyc is a collection of Pathway/Genome
Databases.
Each Pathway/Genome Database in the BioCyc collection describes the
genome and metabolic pathways (NO signaling pathways !)
of a single organism, with the exception
of the MetaCyc database, which is a reference
source on metabolic pathways from many organisms. Typical BioCyc accessions: Please note that there are actually NO BioCyc-specific IDs, but for matters of completeness the example gene PTGS2 (COX2) is listed here. - ENSG00000073756: BioCyc uses Ensembl Gene IDs for gene-specific reports, like this one for human PTGS2. - There is also a respective Enzyme (protein)-specific entry for PTGS2. - 1.14.99.1: BioCyc uses the standard EC nomenclature for enzyme reactions, like the synthesis of Prostaglandin-H2 in this example. - There are also specific compound-entries, like for Prostaglandin-H2 in this example. Please refer also to the BioCyc main section. |
| CCDS IDs (EBI, NCBI, UCSC, Sanger) CCDS1371.1 |
CCDS IDs: The CCDS
(Consensus CDS) database, is a collaborative effort to identify
a core set of human protein coding regions that are consistently
annotated and of high quality. Typical CCDS accessions: - CCDS1371.1: This is the CCDS entry of an example gene PTGS2 (COX2). Annotated genes that are included in the CCDS set are associated with a unique identifier number and version number (e.g., CCDS1.1, CCDS234.1). The version number will update if the CDS structure changes, or if the underlying genome sequence changes at that location. A CCDS entry lists accessions which are "included" like RefSeq and Ensembl IDs. Also, links to the major genome browsers (UCSC, NCBI, Ensembl, WTSI) are contained. Please refer also to the CCDS main section. |
| ChEBI IDs (EBI) ChEBI:15365 |
ChEBI IDs: ChEBI, Chemical
Entities of Biological Interest, is a
freely available dictionary of "small molecular entities". The
molecular entities in question are either products of nature or
synthetic products (like drugs). Typical ChEBI accessions: - ChEBI:15365: This is the ChEBI identifier for the substance Aspirin. A ChEBI entry lists the ChEBI name, synonyms, IUPAC name, and database links like to the KEGG Compound database. Note: the substance Diclofenac which is used as example for interference with PTGS2 in sections KEGG IDs and MMDB IDs, is not found in ChEBI, therefore another anti-inflammatory substance was chosen. Note: There is no option in ChEBI to search using gene names like PTGS2, as there is no gene-drug correlation. Please refer also to the ChEBI main section. |
| CleanEx IDs (SIB) HS_PTGS2 AFFY_HG-U133A_204748_at |
CleanEx IDs: CleanEx is a database which provides
access to public gene
expression data via unique approved gene symbols and which
represents
heterogeneous expression data produced by different technologies in a
way that facilitates joint analysis and cross-dataset comparisons. Typical CleanEx accessions: - HS_PTGS2: This is the CleanEx database entry for the human gene PTGS2. It summarizes expression data from different databases corresponding to this gene of interest. - AFFY_HG-U133A_204748_at: This is a CleanEx Target database entry derived from an Affymetrix ProbeSet corresponding to the gene PTGS2, as contained on the human U133A chips. Please refer also to the CleanEx main section. |
| dbSNP IDs (NCBI) rs20426 ss23080 |
dbSNP IDs: The SNP
database (dbSNP)
of
NCBI is a central repository for information related to Single
Nucleotide Polymorphisms in the genomes of various species. Typical dbSNP accessions: - rs20426: This is a typical dbSNP database record, a Reference SNP record which shows a polymorphism affecting the first amino acid of the human PTGS2 protein (Met/Ile). Such a record stores all SNP detail information, like method, submitter, a variation summary, and a validation summary. These Reference SNP records provide a summary list of individual submitter records (useful in cases where several records address the same variation) in dbSNP and a list of external resource and database links. Reference SNP identifiers will also be exported as standardized features for annotation in other NCBI resources. Reference SNP cluster 'rs' ID's are created by NCBI during periodic 'builds' of the database. Reference SNP clusters define a non-redundant set of markers that are used for annotation of reference genome sequence and integration with other NCBI resources. New submissions that match existing data will be merged into an existing refSNP cluster. A reference SNP cluster record has the format NCBI | rs[NCBI SNP ID] where 'rs' is always lower case. Note that from the GeneView it is easy to retrieve the complete list of SNPs in the respective transcript region. - ss23080: This is a dbSNP Assay ID ('ss'), representing an individual submission record. Please refer also to the dbSNP main section. Please refer also to this dbSNP identifiers information page. |
| Ensembl IDs (EBI+Sanger) ENSG00000073756 ENSMUSG00000032487 ENST00000186982 ENSMUST00000035065 ENSP00000186982 ENSMUSP00000035065 ENSF00000001307 ENSE00001002288 |
Ensembl IDs: Ensembl is
a joint project
between EMBL-EBI and
the Sanger Centre to develop a
software system which produces and maintains automatic annotation
on eukaryotic genomes. The resulting databases contain genomic
sequences with features attached. Typical Ensembl accessions: Note: These links are related to the example gene / protein PTGS2 (COX2). - ENSG00000073756: This is a human Gene Report, with links to the genome browser display, to related Ensembl transcript, family, etc. reports, to orthologous sequences, protein domains, motifs, GO terms, and links to all major databases. - ENSMUSG00000032487: A mouse Gene Report, similar to human. - ENST00000186982: A human Transcript report. Similar to Ensembl Gene reports, but showing a very useful feature which displays the transcript sequence as colored codons, exons, and also SNPs. - ENSMUST00000035065: A mouse Transcript report. - ENSP00000186982: A human Protein Report. This report focuses on protein domains and motifs, but also displays very nicely the positions of alternating exons and SNPs. - ENSMUSP00000035065: A mouse Protein Report. NOTE: A search via the Ensembl search field using a Transcript ID or a protein ID will initially retrieve the Gene report which then links to the other entries. - ENSF00000001307: A Protein Family Report. This report "unifies" in one display all protein sequences from all species available in Ensembl which belong to the same protein family. It is possible to produce multiple alignments and to download the sequences. NOTE: There is an individual Ensembl Family report for each species (like human in the example) as in the upper part of the entry a chromosomal map is shown which presents the species-specific positions of the genes belonging to the family, whereas in the lower part all the other species are listed. - ENSE00001002288: This is an Ensembl Exon Report, corresponding to the first of the 10 exons of the human PTGS2 gene. Please refer also to the Ensembl Databases main section. |
| Entrez Gene IDs (NCBI) 5743 |
Entrez Gene IDs:
Entrez
Gene is one of the Entrez databases, which was constructed to replace
the widely known and used LocusLink database in the year 2004.
Entrez Gene integrates information from
LocusLink and from genes annotated on Reference Sequences
from completely sequenced genomes. Typical Entrez Gene accessions: - 5743: The Entrez Gene report of the human PTGS2 (COX2) gene. Entrez Gene IDs consist of a simple number without any letters. Entrez Gene entries include information from many resources, like a concise summary what is known about a certain gene, PubMed links, transcripts, genomic context, described interactions, GO terms, and much more. Please refer also to the Entrez Gene main section. |
| Enzymes IDs including: IntEnz IDs (EBI) ENZYME IDs (ExPASy) EC 1.14.99.1 GO:0004666 |
Enzymes IDs: In
general, there is a standardized enzyme nomenclature, all enzyme IDs
start with the prefix "EC" followed by a number which is
separated in 4 sections. The following examples are derived from enzyme
entries in different enzyme databases. Typical Enzyme accessions: - EC 1.14.99.1: This is the IntEnz entry for the enzyme prostaglandin synthetase. - EC 1.14.99.1: This is the ENZYME (ExPASy) entry for the enzyme prostaglandin synthetase. - EC 1.14.99.1: This is the KEGG LIGAND database entry for the enzyme prostaglandin synthetase (see also section KEGG IDs). - GO:0004666: This is the QuickGO database entry for the enzyme prostaglandin synthetase (see also section GO IDs). Please refer also to the Enzymes main section. |
| GenBank IDs (NCBI) AY462100 U04636 L15326 U20548 |
GenBank IDs: GenBank
is the NIH genetic sequence database, an annotated
collection of all publicly available DNA sequences. Since 1992
it has been based at the National Center for
Biotechnology Information (NCBI), a division of the National Library of
Medicine, located on the NIH campus. GenBank
records are annotated using a standard set of biological terms and show
these annotations in a Feature Table. GenBank is part of the International
Nucleotide Sequence Database Collaboration,
which comprises the DNA DataBank of Japan (DDBJ) at the National
Institute of Genetics (NIG), the European Molecular
Biology Laboratory (EMBL-Bank)
, and GenBank at
NCBI. Typical GenBank accessions: A typical GenBank entry includes a concise description of a sequence, the taxonomy of the source organism, bibliographic references and a table of sequence features (like CDS, polyadenylation signals, etc.), contact information (eventually information on clone distribution), literature references, and of course the sequence itself. The GenBank accession number is a stable and unique identifier which is shared across GenBank-EMBL-DDBJ and which remains constant even when there is a change to the sequence or to the annotation. The DNA sequence is also assigned a unique NCBI identifier, called "gi". Note: When a change is made to the sequence, a new gi number is issued to the sequence and the version extension of the "accession.version" identifier is incremented. The accession number of the record as a whole remains unchanged and the older sequence remains available under the old "accession.version" identifier and gi. Note: A similar system is applied to protein translations corresponding to nucleotide entries. - AY462100: Human PTGS2 mRNA (CDS only). - U04636: Human PTGS2 mRNA (full mRNA including UTRs, but generated from genomic DNA ! ("join..."); reference for RefSeq NM_000963). - L15326: Human PTGS2 mRNA (full mRNA including UTRs, generated from mRNA molecule). - U20548: Human PTGS2 promoter sequence. Please refer also to the GenBank main section. |
| GeneCards IDs (Weizmann Institute) GC01M183372 |
GeneCards IDs:
GeneCards
at Weizmann Inst. (mirror: GeneCards at Stanford)
is a database of human genes, their products and their involvement in
diseases. Typical GeneCards accessions: - GC01M183372: GeneCard for the human PTGS2 gene. A typical "GeneCard" includes related sequences, SNPs, medical news, disorders and mutations, MIPS PEDANT Viewer report (!), links to UCSC and Ensembl, PubMed search and many more. In addition, links to gene expression data (Arrays, ESTs, links to SOURCE) are available. Please refer also to the GeneCards main section. |
| GEO IDs (NCBI) GPL96 GSE973 GSM15390 GDS649 |
GEO IDs: GEO is a gene
expression and hybridization
array data repository, as well as an online resource for the
retrieval of
gene expression data from any organism or artificial source. Many types
of gene expression data including microarray-based
experiments measuring mRNA, genomic
DNA and protein abundance, as well as non-array techniques such
as serial analysis of gene expression (SAGE), and mass
spectrometry proteomic data, are accepted,
accessioned, and archived as public data sets. Typical GEO accessions: - GPL96: This is a GEO Platform record (GPL) describing the Affymetrix GeneChip Human Genome U133 Array Set HG-U133A. GPLs describe the technology of the platforms (e.g. arrays) used, meaning the lists of elements on the array (e.g., cDNAs, oligonucleotide probesets, ORFs, antibodies) or the list of elements that may be detected and quantified in that experiment (e.g., SAGE tags, peptides). Each platform record is assigned a unique and stable GEO accession number (GPLxxx). A platform may reference many samples that have been submitted by multiple submitters. - GSE973: This is a GEO Series Record (GSE) describing a microarray experiment where HUVEC were treated with the inflammatory cytokine Interleukin-1. GSEs contain detailed descriptions of an experiment, including submitter details and literature references. A GSE record also provides a list of all single sample records (GSMs) which are part of this experiment. GSEs therefore define a set of related samples considered to be part of a group, how the samples are related and if and how they are ordered. Each series record is assigned a unique and stable GEO accession number (GSExxx). - GSM15390: This is one of the GEO Sample records (GSM) which belong to the GSE973 series. GSMs describe the conditions under which an individual sample was handled, the manipulations it underwent and the abundance measurement of each element derived from it. Example: In the case of an Affymetrix array experiment, the GSM provides the complete list of ProbeSets, and their measured values. Each sample record is assigned a unique and stable GEO accession number (GSMxxx). A sample entity must reference only one platform, but may be included in multiple series. - GDS649: This is the GEO DataSet (GDS) record which corresponds to the experiment described in GSE973. GDS records are curated sets of GEO sample data. A GDS record represents a collection of biologically and statistically comparable GEO samples (GSMs) and forms the basis of GEO's suite of data display and analysis tools. Samples within a GDS refer to the same platform, that is, they share a common set of probe elements. Value measurements for each sample within a GDS are assumed to be calculated in an equivalent manner, that is, considerations such as background processing and normalization are consistent across the dataset. Information reflecting experimental design is provided through GDS subsets. NOTE: If you want to know the expression profile of the example gene PTGS2 within this experiment, simply enter "PTGS2 GDS649" into the query field of the Entrez GEO Profiles page. Please refer also to the GEO main section. |
| GO IDs (AmiGO) GO:0004666 |
GO IDs: The goal of
the Gene Ontology Consortium
is to produce a dynamic
controlled vocabulary that can be applied to all organisms
even as knowledge of gene and protein roles in cells is accumulating
and changing. The three organizing principles of GO are molecular
function, biological process and cellular component. Typical GO accessions: - GO:0004666: A GO entry of the branch "molecular function", namely "prostaglandin-endoperoxide synthase activity" which was attributed to the example gene PTGS2 (COX2). A Gene Ontology accession always starts with the prefix "GO", followed by a number. Please refer also to the GO main section. |
| HGMD IDs (University of Wales) CM024574 |
HGMD IDs: HGMD
- Human Gene Mutation Database is
maintained by the Institute of Medical Genetics, Cardiff, University of
Wales and is the leading database storing
not only mutations in human genes but also curated polymorphisms
showing clear phenotypes. HGMD is also directly linked via NCBI
LocusLink entries. Typical HGMD accessions: - CM024574: This is the HGMD accession for one of the mutations described in the human PTGS2 (COX2) gene (Note that the link referes to the overview page of all described PTGS2 mutations). Mutations are grouped either by mutation type (like missense/nonsense, splicing, deletions, insertions,...) or phenotype (like diabetes mellitus, colorectal cancer risk,...). The entry itself lists codon and amino acid exchanges, as well as the proposed phenotype and the primary literature reference. Please refer also to the HGMD main section. |
| H-InvDB IDs (JBIRC + DDBJ) HIX0001429 HIT000036341 |
H-InvDB IDs: H-Invitational
Database (H-InvDB) is a human gene database opened to the
public in April 2004, which is hosted by the Japan Biological
Information Research Center (JBIRC) and by the
DNA Databank of Japan (DDBJ),
with contributions from more than 40 institutes worldwide, like the
german DKFZ. The scope of H-InvDB is to provide an
integrative annotation of full-length cDNA clones available
from high throughput cDNA sequencing projects. Typical H-InvDB accessions: - HIX0001429: This is the Locus view (HIX# ID) of the example gene PTGS2, which collects all gene-centered information and links, like exon-intron organization, cDNA multiple alignments, ORF alignments, gene expression profiles, and disease information. - HIT000036341: This is the cDNA view (HIT# ID) of the example gene PTGS2, which provides information concerning function (HUGO, PubMed, and to the KEGG database for metabolic pathway information), mapping information (including external links like Ensembl, GeneLynx, Refseq, OMIM), predicted ORF (incl. Interpro and GO IDs), evolutionary features (orthologs in other species), secondary and tertiary structures (GTOP database), subcellular localization (incl. the output of several programs like PSORT, TargetP and TMHMM; and links to the TOPO viewer), and cDNA information (incl. SNPs, PolyA sites, repeats, and more). Please refer also to the H-InvDB main section. |
| HPR IDs (HPR program, Sweden) CAB000113 |
HPR IDs: HPR - the Human Protein Atlas, contains
hundreds of
thousands of images of protein expression in normal
human tissues and cancer cells. Typical HPR accessions: - CAB000113: This is the HPR entry for the gene / protein PTGS2 (COX2). In fact, the ID refers to the PTGS2 specific antibody. Links to Ensembl gene and transcript IDs as well as general protein specific data are indicated on top. Lists of normal and cancer tissues are presented together with symbols referring to the intensity of the staining in these tissues. Each tissue can be selected to show the corresponding high-quality immuno-histochemical staining. Note that the link "antibody info" will present additional gene data, including the important links to the major databases, a gene summary, assigned GO terms and more. Please refer also to the HPR main section. |
| HPRD IDs (Johns Hopkins School of Medicine, Baltimore, and Institute of Bioinformatics, Bangalore, India) 02599 |
HPRD IDs: HPRD - Human Protein Reference
Database represents a centralized platform
to visually depict and integrate information pertaining to domain
architecture, post-translational modifications, interaction
networks
and disease association for each protein in the human proteome.
All the
information in HPRD has been manually extracted from the
literature by
expert biologists who read, interpret and analyze the published data. Typical HPRD accessions: HPRD IDs consist of a simple number without any letters. Note that the HPRD ID is only displayed in the URL of a protein record, it is not shown within the record itself (although there is the option to query using the HPRD ID). - 02599: This is the HPRD entry for the protein PTGS2 (COX2). In particular, have a look at the tab "Interactions". Interestingly, there is no entry at the tab "PTMs and Substrates". Please refer also to the HPRD main section. |
| IntAct IDs (EBI) EBI-298933 |
IntAct IDs: IntAct provides a freely
available, open source database system and analysis tools for protein
interaction data. Typical IntAct accessions: - EBI-298933: This is the IntAct entry for the mouse protein Ptgs2. IMPORTANT NOTE: This tabular form is somehow misleading as one could believe that Ptgs2 itself interacts with all the molecules listed. But this is not the case as can be seen when hitting the link "Number of interactions", which will display the experimental details, the technical protocol used to verify the interaction, and the PubMed link. You can see that Ptgs2 is only one of the molecules which were identified as interaction partners of Protein kinase C, epsilon type (Kpce) which was used as the bait in this experiment. So, the table is actually a list of partners of Kpce and not of Ptgs2. There are several display options for interaction networks: "Graph" displays all interaction partners in a "hierarchical view". "Path" computes the "minimal connection network" of the components which have been selected via the checkboxes. Please refer also to the IntAct main section. |
| InterPro IDs (EBI) IPR006209 |
InterPro IDs: InterPro is a
database of protein families, domains and functional sites. InterPro
searches simultanously in a whole list of databases like Pfam,
PRINTS, ProDom, PROSITE,
SMART, SWISS-PROT, TIGRFAMs, PIRSF (PIR Superfamily), and Superfamily
for domains, families, repeats and short
sequence motifs. Typical InterPro accessions: - IPR006209: This is a domain-type InterPro entry, namely EGF-like domain, which is found in the example protein PTGS2. Besides a description of the domain itself, it lists many links to related InterPro entries, it shows the taxonomic coverage of the entry, example proteins, and more. Please refer also to the InterPro main section. |
| IPI IDs (EBI) IPI00018109 |
IPI IDs: The International Protein
Index (IPI) provides a top level guide to the main databases
that
describe the human, mouse and rat proteomes. IPI is
assembled from protein sequence information taken from the following
data sources: UniProt, Swiss-Prot, TrEMBL, RefSeq NPs, RefSeq XPs,
Ensembl, TAIR, and H-InvDB. Typical IPI accessions: - IPI00018109: IPI entry of the example protein PTGS2. Similar to Swiss-Prot, there is a "raw version" and a "pretty-view" version of this IPI entry available, both retrievable via SRS-based systems. Note that, besides the "usual" database links, IPI entries also provide links to "more exotic" databases like trome, UTRdb, or CleanEx. Please refer also to the IPI main section. |
| JASPAR IDs (CGB, Karolinska) MA0061 |
JASPAR IDs: JASPAR
is an open-access database of transcription factors and their
binding
site profiles, which gained tremendous importance as the "mother"
database for TF information, TRANSFAC, has been largely commercialized.
Typical JASPAR accessions: - MA0061: This is the MAtrix of the binding profile for the transcription factor NF-kappaB (REL). Note: There is no individual URL for each TF, but all TFs can be browsed by using the "Browse by..." buttons at the JASPAR start site. Please refer also to the JASPAR main section. |
| KEGG IDs (Kyoto University) hsa:5743 K00509 hsa00590 ot00590 map00590 EC 1.14.99.1 R00073 |
KEGG IDs: KEGG is part
of the GenomeNet project
of the Kyoto University. KEGG turns sequence information from a number
of organisms into metabolic
or regulatory pathways. This site makes it easy to place genes into
a functional context, and to look for as yet unknown genes that
might exist in an organism. Typical KEGG accessions: - hsa:5743: This is the "gene-centered" KEGG report for the example gene human PTGS2, which can be retrieved by searching the KEGG GENES database. Besides the aa and nt sequences, the report lists internal links to other KEGG databases as well as external links. - K00509: This is a KEGG ORTHOLOGY (KO) database report for the enzyme function "prostaglandin-endoperoxide synthase" which is related to the example protein PTGS2. The KO database contains a manually curated set of orthologous gene groups in the complete genomes, which are linked to the nodes (boxes) indicating gene products (mostly proteins) in the KEGG pathway maps. Thus, the KO database accession number, or the K number, represents the common identifier of the pathway node of the KEGG PATHWAY database and the ortholog group of the KEGG GENES database. - hsa00590; ot00590, map00590: These accessions are KEGG PATHWAY reports for prostaglandin and leukotriene metabolism, the first one is the human pathway, the second is the same pathway related to ALL organisms in KEGG, the third one is the so-called reference pathway. Pathway reports in general provide a graphical representation of metabolic (like glycolysis or ATP synthesis) and regulatory pathways (like apoptosis or cell cycle). - EC 1.14.99.1: This is a KEGG report specific for enzymes, like prostaglandin synthetases in this example, which lists the different names of an enzyme, reactions it catalyzes, substrates, inhibitors, pathways, genes involved, and more. - R00073: This is a KEGG report specific for enzymatic Reactions, like prostaglandin reductase reaction in this example, which includes the equation, the chemical structures, as well as a link to the respective pathway. - cpd:C01690: This is a KEGG compound ID, which refers to chemical compounds like Diclofenac in this example, which is a described inhibitor of PTGS2 action. Please refer also to the KEGG main section. |
| MGI IDs (Jackson Laboratory, Maine, USA) MGI:97798 |
MGI IDs: MGI (Mouse Genome
Informatics) is maintained at Jackson Laboratory,
Maine, USA and collects all data about mouse genes,
including nomenclature,
map positions, expression data and more. Typical MGI accessions: - MGI:97798: This is the MGI gene entry for the mouse Ptgs2 (Cox-2) gene. It contains the majority of the major database links for this gene, including links to the specific MGI datasets, like expression information including RT-PCR, Northern Blot and Western Blot data (stored in the GXD database). Please refer also to the MGI main section. |
| MMDB IDs (NCBI) 23795 |
MMDB IDs: The NCBI Structure group
maintains MMDB,
a
database of macromolecular 3D structures, as well as tools
for their visualization and comparative analysis. MMDB, the Molecular
Modeling Database, contains experimentally determined biopolymer
structures obtained from the Protein Data Bank (PDB). Typical MMDB accessions: - 23795: This is the MMDB accession for the crystal structure of Diclofenac bound to the cyclooxygenase active site of the example protein Ptgs2 (Cox-2) (mouse). MMDB entries can be displayed in 3D using the NCBI software Cn3D which is very easy to install and to handle. Please refer to the Cn3D section for information. NOTE: Usually, there is always a corresponding PDB entry to each MMDB entry (see PDB IDs). Please refer also to the MMDB main section. |
| OMIM IDs (NCBI) 600262 601373.0001 |
OMIM IDs: OMIM
is a catalog
of human genes and genetic disorders. The database contains
textual information (like "mini-reviews" !),
pictures, and reference information. It also contains links to
NCBI's Entrez database of MEDLINE articles and sequence information. Typical OMIM accessions: - 600262: OMIM IDs consist of a simple number without any letters. This is the OMIM entry of the example gene PTGS2. Note: Each OMIM entry is assigned a unique six-digit number whose first digit indicates whether its inheritance is autosomal (1, 2, and 6 depending on date of creation), X-linked (3), Y-linked (4), or mitochondrial (5). In addition, OMIM entries are categorized by content, which is displayed by symbols preceding the MIM number: "*" (asterisk) indicates an entry of a gene of known sequence. "#" (number symbol) indicates a descriptive entry, usually a phenotype, and does not represent a unique locus. "+" (plus sign) indicates an entry of gene AND phenotype. "%" (percentage sign) indicates confirmed phenotype for which the molecular basis is unknown. "^" (caret symbol) indicates that the entry was removed from the database. - 601373.0001: This is one of the allelic variants of the gene CCR5 (32bp deletion), conferring resistance to HIV infection. Allelic variants are given a 10 digit number: the 6-digit number of the parent locus followed by a decimal point and a unique 4-digit variant number. Note that for most genes, only selected mutations are included as specific subentries. Criteria for inclusion include: the first mutation to be discovered, high population frequency, distinctive phenotype, historic significance, unusual mechanism of mutation, unusual pathogenetic mechanism, and distinctive inheritance (e.g., dominant with some mutations, recessive with other mutations in the same gene). Most of the allelic variants represent disease-producing mutations. A few polymorphisms are included, many of which show a positive statistical correlation with particular common disorders. NOTE: OMIM does not accept an allelic variant number as search term (only the parent number) ! Please refer also to the OMIM main section. |
| PDB IDs (RCSB) 1PXX |
PDB IDs: The PDB, Protein Data
Bank, is maintained by the consortium RCSB (Research
Collaboratory for Structural Bioinformatics. PDB makes all published
macromolecular
structures available. So the PDB is the most comprehensive
place to look for proteins, DNA, RNA, and polysaccharides. PDB files
contain atomic coordinate data for each structure. Typical PDB accessions: - 1PXX: This is the PDB accession for the crystal structure of Diclofenac bound to the cyclooxygenase active site of the example protein Ptgs2 (Cox-2) (mouse). Note that PDB accessions in general have a characteristic 4-character code. Note: You may want to refer to the PDB entry in cases where a structure is composed of several molecules and you want to know which chain in the 3D structure (as displayed by e.g. Cn3D) corresponds to which molecule. NOTE: Usually, there is always a corresponding MMDB entry to each PDB entry (see MMDB IDs). Please refer also to the PDB main section. |
| Pfam IDs (Sanger) PF00008 CL0001 |
Pfam IDs: Pfam is a
large collection
of multiple
sequence alignments and hidden Markov models covering many common protein
domains. For each family in Pfam you can retrieve multiple
alignments,
view protein domain architectures, examine species distribution, follow
links to other databases, and view known protein structures. Typical Pfam accessions: - PF00008: This is the same entry as described for InterPro IDs (EGF-like domain, which is found in the example protein PTGS2). Besides a description of the domain itself, Pfam offers interesting tools to generate multiple alignments, and to investigate the domain organization, the species distribution, or to generate a phylogenetic tree. - CL0001: This is a typical Pfam clan accession number. This entry refers to the EGF superfamily clan. A clan contains two or more Pfam families that have arisen from a single evolutionary origin, and thus represents a protein superfamily. Please refer also to the Pfam main section. |
| PharmGKB IDs (Stanford) PA293 PA448871 PA444552 |
PharmGKB IDs: PharmGKB - the
"Pharmacogenetics and
Pharmacogenomics Knowledgebase", is a research tool which aims to aid
researchers in
understanding how genetic
variation among individuals contributes to differences in reactions to drugs.
The PharmGKB database is a central repository for genetic and clinical
information. In
addition, genomic data, molecular and cellular
phenotype data, and clinical
phenotype data are accepted from the scientific community at large. Typical PharmGKB accessions: - PA293: This is the PharmGKB Gene entry for the gene PTGS2. Besides cross-references to all major "outside-databases", links to related drugs and related diseases are listed. - PA448871: This is a PharmGKB Drug entry for the substance celecoxib (Celebrex) which interferes with the action of PTGS2. Interestingly, there is no correlation between PTGS2 and the drug Diclofenac, although present in the database (PA449293). - PA444552: This is a PharmGKB Disease entry for the disease hypertension, which is related to several genes, like PTGS2. Interestingly, there is no correlation between PTGS2 and the disease inflammation, although present in the database (PA444620). Please refer also to the PharmGKB main section. |
| PolyA_DB IDs (University of Medicine and Dentistry of New Jersey) p.5743.5 |
PolyA_DB
IDs: PolyA_DB, maintained at the
University of Medicine and Dentistry of New Jersey (UMDNJ), is a database which provides
several types of information regarding polyadenylation in
mammalian species. Typical PolyA_DB accessions: - p.5743.5: This is the Poly(A) site ID of the human gene PTGS2. The PolyA_DB has the format of p.###.*, where ### is the Entrez Gene ID (LocusLink ID) for the corresponding gene, * is a order number (ordered for all poly(A) sites of the gene from 5' to 3' of the transcript). Please refer also to the PolyA_DB main section. |
| PRINTS IDs (Manchester University) PR00457 |
PRINTS IDs: PRINTS
is a compendium of protein fingerprints, provided by
the Manchester University.
A fingerprint
is a group of conserved motifs used to characterise a protein family;
its diagnostic power is refined by iterative scanning of a SWISS-PROT /
TrEMBL composite. Typical PRINTS accessions: - PR00457: This is a PRINTS entry for Anperoxidase, a domain found in the example gene PTGS2, displayed by SPRINT ("pretty-view"). A detailed documentation about the domain is presented along with a list of proteins from diverse species which bear this domain. Also, a list of "initial motifs" and "final motifs" is presented. - PR00457: This is the output which is displayed when searching the PRINTS database. Please refer also to the PRINTS main section. |
| PROSITE IDs (ExPASy) PS50026 |
PROSITE IDs: PROSITE is a database
of protein
families and domains. It consists of biologically significant
sites, patterns and profiles that help to reliably identify to
which known protein family (if any) a new sequence belongs. Typical PROSITE accessions: - PS50026: This is the PROSITE entry for the same domain described for InterPro or Pfam IDs (EGF-like domain, which is found in the example protein PTGS2). Please refer also to the PROSITE main section. |
| PubChem IDs (NCBI) CID:3033 SID:364811 |
PubChem IDs: PubChem is a
collection of databases provided by the NCBI, which contains the
chemical structures of small organic molecules and information
on their biological activities. PubChem is organized as three
linked databases within the
Entrez/PubMed information retrieval system, meaning that all 3
databases can be searched "in one run". These are PubChem Substance,
PubChem Compound, and PubChem BioAssay. Typical PubChem accessions: - CID:3033: This is the PubChem Compound ID for the substance Diclofenac, a known inhibitor of PTGS2 action. The entry contains structural data of the substance, references, synonyms, a description of the pharmacological action and more. - SID:364811: This is the PubChem Substance ID for the substance Diclofenac. Please refer also to the PubChem main section. |
| Reactome IDs (CSHL, EBI, GO Consortium) 61606 140180 |
Reactome IDs: Reactome
(formerly
known as "Genome KnowledgeBase) is a collaborative effort
to develop a curated resource of core pathways and reactions in
human biology. Typical Reactome accessions: Note: Actually there are no "typical" Reactome IDs, instead reactions, pathways, and single molecules are attributed a certain number to be retrieved in the Reactome Eventbrowser. - 61606: This is a typical Reactome-entry for a specific gene/protein displaying concise information on COX2 (PTGS2), linking to major external databases as well as to the reactions stored in Reactome where this molecule is involved. - 140180: This is a typical Reactome-entry for a specific type of reaction, displaying information on COX reactions, meaning reactions performed by the enzymes COX1 and COX2 (PTGS2). Note that both enzymes perform the same reactions but under different stimulatory conditions. In this case there are links to 2 sub-reactions, displayed in individual pages. Please refer also to the Reactome main section. |
| RefSeq IDs (NCBI) NM_000963 NP_000954 |
RefSeq IDs: The
Reference Sequence (RefSeq)
collection aims to provide a
comprehensive, integrated, non-redundant set of sequences, including
genomic DNA, transcript (RNA), and protein products, for major
research
organisms. Typical RefSeq accessions: - NM_000963: This is a RefSeq mRNA record for human PTGS2. RefSeq entries look similar to "normal" GenBank records, in fact RefSeqs are actually derived from GenBank records which were adapted by NCBI staff. - NP_000954: This is a RefSeq protein record for human PTGS2. Note: Further accession numbers include "NC_", "NG_", "NT_", "NW_", NZ_" for genomic DNA and "NR_" for non-coding RNAs. "XM_", "XP_" and "XR_" designate model mRNAs, proteins, and non-coding transcripts generated by automated genome annotation pipelines. Please refer to this RefSeq accessions page for a full list of IDs ! Please refer also to the RefSeq main section. Note: RefSeq was started by the NCBI, while other institutes like EBI-Ensembl also began to generate such "non-redundant sets of sequences". As a consequence, a new database was created to integrate these datasets into one common identifier for each gene; please refer to the CCDS section for details. |
| RESID IDs (EBI and NCIFCRF) AA0151 |
RESID IDs:
The RESID Database of
Protein
Modifications is a comprehensive collection of annotations
and structures for protein
modifications and
cross-links including pre-, co-, and post-translational modifications. Typical RESID accessions: - AA0151: This is the RESID database entry for N4-glycosyl-L-asparagine, which is found in N-glycosylated proteins. This modification typically occurs in extracellar peptides with an N-X-[ST] motif. Note: All RESID entries start with the prefix "AA" followed by a four-letter code. Please refer also to the RESID main section. |
| Rfam IDs (Sanger and Washington University) RF00254 miRBase IDs (Sanger) MI0000070 MIMAT0000069 |
Rfam IDs: Rfam is a large
collection of multiple
sequence alignments and covariance models covering many common non-coding
RNA families. Typical Rfam accessions: - RF00254: This is the Rfam database entry for the mir-16 microRNA precursor family. miR-16 microRNA was shown to be involved in the mRNA-destabilization of inflammatory mediators like TNFalpha and PTGS2 (COX2), as shown in Jing et al., Cell 2005. Please refer also to the Rfam main section. miRBase IDs: miRBase contains all published miRNA sequences, genomic locations and associated annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available. Typical miRBase accessions: - MI0000070: This is the stem-loop sequence entry of the human miR-16-1 microRNA. Note that this file also contains the data of the mature sequence of this microRNA, with accession MIMAT0000069. Please refer also to the miRBase main section. |
| SMART IDs (EMBL) SM00181 |
SMART IDs: SMART (a Simple
Modular
Architecture Research Tool) allows the identification and annotation of
genetically mobile domains and the analysis of domain architectures.
More than 500 domain families found in signalling,
extracellular and chromatin-associated proteins are detectable. Typical SMART accessions: - SM00181: This is the same entry as described for InterPro IDs and Pfam IDs (EGF-like domain). There are obviously strong overlaps concerning content and functionality of these entries. Please refer also to the SMART main section. |
| Swiss-Prot IDs TrEMBL IDs UniProt IDs (EBI, SIB, PIR) P35354 PGH2_HUMAN Q6ZYK7 Q6ZYK7_HUMAN |
Swiss-Prot IDs / TrEMBL IDs / UniProt
IDs: The Swiss-Prot
Protein
Sequence Database is the "mother database" of protein
sequences. It contains high-quality annotation, is
non-redundant,
and cross-referenced to several other databases. TrEMBL (also
known as SPTREMBL) is a computer-annotated protein sequence
database supplementing the SWISSPROT
Protein Sequence Data Bank. In 2002, EBI,
SIB
(Swiss Institute of Bioinformatics), and PIR (Protein Information
Resource) joined forces as the UniProt consortium. UniProt
is
essentially built of Swiss-Prot
and TrEMBL. Typical Swiss-Prot accessions: Note: These links are related to the example gene / protein PTGS2 (COX2). - P35354: A typical Swiss-Prot entry lists the definition of a protein sequence, the source organism, literature references, keywords concerning function and cellular localization, GO terms, protein domains, motifs, interaction partners, (potential) sites of post-translational modification, and of course the sequence itself. Typical Swiss-Prot/UniProt accessions: - PGH2_HUMAN: shows (almost) the same information content as the Swiss-Prot entry, but in a more structured layout. Typical TrEMBL accessions: - Q6ZYK7: Somehow similar to Swiss-Prot entry but usually shorter. Typical TrEMBL/UniProt accessions: - Q6ZYK7_HUMAN: shows (almost) the same information content as the TrEMBL entry, but in a more structured layout. Please refer also to the Swiss-Prot and TrEMBL main section as well as to the UniProt main section. |
| TRANSFAC IDs (BIOBASE, Germany) G000316 M00054 R01634 T00590 |
TRANSFAC IDs: TRANSFAC
is
"historically" the most important transcription factor database.
TRANSFAC is maintained by BIOBASE,
Germany. TRANSFAC contains
data of transcription factors, transcription factor matrices, and their
binding sites. Thus, TRANSFAC is divided into several databases, all
containing entries with characteristic accession numbers. Typical TRANSFAC accessions: NOTE: The first link points to the BIOBASE entry (which demands prior free subscription), the second link points to the free SRS-based entry. SRS databases can be selected via the list of public SRS servers. - G001237; G001237: TRANSFAC TFGene Table entry for the example gene PTGS2. This entry shows a certain gene, where the promoter was experimentally analyzed and the binding TFs ("T...") and TF binding sites ("R...") were chracterized. - M00109; M00109: TRANSFAC TFMatrix Table entry for the TF CEBPbeta. This entry shows a matrix, which is built by a series of individual binding sites related to a specific TF. Often, binding sites of several species are "merged". Such TF matrices are used by several programs to predict TFBS in sequences. Note: This matrix entry is derived from CEBPbeta instead of CEBPdelta (which was described in the context of the regulation of the PTGS2 promoter) as there is no matrix for this TF available in TRANSFAC 6.0 public. - R08091; R08091: TRANSFAC TFSite Table entry. This entry shows an individual short binding sequence within the PTGS2 promoter, which is recognized by the TF CEBPdelta (NF-IL6). The relative position to the transcription start site is indicated. Links to the TFGene entry and to the binding factor(s) are contained. - T01114; T01114: TRANSFAC TFFactor Table entry for the TF CEBPdelta. This entry shows the protein sequence of a TF, literature references, functional annotation, cell specificity, and links to the orthologs in other species, as well as to the binding site entries. Please refer also to the TRANSFAC main section. |
| UniGene IDs (NCBI) Hs.196384 Mm.292547 |
UniGene IDs: UniGene
clusters all
EST- sequences that belong to a single gene. UniGene provides links to
databases like Entrez Gene,
OMIM, and HomoloGene. Note: In contrast to databases like TIGR, there
is NO consensus sequence assembly, and NO graphical
output. Typical UniGene accessions: - Hs.196384: A human UniGene entry (PTGS2 gene) always shows the prefix "Hs", followed by a number. - Mm.292547: A mouse UniGene entry (Ptgs2 gene) always shows the prefix "Mm", followed by a number. Please refer also to the UniGene main section. |
| VEGA IDs (Sanger) OTTHUMG00000035473 OTTMUSG00000010099 OTTHUMT00000086157 OTTMUST00000023494 OTTHUMP00000033524 |
VEGA IDs: The VEGA (Vertebrate Genome
Annotation) database is a central
repository for high quality, frequently updated, manual annotation
of
vertebrate finished genome sequence. The website
is built upon code from the Ensembl
project. Typical VEGA accessions: Note: These links are related to the example gene / protein PTGS2 (COX2). - OTTHUMG00000035473: This is a human "curated locus report", very similar to the Ensembl Gene report, with links to the genome browser display, to related transcript, family, etc. reports, to orthologous sequences, protein domains, motifs, GO terms, and links to all major databases. Note: This ID is different from the Ensembl ID for the same gene (see section Ensembl IDs), but both reports (Ensembl AND Vega) can also be retrieved by searching the Ensembl website. Note: "OTT" indicates that the reports are manually annotated in the so-called Otter database. Otter is an extended Ensembl database with an associated client/server system that is able to support interactive updating of annotation. Please refer also to the VEGA publication in NAR (Jan. 2005) for details. - OTTMUSG00000010099: A mouse "curated locus report", similar to Ensembl Gene Report. - OTTHUMT00000086157: A human VEGA Transcript report, similar to Ensembl Transcript reports. Note: VEGA contains 3 different transcripts for this gene (the other acc. are OTTHUMT00000086158, and OTTHUMT00000086159), in contrast to Ensembl (only 1 transcript, see section Ensembl IDs). - OTTMUST00000023494: A mouse VEGA Transcript report, similar to Ensembl Transcript reports. - OTTHUMP00000033524: A VEGA human protein report. Please refer also to the VEGA main section. |