EUKARYOTIC PROMOTER DATABASE
USER MANUALPhilipp
Bucher, Rouaida Cavin Périer, Viviane Praz and Christoph Schmid
EPFL School of Life Sciences - SV
and Swiss Institute for Experimental Cancer Research - ISREC
Computational Cancer Genomics Group
EPFL SV ISREC GR-BUCHER Station 15
CH-1015 /Lausanne
Switzerland
Electronic mail:
This manual and the database it accompanies may be copied and redistributed freely, without advance permission, provided that this statement is reproduced with each copy.Published Research assisted by the Eukaryotic Promoter Database should cite:
EPD in its twentieth year: towards complete promoter coverage of selected model organisms
Schmid, C.D., Perier, R., Praz, V. and Bucher, P. (2006) Nucleic Acids Res, 34, D82-85.
EPD RELEASE 109, November 2011
EPD release history
CONTENTS
- INTRODUCTION
- PROMOTER SELECTION
- ASSIGNMENT OF INITIATION SITE
- FORMAT CONVENTIONS
- The title line
- Promoter entries
- The ID line
- The AC line
- The DT line
- The DE line
- The OS line
- The HG line
- The AP line
- The NP line
- The DR line
- The RN, RX, RA, RT and RL lines
- The ME line
- The SE line
- The FL line
- The IF line
- The TX line
- The KW line
- The FP, DO and RF lines
- The // line
- Line types retained from the old format
- Distinct format of 'preliminary' entries in epd_bulk.dat
- CLASSIFICATION
- HOMOLOGOUS PROMOTERS
- PROMOTER SEQUENCE RETRIEVAL
- REFERENCES
1 INTRODUCTION
The Eukaryotic Promoter Database EPD was designed and developed at the Weizmann Institute of Science in Rehovot (Israel) and is currently maintained at ISREC in Epalinges s/Lausanne (Switzerland). EPD is a specialized annotation database of the EMBL Data Library. It provides information about eukaryotic promoters available in the EMBL Data Library and is intended to assist experimental researchers, as well as computer analysts, in the investigation of eukaryotic transcription signals. The present version originated from a previous compilation published in an article (1) and is organized as a hierarchically ordered and documented "functional position set" (2) pointing to transcription initiation sites. All information is either directly extracted from scientific literature or, starting from release 73, compiled by a new in silico primer extension method (16). Thus promoter information in EPD is independent of the EMBL sequence entry descriptions. As a consequence, many of the initiation sites referred to in EPD do not appear in corresponding EMBL feature tables.A coordinated updating procedure has been set up by the two laboratories that will ensure future compatibility between the position references in EPD and the sequence data in the main data library. Investigators who access EMBL via publicly available programs should be aware of the fact that software producers occasionally modify the sequence data in ways that render position references inaccurate. EPD is generally not compatible with sequence data of another release because EMBL sequence entries are not designed as stable data units. The completeness and accuracy of EPD greatly benefits from user-feedback. Any report of mistakes or omissions would be very much appreciated. Direct communication of newly published transcript mapping or gene expression data is also welcome. Please forward all correspondence to the address given on top of this document. Use electronic mail if possible.2 PROMOTER SELECTION
EPD is a rigorously selected database. In order to be included in EPD, a promoter must be:- recognized by eukaryotic RNA POL II,
- active in a higher eukaryote,
- experimentally defined, or homologous and sufficiently similar to an experimentally defined promoter,
- biologically functional,
- available in the current EMBL release,
- distinct from other promoters in the database.
- Transcription by RNA POL II is bona fide assumed for protein coding genes but must be supported by alpha-amanitin data if the end product is an RNA.
- All eukaryotes except phycophyta, fungi, myxomycetes, and protozoa are considered higher eukaryotes. Note that the expression "active in" does not always refer to the source organism of the promoter (e.g. in viruses). EPD contains currently promoter sequences from 139 different species.
- A promoter is experimentally determined if a corresponding transcription initiation site is mapped with a precision of +/- 5 bp or higher. Any technique that characterizes the 5'terminus of an in vivo or in vitro generated RNA is acceptable. Single nuclease-protection or primer-extension data must be accompanied by additional evidence unless the gene's intron-exon organization is well established. Similarity is considered "sufficient" if percent identity (as defined in Section 6) is >=60% between -79 and +20 or >=75% between -49 and +10.
- A promoter is biologically functional if it contributes to the source organism's survival and/or reproduction. This is bona fide assumed except for promoters of pseudogenes, minor transcription initiation sites (<20% of total gene transcripts), promoters giving rise to an unstable RNA product, and mutant promoter.
- The minimum sequence requirement is 45 bp between -49 and +10.
- Promoters are considered distinct if they originate from different gene loci or different species. Identity is assumed if two promoters from the same species exhibit >95% similarity between -79 and +20 while their genetic relationship is unknown. Multiple isolates of viruses or transposable elements are considered distinct if at least one promoter region fails to fulfill the above similarity criterion.
3 ASSIGNMENT OF TRANSCRIPTION INITIATION SITE
A eukaryotic promoter is defined as a DNA sequence around a transcription initiation site. The position reference to the initiation site is therefore the central part of a promoter entry. Its assignment is based directly on experimental data shown in an article, proposed adjustments originating from consensus sequence considerations being ignored. In the case of minor discrepancies between different publications averaged positions are given. Position references are subject to permanent re-evaluation. A transcription initiation site may be reassigned upon publication of new data. Position references are replaced if longer upstream sequences of the same promoter become available in a new EMBL sequence entry.Several initiation sites preceding the same gene appear as alternative promoters if they are clearly separated from each other or differentially regulated. The minimum distance required between two alternative initiation sites is 20 bp. Otherwise, they are considered a single promoter region.
Four types of promoters are distinguished by one-letter codes in order to account for the variety of transcription initiation patterns in eukaryotes:
- S: Single initiation site: >90% of all reported transcripts initiate within 10 bp (the experimental data usually do not allow distinction between a single cap-site and small mRNA 5' heterogeneity).
- M: Multiple initiation sites: >75% of all reported transcripts initiate within 20 bp.
- R: Initiation region: >75% of all reported transcripts initiate within 100 bp.
- U: Undefined transcription initiation pattern, exclusively in 'preliminary' entries in epd_bulk.dat (see next section).
In sequence entries that contain a complete RNA or DNA genome of a retrovirus or a retrovirus-like transposable elements, the position reference points to the U3/R boundary of the 3'terminal LTR.
4 FORMAT CONVENTIONS
EPD is distributed as two ASCII flatfiles (epd.dat, epd_bulk.dat) in essentially identical format. Differences in the format of 'preliminary' entries in 'epd_bulk.dat' are described in paragraph 4.4. EPD files contain a title line followed by a number of promoter entries. Interspersed are group headings whose function and format are described in the next section. The title line and parts of the promoter entries are rigidly formatted so that the entire database conforms to the standards of an FPS file (functional position set) of our current signal search analysis (1,2) software.4.1. The title line
The title line of EPD is shown below:TI EPD83 Eukaryotic Promoter Database / Release 83 EPThe TI line contains the following fields:
| columns | data type |
|---|---|
| 1- 2 | "TI" |
| 3- 5 | (blank) |
| 6-15 | FPS name |
| 16-70 | title |
| 71-72 | FPS code |
- FPS name and FPS code are used by our data extraction software to generate default names for output files.
4.2. Promoter entries
An EPD entry contains the following types of information:- Promoter identification and description.
- Machine-readable pointers to the transcription initiation site in corresponding sequence entries.
- Description of the experimental evidence defining the transcription start site.
- Various kinds of promoter classifications useful for extraction of biologically meaningful promoter subsets.
- Information on regulatory properties.
- Cross-references to other databases.
- Bibliographic references.
ID - IDentification.Spacer lines (XX) are inserted in order to make the promoter database easier to read by eye. Some line types occur many times in a single entry. Each entry must begin with an identification line (ID) and end with a terminator line (//). Text does not exceed column 72. Below is an example of a promoter entry:
AC - ACcession number(s).
DT - DaTe.
DE - DEscription.
OS - Organism Species.
HG - Homology Group.
AP - Alternative Promoter.
NP - Neighbouring Promoter.
DR - Database cross-References.
RN - Reference Number.
RX - Reference cross-references.
RA - Reference Authors.
RT - Reference Title.
RL - Reference Location.
ME - MEthods.
SE - SEquence.
FL - Full Length.
IF - Initiation Frequency.
TX - TaXonomy.
KW - KeyWords.
FP - Functional Position.
DO - DOcumentation.
RF - literature ReFerence.
// - Termination line.
ID HS_MYC_2 standard; single; VRT.A detailed description of each line type is given below.
XX
AC EP11148;
XX
DT ??-APR-1987 (Rel. 11, created)
DT 07-MAR-2005 (Rel. 82, Last annotation update).
XX
DE c-myc (cellular homologue of myelocytomatosis virus 29 oncogene),
DE promoter 2.
OS Homo sapiens (human)
XX
HG Homology group 53; Mammalian c-myc proto-oncogene, promoter 2
AP Alternative promoter #2 of 2; exon 1; site 2; major promoter.
NP none.
XX
DR GENOME; NT_008046.15; NT_008046; [-41966656, 15188617].
DR EPD; EP11146; HS_MYC_1; alternative promoter; [-162; +].
DR CLEANEX; HS_MYC.
DR EMBL; AC103819.3; [-87815, 60206].
DR EMBL; X00364.2; [-2489, 8507].
DR EMBL; D10493.1; [-2487, 5569].
DR EMBL; K01910.1; [-2451, 49].
DR EMBL; M16261.1; [-1843, 1048].
DR EMBL; J03253.1; [-1759, 461].
DR EMBL; L00057.1; [-810, 2795].
DR EMBL; K03015.1; [-555, 458].
DR EMBL; X00196.1; [-532, 2792].
DR EMBL; M12026.1; [-511, 678].
DR EMBL; K01708.1; [-410, 500].
DR EMBL; K00559.1; [-345, 1020].
DR EMBL; K02280.1; [-302, 178].
DR EMBL; K01909.1; [-266, 1365].
DR EMBL; S65124.1; [-266, 1023].
DR EMBL; M14206.1; [-266, 446].
DR EMBL; M20013.1; [-240, 982].
DR EMBL; AF111270.1; [-142, 264].
DR EMBL; K02275.1; [-96, 780].
DR EMBL; X00675.1; [-96, 404].
DR EMBL; K02277.1; [-96, 157].
DR SWISS-PROT; P01106; MYC_HUMAN.
DR TRANSFAC; R01157; HS$CMYC_01; [-211, -189]; by position.
DR TRANSFAC; R01158; HS$CMYC_02; [-168, -145]; by position.
DR TRANSFAC; R01804; HS$CMYC_04; [-300, -283]; by position.
DR TRANSFAC; R01851; HS$CMYC_05; [-65, -57]; by position.
DR TRANSFAC; R01852; HS$CMYC_06; [-42, -34]; by position.
DR TRANSFAC; R04076; HS$CMYC_12; [-251, -228]; by position.
DR TRANSFAC; R04076; HS$CMYC_12; [-252, -229]; by position.
DR TRANSFAC; R04076; HS$CMYC_12; [-253, -230]; by position.
DR TRANSFAC; R04621; HS$CMYC_17; [-313, -262]; by position.
DR TRANSFAC; R08503; HS$CMYC_18; [-50, -41]; by position.
DR TRANSFAC; R16688; HS$CMYC_24; [-7, 41]; by position.
DR TRANSFAC; R16689; HS$CMYC_25; [-7, 41]; by position.
DR TRANSFAC; R17051; HS$CMYC_30; [-510, -480]; by position.
DR TRANSFAC; R18503; HS$CMYC_31; [-185, -170]; by position.
DR TRANSFAC; R18504; HS$CMYC_32; [-153, -168]; by position.
DR RefSeq; NM_002467.
DR MIM; 190080.
XX
RN [1]
RX MEDLINE; 84026482.
RA Battey J., Moulding C., Taub R., Murphy W., Stewart T., Potter H.,
RA Lenoir G., Leder P.;
RT "The human c-myc oncogene: structural consequences of
RT translocation into the IgH locus in Burkitt lymphoma";
RL Cell 34:779-787(1983).
RN [2]
RX MEDLINE; 84131953.
RA Bernard O.D., Cory S., Gerondakis S., Webb E., Adams J.M.;
RT "Sequence of the murine and human cellular myc oncogenes and two
RT modes of myc transcription resulting from chromosome translocation
RT in B lymphoid tumours";
RL EMBO J. 2:2375-2383(1983).
RN [3]
RX MEDLINE; 87257828.
RA Lipp M., Schilling R., Wiest S., Laux G., Bornkamm G.W.;
RT "Target sequences for cis-acting regulation within the dual
RT promoter of the human c-myc gene.";
RL Mol. Cell. Biol. 7:1393-1400(1987).
RN [4]
RX MEDLINE; 88038843.
RA Broome H.E., Reed J.C., Godillot E.P., Hoover R.G.;
RT "Differential promoter utilization by the c-myc gene in mitogen-
RT and interleukin-2-stimulated human lymphocytes.";
RL Mol. Cell. Biol. 7:2988-2993(1987).
XX
ME Nuclease protection [1,4].
ME Nuclease protection; transfected or transformed cells [3].
ME Length measurement of an RNA product; low-precision data [1].
XX
SE agggagggatcgcgctgagtataaaagccggttttcggggctttatctaACTCGCTGTAG
XX
TX 6. Vertebrate promoters
TX 6.1. Chromosomal genes
TX 6.1.5. Hormones, growth factors, regulatory proteins
TX 6.1.5.16. Various cellular protooncogenes
XX
KW Proto-oncogene, Nuclear protein, DNA-binding, Glycoprotein,
KW Transcription regulation.
XX
FP Hs c-myc P2+:+S EU:NC_000008.9 1+ 128817660; 11148.053 010*2
XX
DO Experimental evidence: 4,4#,2l
DO Expression/Regulation: +mitogen
RF Cell34:779 EMBOJ2:2375 MCB7:1393 MCB7:2988
//
4.2.1. The ID line
The identification line is always the first line of an entry. The general form of the ID line is:ID ENTRY_NAME data class; initiation site type; TAXONOMIC DIVISION.
- ENTRY_NAME is a unique entry identifier "HS_MYC_2" which obeys rigorous naming conventions. It contains 2 or 3 fields, the first is the species identification code at most 4 alphanumeric characters representing the biological source of the promoter. The second field uses for gene identification the protein code of SWISS-PROT ID (if available). For human EPD entries, instead of the SwissProt ID the official gene symbol approved by the HGNC (HUGO Gene nomenclature committee) (if available) is used. The third field is optional, it is either a number which represents alternative promoters or a letter for promoters of duplicated genes. The `_' sign serves as a separator.
- The data class field relates to the quality of the information: "standard" means that the information is complete and correct according the standards laid down in this document; "preliminary" means that the entry has not yet undergone all quality checks necessary for being classified as "standard".
- The initiation site type is either "single", "multiple", "region" as defined in Section 3.
- TAXONOMIC DIVISION are
- PLN for plant
- NEM for nematode
- ART for arthropode
- MLS for mollusc
- ECH for echinoderm
- VRT for vertebrates.
4.2.2. The AC line
AC EP11148;The accession number consists of the character string "EP" followed by 5 digits representing the EMBL release number followed by the EPD entry order. Most EPD entries currently have only one accession number. If necessary, more then one AC will be used, separated by semicolons and the list is terminated by a semicolon.
4.2.3. The DT line
The date lines show the date of entry or last modification of the entry.DT DD-MMM-YEAR (Rel. XX, Comment)where `DD' is the day, `MMM' the month, `YEAR' the year, and `XX' the EPD release number. The comment portion of the line indicates the action taken on that date.
- The first DT line indicates when the entry first appeared in the database.
- The second DT line indicates when the promoter data was last modified. It is terminated by a period.
4.2.4. The DE line
DE c-myc (cellular homologue of myelocytomatosis virus 29 oncogene),The description lines contain general descriptive information about the promoter. The description is given in ordinary English and is free-format. It contains the swiss-prot gene names when known. In some cases, more than one DE line is required; in this case, the text is divided only between words. The last DE line is terminated by a period.
DE promoter 2.
4.2.5. The OS line
OS Mus musculus (house mouse)The species line specifies the source organism(s) of the promotery. The species names are based on NCBI's taxonomy and thus can be automatically hyperlinked to the NCBI's taxonomy web pages.
4.2.6. The HG line
HG Homology group 53; Mammalian c-myc proto-oncogene, promoter 2The homology group line is optional, it contains 2 fields: a homology group number that allows identification of all sequence-wise similar promoters in EPD, and a homology group name.
4.2.7. The AP line
AP Alternative promoter #2 of 2; 5' exon 1; site 2; major promoter.The AP line is optional and provides information on alternative promoters of the same gene (for more details, see Section 4.3.1.). It contains 3 or 4 fields, separated by semicolons, providing the following types of information:
-
descriptive text fields followed by
- Two numbers indicating, respectively, the promoter's relative position along the gene, and the total number of alternative promoters of the gene. Promoters are numbered in the 5' to 3' directions starting with one.
- A number referring to the exon preceded by the promoters. Note that multiple promoters may be associated with the same (3'-coterminal) exon or with different exons. Known exons are numbered in 5' to 3' direction starting with one.
- A number indicating the promoter's relative position among the subset of promoters preceeding the same exon.
- An optional keyword indicating major promoters.
Note that the nomenclature of 5'-exons in EPD may differ from the usage in the literature.
4.2.8. The NP line
NP Neighbouring Promoter; EP23008; MM_H2B1; [-209; -].The NP line is optional and provides information on promoters which are physically closer to each other than 1000 bp. It contains 3 fields, separated by semicolons, providing the following types of information:
- The EPD accession number of the neighbouring promoter.
- The EPD identifier of the neighbouring promoter.
- The last field indicates, respectively, the position and the direction of the neighbouring promoter relative to the transcription initiation site given in the promoter entry.
- Negative numbers indicate the upstream region of this entry and positive ones indicate the downstream region.
- The sign indicates the transcription direction of the neighbouring promoter relative to the promoter entry:
"+" means same direction
"-" means opposite direction
4.2.9. The DR line
The DR lines contain cross-references to other EPD entries (if there are alternative promoters of the same gene), or to entries from other databases. So far, we have incorporated links to CLEANEX, EMBL (3), GenBank (4), DDBJ (5), SWISS-PROT (6), TRANSFAC (7), Flybase (8), MIM (9) and MGD (10). The precise format of these lines depends on the target database. Note that some cross-references include numbers enclosed in square brackets indicating the relative position of a linked sequence object, or keywords characterising the nature of the relationship between the entries. For instance, the ranges associated with cross-references to EMBL entries define the extensions of the EMBL sequences relative to the initiation site described by the EPD entry. The multiplicity of EMBL cross-references in some entries mirrors the redundancy of the sequence database. The first of these references corresponds to the longest promoter region, except when the sequences are cancelled from EMBL database, but still exist in GenBank or DDBJ.The format of the DR line is shown by the following example lines:
DR GENOME; NT_037436.1; NT_037436; [-14139754, 9212459].Explanations (for detailed information go to Guidelines ):
DR EPD; EP11146; HS_MYC_1; alternative promoter; [-162; +].
DR EMBL; J00120.1; [-2489, 8507].
DR SWISS-PROT; P01106; MYC_HUMAN.
DR SPTREMBL; Q8IQL1.
DR FLYBASE; FBgn0013718; nuf.
DR TRANSFAC; R01804; HS$CMYC_04; [-300, -283]; by position.
DR MIM; 190080.
DR RefSeq; NM_003529.
DR MGD; MGI:88468; Cola2.
DR ENSEMBL; CG32140.
DR TRANSCRIPTOME; DMe000571.
- The first item on the DR line is the abbreviated name of the data collection to which reference is made. The currently defined data bank identifiers are the following:
- The second item is the primary accession number (or an equivalent unique identifier of another data banks) of the entry to which reference is made.
- The third item (if it exists) is a secondary idientifier or name for the cross-referenced database entry.
- The fourth item for EMBL and Transfac indicates the location and extension of the sequences given in these entries relative to the transcription initiation site given in the promoter entry. Negative numbers indicate the upstream region of this site and positive ones indicate the downstream part.
- The fifth item
- in the EPD line, indicates the position and the direction of the alternative promoter as it is defined for the neighbouring promoter in the NP line last field
- in the TRANSFAC line, designates the criteria used to collect the TF entry:
| GENOME | NCBI Reference Sequence (RefSeq) of genomic sequence contigs |
| EPD | Eukaryotic Promoter Database: alternative promoters of the same gene |
| CLEANEX | Gene expression database for human EPD promoters |
| EMBL | Nucleotide sequence database of the EMBL |
| SWISS_PROT | Protein sequence database |
| SPTREMBL | Subset of protein sequence database TrEMBL. It contains the entries which should be eventually incorporated into SWISS-PROT. SWISS-PROT accession numbers have been assigned for all SP-TrEMBL entries |
| FLYBASE | Drosophila genome database |
| TRANSFAC | Transcription factor (TF) database |
| MIM | Mendelian Inheritance in Man Database |
| RefSeq | Reference Sequence Database |
| MGD | Mouse Genome Database |
| ENSEMBL | Metazoan genome annotation |
| TRANSCRIPTOME | Catalog of transcripts and their mapping onto the genome (LICR Lausanne branch) |
| TIGR | 'gene identifiers' from the 'Rice Genome Annotation' project at TIGR |
- by position: The TF binding site is situated between -500 and + 100, +1 being the transcription initiation site
- by function: The TF binding site is known to regulate the corresponding promoter.
4.2.10. The RN, RX, RA, RT and RL lines
These lines comprise the literature citations within EPD. The citations indicate the papers from which the data has been abstracted. The reference lines for a given citation occur in a block, and are always in the order RN, RX, RA, RT, RL. Within each such reference block the RN line occurs once, the RX lines occurs zero or more times, and the RA, RT and RL lines each occur one or more times. If several references are given, there will be a reference block for each.An example of a complete reference is:RN [1]The formats of the individual lines are explained below. >
RX MEDLINE; 84026482.
RA Battey J., Moulding C., Taub R., Murphy W., Stewart T., Potter H.,
RA Lenoir G., Leder P.;
RT "The human c-myc oncogene: structural consequences of
RT translocation into the IgH locus in Burkitt lymphoma";
RL Cell 34:779-787(1983).
4.2.10.1. The RN line
The RN line gives a sequential number to each reference citation in an entry.This number is used to indicate the reference in the ME lines.4.2.10.2 The RX line
The RX line is an optional line which is used to indicate the identifier assigned to a specific reference in PubMed (PMID, from the National Library of Medicine (NLM)). .4.2.10.3 The RA line
The RA lines list the authors of the paper (or other work) cited. The authors are are listed in the order given in the paper. The names are listed surname first followed by a blank followed by initial(s) with periods. The authors' names are separated by commas and terminated by a semicolon. Author names are not split between lines.4.2.10.4 The RT line
The RT lines contain the title of the reference citation.4.2.10.5 The RL line
The RL lines contain the conventional citation information for the reference. In general, the RL lines alone are sufficient to find the paper in question. It includes the journal abbreviation, the volume number, the page range, and the year. Journal names are abbreviated according to the conventions used by the National Library of Medicine (NLM) and are based on the existing ISO and ANSI standards.4.2.11. The ME line
The method lines describe experiments defining the transcription initiation site. The format of the ME line is as follows:ME Method_description [; Qualifier...] [n,...].A complete list of method descriptions is given in Section 4.3.2. Qualifiers may indicate that an experimental gene transcription system was used, that data are of low precision (less +/- 5 bp), or that the experiments were done with a closely related gene. The number(s) enclosed in square brackets links the method descriptions to the bibliographic references included in the promoter entry. The methods line from the example are:
ME Nuclease protection [1,4].
ME Nuclease protection; transfected or transformed cells [3].
ME Length measurement of an RNA product; low-precision data [1].
4.2.12. The SE line
The sequence line shows a short sequence segment corresponding to the -49 to +10 region of the promoter. Transcribed and untranscribed nucleotides are represented by upper and lower case characters, respectively. This line type is not meant to provide sequence data but serves as a control string for sequence extraction.4.2.13. The FL line
The Full length line designates the
large-scale
cDNA sequencing projects : NEDO (11),
MGC (12),
and
BDGP (15).
4.2.13. The IF line
The Initiation Frequency lines reflect the
frequency
at which each nucleotide within the initiation region is found at the
5'end
of bone fide full-length cDNA clone inserts.
4.2.14. The TX line
The TX (TaXonomy) lines define a promoter's location within EPD's hierarchical classification system (see Section 5). Note that starting from release 72, the classification system is no longer maintained.4.2.15. The KW line
The KW lines define a number of keywords describing an entry.4.2.16. The FP, DO and RF lines
These lines pertain to the EPD old format, see next Section.4.2.17. The // line
The // (terminator) line contains no data or comments. It designates the end of an entry.4.3. Line types retained from the old format
The last six lines of a entry present essential information in the more concise, old format. A original description of the old format follows: Each entry starts with an FP line that contains a position reference to a transcription initiation site, and ends with a terminator (//).Below is an example of a promoter entry:FP Hs c-myc P2+:+S EU:NC_000008.9 1+ 128817660; 11148.053 010*2
XX
DO Experimental evidence: 4,4#,<2>
DO Expression/Regulation: +mitogen
RF Cell34:779 EMBOJ2:2375 MCB7:1393 MCB7:2988
//
4.3.1. The FP line
The FP line contains the following fields and subfields:
|
|
|
|
- The promoter name begins with a species code usually followed by a gene locus or gene product name. Species codes consist of the initials of genus and species name. Occasionally, three characters are required to generate unique codes. Standard abbreviations identify viruses. The full names of the organisms are given in appendix B.1. Subspecies or strains are specified in parentheses. Chromosomal locations (genetic or cytogenetic loci, genomic map units, etc.) may appear in square brackets immediately following species codes. Many gene products are referred to by abbreviations explained in appendix B.3. Alternative promoters are identified by right-justified "P" and a digit indicating the corresponding initiation site numbered sequentially from 5' to 3'. An optional "E" and digit refers to the corresponding 5'exons, if known. Identical numbers indicate 3'co-terminal exons. The strongest initiation site is marked by trailing + if known (see also List of alternative promoters)
- genome db codes currently used are 'EM' for EMBL database, and 'EU' for genome contigs or chromosomal genome assemblies of the RefSeq database.
- The EMBL accession number always relates to the first EMBL cross-reference. This one is usually the longest promoter region except when the entry is cancelled from the EMBL database, but still present in GenBank or DDBJ.
- The sequence type indicates whether the sequence is circular or linear. A sequence comprising exactly one repeat unit of a tandem repeat cluster is also considered circular. Note that the annotation as circular or linear sequences in EPD is not always in agreement with the corresponding annotation in EMBL.
- The entry code is a five-digit number which is the only part of a promoter entry that is stable from release to release.
- Alternative promoter identification code: Genes represented by multiple promoter entries in EPD are assigned a promoters group number. The corresponding initiation sites are numbered sequentially from 5' to 3'.
4.3.2. DO lines: Documentation
Documentation of promoter entries is presented on lines starting with "DO". They are essentially free format and so far not processed by specific programs. In the present release, there are two DO lines per entry, the first referring to the transcript mapping experiments that define the promoter, the second giving information about expression and regulation.The varies experimental techniques are identified by number codes.The "Medline's number" and/or "example" in brackets are linked, respectively, to the abstract and/ or to the full text article describing the related experiment.| codes | experiments |
|---|---|
| 1 | Direct RNA sequencing (1634116) |
| 2 | Length measurement of an RNA product (1989694) |
| 3 | Nuclease protection : Length measurement of a nuclease-protected complementary RNA or DNA fragment (2845126) (8294473) |
| 4 | RNA sequencing by primer extension : by dideoxy-terminated primer extension (3396543) |
| 5 | Sequencing of a full-length cDNA (8294473) |
| 6 | Primer extension : Length measurement of a primer extension product (10187799 , example) (9880555 , example) |
| 7 | DNA sequencing of a full-length processed pseudogene (3584116) |
| 8 | Reverse direction primer extension with homologous sequence ladder : Length measurement of an in vitro synthesised DNA primed upstream of the initiation site and blocked by the 5'end of the RNA hybridized to the template (2451027) |
| 9 | Rapid amplification of cDNA ends (RACE) (9116864) |
| 10 | RNA sequencing, type not specifed |
| 11 | Oligo-capping : artificial capping of mRNA followed by sequencing of the 5' end of cDNA (11375929, 11337467 and examples) |
| 12 | Mammalian gene collection (MGC) full-length cDNA cloning (10521335 and example) |
| 13 | 5' end confirmed by alignment of first 100 downstream nucleotides to EST database. |
| 14 | Oligo-capping: Berkeley Drosophila Genome Project (12537569) |
| 15 | Oligo-capping: Rice full-length cDNA cloning (12869764) |
Special characters appended to the number codes designate an
experimental
gene expression system where the RNA for the corresponding experiments
was synthesized.
| * | RNA POL II in vitro system |
| o | injected amphibian oocytes |
| # | transfected or transformed cells, injected neurons |
| ! | transgenic organisms |
| r | experiments performed with closely related gene |
| h | homologous sequence ladder used for length measurement of nuclease protection or primer extension product |
| l | low-precision data (error > +/- 5 bp) |
- The full-length assumption of a cDNA clone or a proccessed pseudogene is based on consistency with accompanying nuclease-protection or primer extension data or, alternatively, the existence of multiple 5'coterminal clones or pseudogenes.
- Semicolon delimits the two fields : expression and regulation.
- Comma delimits alternative keywords (e.g. liver, kidney)
- "+" means "induced by" or "strongly expressed in".
- "-" means "repressed by" or "weakly expressed in".
- "~" means "modulated by".
- Cell cycle stages are given in square brackets.
4.3.3. RF line: Literature references
The first four references from the RN, RX,
RA,
RT and RL lines are repeated in a highly condensed form. Each reference
is spaced by 15 letters and indicates journal, volume, and starting
page
of the referred article (maximal 14 letters). The journal code
explained
in Appendix B.2.
They primarily point to the articles where the experimental promoter
evidence is presented. Additional potential subjects are homology to
other
promoters, gene expression and regulation, nomenclature. Papers
containing
only sequence data are usually not referred to because they are easy to
find via the corresponding EMBL sequence entry descriptions.
4.3.4. Miscellaneous
- Greek letters are sometimes represented by corresponding latin letters followed by apostrophe:
- Sub- and superscripts are sometimes indicated by preceding "_" and "^", respectively.
| a' = alpha | b' = beta | g' = gamma | d' = delta | e' = epsilon |
| z' = zeta | h' = eta | th'= theta | k' = kappa | l' = lambda |
| n' = nu | r' = rho |
4.4. Distinct format of 'preliminary' entries in epd_bulk.dat
4.4.1. The title line:
TI epd83 Bulk Section Eukaryotic Promoter Database / Release 83 EP
4.4.2. The ID line
The identification line is always the first line of an entry. The form of the ID line in 'epd_bulk.dat' is:ID OS_bAAAA preliminary; undefined; TAXONOMIC DIVISION.
- An unique entry identifier "OS_bAAAA" is contructed using the species identification code ('OS') with at most 4 alphanumeric characters representing the biological source of the promoter and a 'b' (for bulk) followed by an arbitrary 4 letter code
- "preliminary" data class field indicates that the entry has not (yet) undergone all quality checks necessary for being classified as "standard".
- "undefined" as initiation site type due to insufficient data to define transcription initiation patterns (Section 3).
- TAXONOMIC DIVISION are
- PLN for plant
- NEM for nematode
- ART for arthropode
- MLS for mollusc
- ECH for echinoderm
- VRT for vertebrates.
4.4.3. The AC line
AC EP00001;The accession number consists of the character string "EP" followed by 5 digits. Previously the first two digits of the AC designated the release number of initial appearance of the specific entry followed by the EPD entry order. AC numbers in 'epd_bulk.dat' are continuous numbers, excluding ACs already used for entries in the main file 'epd.dat'.
5 CLASSIFICATION
Starting from release
72,
the classification system is no longer maintained. New entries are
presently
added by default to an '?Unclassified' category. The classification
system
might still provide valuable information for entries added before
release
72. However for any category, consider the possible existence of
additional,
potentially corresponding EPD entries in the default categories.
The entries of the Eukaryotic Promoter Database are embedded
in a hierarchical
classification
system. A promoter's taxonomic location is made clear by interspersed
group
headings. The example shown below is taken from top of the database. A
contrasting format has been chosen to emphasize the very different
nature
of this information.
*----------------------------------------------------------------------*A group heading consists of a series of node numbers and a title. The highest classification level distinguishes between promoters active in major eukaryotic taxa (phyla). Further below, grouping considers replicon type and functional properties of gene products. On the lowest level, homology (as defined in section 6) is the criterion. A survey of the upper part of the classification pyramid is presented in appendix A.The proposed classification system has a highly tentative character as it is often unclear how a new promoter should be classified, especially if the gene product is a multifunctional protein. Users should therefore not be surprised or discouraged if they don't find a promoter at the initially expected place.
* 1. Plant promoters *
*----------------------------------------------------------------------*
* 1.1. Chromosomal genes *
*----------------------------------------------------------------------*
* 1.1.1. Small nuclear RNAs *
*----------------------------------------------------------------------*
6 HOMOLOGOUS PROMOTERS
Homology is defined as sequence similarity due to common phylogenetic origin. In EPD, two promoters are considered homologous if they exhibit >=50% sequence similarity between -79 and +20. Similarity is calculated from optimal alignments generated with the aid of the UWGCG subroutine ShiftAlign (13) using the following symbol comparison table:| A | C | G | N | T | |
| 1.0 | 0.0 | 0.0 | 0.5 | 0.0 | A |
| 1.0 | 0.0 | 0.5 | 0.0 | C | |
| 1.0 | 0.5 | 0.0 | G | ||
| 0.5 | 0.5 | N | |||
| 1.0 | T |
Gap weight and gap length weight are specified as 3 and 0,
respectively.
Terminal gaps are ignored. Percent similarity is understood as
alignment
score divided by segment length, times 100. Groups of homologous
promoters
are identified by homology group numbers (see 4.2.1.). Definition of
these
groups is based on similarity scores as defined above and a tree
generation
method called UPGMA (14).
In a few cases, similarities between 50% and 56% were ignored
if the protein sequences of the corresponding genes were not related.
Similarities
were also ignored between alternative promoter sequences that are
spaced
by less than 50 bp. A subset of "independent" promoters is
marked
by "+" in column 27 of the FP line. This set contains only one member
per
homology group (usually, the promoter with the longest upstream
sequence
available) and is intended to be used for statistical analysis of
functional
patterns where it is important to avoid bias by multiples of closely
related
sequences.
7 PROMOTER SEQUENCE RETRIEVAL
Promoter sequence listings have not been incorporated into EPD for two reasons: (i) to avoid duplication of data already existing elsewhere in the EMBL data library, and (ii) to encourage usage of FPS-dependent sequence retrieval programs which enables the user to specify suitable 5'- and 3'boundaries of the requested sequence segments himself. Effort is under way to motivate producers of standard nucleotide sequence analysis packages to provide such tools in the future. In the meantime, users with some programming experience will find it easy to write their own routines. Our local sequence extraction programs run in a UWGCG environment (13) and have been implemented at several sites in Europe and the United States. They are documented and freely available on request.8 REFERENCES
- Bucher, P. & Trifonov, E.N., Compilation and analysis of eukaryotic POL II promoter sequences, Nucl. Acids Res. 14, 10009-10026 (1986). (3808945)
- Bucher, P. & Bryan, B., Signal search analysis: a new method to localize and characterize functionally important DNA sequences, Nucl. Acids Res. 12, 287-305 (1984). (84118736)
- Stoesser, G., Tuli,M.A., Lopez, R. and Sterk, P., The EMBL nucleotide sequence database, Nucleic Acids. Res., 27, 18-24 (1999). (99063644)
- Benson, D.A., Boguski, M.S., Lipman, D.J., Ostell, J., Ouellette B.F.F, Rapp, B:A: and Wheeler, D.L., GenBank, Nucleic Acids. Res., 27, 12-17 (1999). (99063643)
- Sugawara, H., Miyazaki, S., Gojobori, T. and Tateno, Y.,DNA Data Bank of Japan dealing with large-scale data submission, Nucleic Acids. Res., 27, 25-28 (1999). (99063645)
- Bairoch, A. and Apweiler, R., The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999, Nucleic Acids Res., 27, 49-54 (1999). (99063650)
- Heinemeyer, T., Chen, X., Karas, H., Kel, A.E., Kel, O.V., Liebich, I., Meinhardt, T., Reuter, I., Schacherer, F. and Wingender, E., Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms, Nucleic Acids. Res., 27, 318-322 (1999). (99063727)
- The FlyBase consortium, The FlyBase database of the drosophilia genome projects and community litterature, Nucleic Acids. Res., 27,85-88 (1999). (99063659)
- Pearson, P., Francomano, C., Foster, P., Bocchini, C., Li, P. and McKusick, V., The status of online Mendelian inheritance in man (OMIM) medio 1994, Nucleic Acids Res., 22, 3470-3473 (1994). (95023074)
- Blake, J.A., Richardson, J.E., Davisson, M.T., Eppig, J.T. and the Mouse Genome Database Group, The Mouse Genome Database (MGD): genetic and genomic information about the laboratory mouse, Nucleic Acids Res., 27, 95-98 (1999). (99063661)
- Suzuki Y., Yamashita R., Nakai K., Sugano S., DBTSS: database of human transcriptional start sites and full-length cDNAs. Nucleic Acids Res. 30(1):328-331(2002). (11752328)
- Strausberg, R.L., Feingold, E.A., Klausner, R.D., Collins, F.S., The Mammalian Gene Collection. Science, 286, 455-457 (1999). (10521335)
- Devereux,J., Haeberli,P., & Smithies,O. A comprehensive set of sequence analysis programs for the VAX, Nucl. Acids Res. 12, 387-395 (1984). (84118744)
- Sneath,H.A. & Sokal,R.R., Numerical taxonomy, W.H. Freemann, San Francisco, London (1973).
- Stapleton M., Liao GC., Brokstein P., Hong L., Carninci P., Shiraki T., Hayashizaki Y., Champe M., Pacleb J., Wan K., Yu C., Carlson J., George R., Celniker S., and Rubin GM., The Drosophila Gene Collection: Identification of Putative Full-Length cDNAs for 70% of D. melanogaster Genes. Genome Res., 12:1294-1300 (2002). (12176937)
- Schmid C.D., Praz V., Delorenzi M., Périer R., and Bucher P., The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucleic Acids Res. 32, D82-5 (2004). (14681364)
A. APPENDIX A : SURVEY OF RELEASE
B. APPENDIX B : CODES AND ABBREVIATIONS
B.1. SPECIES CODES
B.2. JOURNAL CODES
| Code | Journal name |
|---|---|
| ARB | Annual Review of Biochemistry |
| ARP | Annual Review of Physiology |
| BBA | Biochimica Biophysica Acta |
| BBRC | Biochemical and Biophysical Research Communications |
| Bch | Biochemistry |
| Bchi | Biochimie |
| BchJ | Biochemical Journal |
| BCHS | Biological Chemistry Hoppe-Seyler |
| BrJR | British Journal of Rheumatology |
| BrainR | Brain Research |
| Btech | Biotechnology |
| CanR | Cancer Research |
| Cell | Cell |
| CGD | Cell Growth Differentiation |
| Chrom | Chromosoma |
| CSHS | Cold Spring Harbor Symposia on Quantitative Biology |
| CTMI | Current Topics in Microbiology and Immunology |
| CurG | Current Genetics |
| DCB | DNA and Cell Biology |
| DevB | Developmental Biology |
| Diab | Diabetes |
| DNA | DNA |
| ECR | Experimental Cell Research |
| EJBc | European Journal of Biochemistry |
| EJCB | European Journal of Cellular Biology |
| EMBOJ | EMBO Journal |
| EMBOR | EMBO Reports |
| Evo | Evolution |
| FEBS | FEBS Letters |
| GDev | Genes and Development |
| Gene | Gene |
| GChC | Genes Chromosomes Cancer |
| GnmR | Genome Research |
| Gnms | Genomics |
| Gnts | Genetics |
| HGEN | Human Genetics |
| IJCa | International Journal of Cancer |
| ImTo | Immunology Today |
| JBC | Journal of Biological Chemistry |
| JBch | Journal of Biochemistry |
| JCB | Journal of Cell Biology |
| JEM | Journal of Experimental Medicine |
| JGV | Journal of General Virology |
| JI | Journal of Immunology |
| JMAG | Journal of Molecular and Applied Genetics |
| JMB | Journal of Molecular Biology |
| JME | Journal of Molecular Evolution |
| JMEnd | Journal of Molecular Endocrinology |
| JNeSc | Journal of Neuroscience |
| JVir | Journal of Virology |
| MB | Molecular Biology |
| MBE | Molecular Biology and Evolution |
| MBM | Molecular Biology and Medicine |
| MBR | Molecular Biology Reports |
| MCB | Molecular and Cellular Biology |
| MCEnd | Molecular and Cellular Endocrinology |
| MEnd | Molecular Endocrinology |
| MImm | Molecular Immunology |
| MEnz | Methods in Enzymology |
| MGG | Molecular and General Genetics |
| MNeub | Molecular Neurobiology |
| MPMI | Molecular Plant-Microbe Interactions |
| NAR | Nucleic Acids Research |
| Nat | Nature |
| Oncg | Oncogene |
| OncR | Oncogene Research |
| Pla | Planta |
| PlJ | Plant Journal |
| PMB | Plant Molecular Biology |
| PSL | Plant Science Letters |
| RPHR | Recent Progress in Hormone Research |
| PNAS | Proceedings of the National Academy of Sciences of the United States of America |
| Sci | Science |
| SCMG | Somatic Cell and Molecular Genetics |
| TiG | Trends in Genetics |
| Vir | Virology |
| VirR | Virus Research |
B.3. ABBREVIATIONS
| 1-25OH2D3 | 1,25-(OH)_2 vitamin D_3 |
| 20-OHE | 20-Hydroxyecdysone |
| 4CL | 4-coumarate coenzyme A ligase |
| a1 | Gene locus 1 involved in anthocyanin biosynthesis |
| abd-g. | Abdominal ganglion |
| abl | Abelson murine leukemia virus oncogene |
| ACC | 1-aminocyclopropane-1-carboxylic acid |
| AChR | Acetylcholin receptor |
| ACP | b'-ketoacyl-acyl carrier protein of fatty acid synthase |
| ACTH | Adrenocorticotropic hormone |
| ADA | Adenosine deaminase |
| ADH | Alcohol dehydrogenase |
| ADPg-s | GT ADPglucose-starch glucosyltransferase |
| adult-HA | Adult hermaphrodite |
| AFW1 | Adult fast-white (myosin heavy chain) 1 |
| Ag | Antigen |
| (AGM) | "from african green monkey" |
| AGP | Acid glycoprotein |
| AGPP | ADP glucose pyrophosphorylase |
| AIRS | Aminoimidazole ribonucleotide synthase |
| ALA-synt. | 5-Aminolevulinate synthase |
| ALDH_2 | Aldehyde dehydrogenase 2 |
| AlkExo | Alkaline exonuclease |
| Amy | Amylase |
| antp | "antennapedia" locus |
| aP2 | Adipocyte homologue of myelin P2 |
| apolipop. | Apolipoprotein |
| apoVLDLII | Very low densitiy apolipoprotein II |
| APRT | Adenine phosphoribosyltransferase |
| AR | Adrenergic receptor |
| ARF | ADP-ribosylation factor |
| arg | Arginine |
| AS | Argininosuccinate synthetase |
| AS-C | "achaete-scute" complex locus |
| AspAT | Aspartate aminotransferase |
| ass. | Associated |
| AT | Antitrypsin |
| ATIII | Antithrombin III |
| ATCase | Aspartate transcarbamylase |
| ATP | Adenosinetriphosphate |
| awd | "abnormal wing disk" locus |
| BB | Bowman-Birk (protease inhibitor) |
| BCKDHA | Branched-chain alpha-keto acid dehydrogenase complex |
| Bcl-2 | B-cell leukemia/lymphoma 2 proto-oncogene |
| BMMC | Bone marrow-derived mast cell |
| BPTI | Bovine pancreatic trypsin inhibitor |
| BSF | B-cell stimulating factor |
| bsg25D | Blastoderm specific locus 25D |
| c- | Cellular protooncogene .. |
| c1 | Regulatory locus of anthocyanin synthesis (maize) |
| C4BP | Complement component C4-binding protein |
| CA | Carbonic anhydrase |
| CAD | Carbamoyl-phosphate synthetase (glutamine-hydrolysing)/aspartate carbamoyl transferase/dihydroorotase |
| cab | Chlorophyll a/b-binding protein |
| cAMP | Cyclic AMP (Adenosinemonophosphate) |
| card-m. | Cardiac muscle |
| cc-ind. | Cell cycle-independent |
| CD3 | T-cell differentiation antigen CD3 |
| CD4 | T-cell differentiation antigen CD4 |
| CD8 | T-cell differentiation antigen CD8 |
| CEA | Carcinoembryonic antigen |
| CG | Chorionic gonadotropin |
| CNS | Central nervous system |
| CNTF | Ciliary neurotrophic factor |
| car. | Cartilage |
| col. | Collagen |
| conglyc. | Conglycinin |
| cor. | Cornea |
| cotyl. | Cotyledon |
| cp | Cytoplasm(ic) |
| CPS | Carbamyl-phosphate synthetase |
| CRF | Corticotropin-releasing factor |
| CRP | C-reactive protein |
| cs | Cytosol(ic) |
| CSF | Colony stimulating facter |
| cyt | Cytokinin gene (coding for isopentenyltransferase) |
| DAF | Decay-accelerating factor |
| dbp | DNA binding protein |
| DDC | DOPA decarboxylase |
| DDH | Dihydrodiol dehydrogenase |
| dep. | dependent |
| dev. | Development(ally) |
| DHFR | Dihydrofolate reductase |
| diff. | differentiation, differentiated |
| DL/R | Left and right duplicated region |
| dnc | "dunce" locus |
| dUTPase | Deoxyuridinetriphosphatase |
| E | 1. Early, 2. Erythroid cell-specific |
| E8 | Ethylene inducible gene during fruit ripening 8 |
| EAS | 5-epi-aristolochene synthase (sesquiterpene cyclase) |
| EBNA | Epstein-Barr virus nuclear antigens |
| ecd-ind. | Ecdysone-inducible |
| EDF | Eosinophil differentiation factor |
| EFW1 | Embryonic fast-white (myosin heavy chain) 1 |
| EGF | Epidermal growth factor |
| EIa | Adenovirus early Ia region (transactivating element) |
| Eip | Ecdysone-induced protein |
| ELH | Egg-laying hormone |
| em | Embryo, embryonic |
| epithel | epithelial or epithelium |
| EPSP | 5-Enolpyruvylshikimate-3-phosphate |
| erbA,B | (Avian) erythroblastosis virus oncogene A,B |
| E-resp. | Estrogen-responsive |
| ERV3 | Endogenous retrovirus 3 |
| E.Tn | Early transposon |
| et-hypocot. | Etiolated hypocotyl |
| ev1 | (Avian) endogenous virus 1 |
| eve | "even-skipped" locus |
| exch. | Exchanger |
| f. | Factor |
| fib. | Fibers |
| fibrob. | Fibroblasts |
| FMRFamide | Phe-Met-Arg-Phe-NH(2) neuropeptide |
| FNR | Ferredoxin-(NADP+)-oxidoreductase |
| FBP | Folate Binding Protein |
| fos | FBJ (Finkel-Biskis-Jinkins) osteosarcoma virus oncogene |
| FSH | Follicle stimulating hormone |
| ftz | "fushi tarazu" locus |
| g. | Gene |
| G0S.. | G0/G1 switch regulatory gene .. |
| G6PD | Glucose-6-phosphate dehydrogenase |
| GA | Gibberellic acid |
| GADPH | Glyceraldehyde-3-phosphate dehydrogenase |
| GARS | Glycinamide ribonucleotide synthase |
| Gart | "Gart" locus (-> GARS, AIRS, GART) |
| GART | Glycinamide ribonucleotide transformylase |
| gC | Glycoprotein C |
| G-CSF | Granulocyte colony stimulating factor |
| gD | Glycoprotein D |
| GdX | X-linked gene downstream of G6PD gene |
| gE | Glycoprotein E |
| GFAP | Glial fibrillary acidic protein |
| g'GT | g'-Glutamyl transpeptidase |
| gln | Glutamine |
| globul-12s | 12s globulin (oat seed storage protein) |
| glucc | Glucocorticoid |
| GLUT1 | Glucose transporter type 1 |
| GM-CSF | Granulocyte/Macrophage colony stimulating factor |
| GnRH | Gonadotropin-releasing hormone |
| gp | Glycoprotein |
| GPD | Glycerol-3-phosphate dehydrogenase |
| GPT | UDP-GlcNAc:dolichol phosphate N-acetylglucosamine-1-phosphate transferase |
| granulo-c | Granulocyte |
| GRF | Growth hormone-releasing factor |
| GRP | Glycine-rich (cell wall) protein |
| GS17 | Gastrula-specific transcript 17 |
| GSHPx | Gluthathione peroxidase |
| G-spec. | Gastrula-specific |
| GST | Gutathione S-transferase |
| H | 1. Heavy chain, 2. Housekeeping-type promoter |
| Ha-ras | Rat-derived Harvey murine sarcoma virus oncogene |
| haptoblob | haptoglobin |
| hb | "hunchbank" locus |
| Hc | High-cysteine (chorion protein) |
| HDC | L-histidine decarboxylase |
| hematop. | hematopoietic |
| HGT | High-(glycine+tyrosine) keratin |
| hist. | Histone |
| HMG- | High mobility group chromosomal protein |
| HMG-CoA | 3-Hydroxy-3-methylglutaryl coenzyme A |
| HPRT | Hypoxanthine phosphoribosyltransferase |
| hs | Heatshock |
| hsc | Constitutive analogue of heatshock gene/protein |
| HSF | Hepatocyte-stimulating factor |
| hsp | Heatshock protein |
| Ht | Testicular histone |
| HTF | Restriction endonuclease HpaII tiny fragments |
| I-FABP | Intestinal fatty-acid binding protein |
| IAA | Indolacetic acid |
| IAP | Intracisternal A-particles |
| ICP | Infected cell protein |
| IE | Immediate early (gene, RNA) |
| IF | Intermediate filament |
| IFI | Interferon-induced gene/protein |
| IFN | Interferon |
| Ig | Immunoglobulin |
| IGF | Insulin-like growth factor |
| IL | Interleukin |
| inf. | Infected |
| inh. | Inhibitor |
| iNOS | Inducible nitric oxide synthase |
| IRF | Interferon regulatory factor |
| ISG | Interferon-stimulated gene |
| k. | Kinase |
| keratino-c | Keratinocyte |
| Ki-ras | Rat-derived Kirsten murine sarcoma virus oncogene |
| L | 1. Light chain; 2. Late |
| larva-1,2,.. | First, second, .. instar larva |
| LAT.. | Lycopersicon anther-specific gene .. |
| LCAT | Lecithin-cholesterol acyltransferase |
| lck | T-cell- or lymphocyte-specific tyrosine kinase |
| LDH | Lactate dehydrogenase |
| leghem. | Leghemoglobin |
| LeIF | Leukocyte interferon |
| leuko-c | Leukocyte |
| LH | Luteinizing hormone |
| LHC | Light-harvesting complex |
| LHRH | Luteinizing hormone-releasing factor |
| liv. | liver |
| LMW | Low molecular weight |
| LPH | Lipotropic hormone |
| LPS | Lipopolysaccharide |
| LTR | Long Terminal Repeat |
| lympho-c | Lymphocyte |
| lys | Lysosomal |
| MBP | Myelin basic protein |
| (MAC) | Macaque |
| MC | Methylcholanthrene |
| MCK | Muscle-specific creatine kinase |
| mGK | Submaxillary gland kallikrein |
| MHCI/MHCII | Class I/II transplantation antigens of major histocompatibility complex |
| MIF | Macrophage migration inhibitory factor |
| minipara | Miniparamyosin |
| mit | Mitochondrial |
| mono-c | Monocyte |
| mononuc-c. | Mononuclear cells |
| MOPC.. | Mineral oil-induced plasmacytoma |
| mos | Moloney murine sarcoma virus oncogene |
| MP | Macrophage |
| MPC.. | Mouse plasma cell tumor |
| MRP | MIF-related protein (see MIF) |
| MSF | Megakaryocyte stimulating factor |
| msp | Major sperm protein gene |
| MT | Metallothionein |
| mst | Male-specific transcript |
| MUP | Major urinary protein |
| myb | (Avian) myeoloblastosis virus oncogene |
| myc | Myelocytomatosis virus 29 oncogene |
| NCA | nonspecific cross-reacting (with -> CEA) antigen |
| nerv. sys | Nervous system |
| neu | Ethyl-nitrosurea-induced rat neuroblastoma oncogene |
| neuropep. | Neuropeptide |
| NGF | Nerve growth factor |
| ninaE | "neither inactivation nor afterpotential" locus E |
| NMDH | NADP-malate dehydrogenase |
| NOS | Nitric oxide synthase |
| nos | Nopaline synthetase |
| NR | Nitrate reductase |
| N-ras | Neuroblastoma ras-like (-> Ha-ras) oncogene |
| NS | Nervous system |
| OAT | Ornithine aminotransferase |
| ocs | Octopine synthetase |
| ODC | Ornithine decarboxylase |
| Ori | Origin of replication |
| OTC | Ornithine transcarbamylase |
| ovalb. | Ovalbumin |
| p. | Protein |
| P-450 | Cytochrome P-450 |
| p53 | 53K phosphoprotein |
| panc. | pancreas, pancreatic |
| parath. | Parathyroid |
| PB | Phenobarbital |
| PBGD | Porphobilinogen deaminase |
| PCNA | Proliferating cell nuclear antigen |
| PDEase | cAMP phosphodiesterase |
| PDGF | Platelet-derived growth factor |
| PEPCase | Phosphoenolpyruvate carboxylase |
| PEPCK | Phosphoenolpyruvate carboxykinase |
| PG | Prostaglandin |
| PGK | 3-Phosphoglycerate kinase |
| PHA | Phytohemagglutinin |
| PK | Protein kinase |
| P_L | Late promoter |
| PLP | Proteolipid protein |
| POL | Polymerase |
| POMC | Proopiomelanocortin |
| pp.. | Phosphoprotein .. |
| PR1a | Pathogenesis-related protein 1a |
| PRBP | Plasma retinol-binding protein |
| PRL | Prolactin |
| prog. | Progesterone |
| prolyl | 4-hydr. Prolyl 4-hydroxylase |
| PrP | Prion protein |
| PSG1,PSG2,. | Pregnancy-specific glycoproteins 1,2,. |
| PSBP | Prostatic steroid binding protein |
| PSP | Parotid secretory protein |
| PTH | Parathyroid hormone |
| pTiN | Nopaline type tumor inducing plasmid |
| pTiO | Octopine type tumor inducing plasmid |
| r | "rudimentary" locus |
| R | 1. Regulatory subunit, 2. Erythroid cell-specific |
| RAB | Gene responsive to ABA |
| ras | Homologue of -> Ha-ras, Ki-ras, etc. |
| rec. | Receptor |
| red. | Reductase |
| reg. | Regulated |
| rep-dep. | Replication-dependent |
| rig | Rat insulinoma gene |
| RnBP | Renin-binding protein |
| RNR1, | RNR2 Ribonucleotide reductase large, small subunit |
| rp | Ribosomal protein |
| rTn | Retrotransposon |
| RuBPCss | Ribulose-1,5-biphosphate carboxylase small subunit |
| RuBPCA | Ribulose-1,5-biphosphate carboxylase/oxygenase activase |
| s. | Small |
| saliv-g. | Salivary gland |
| SBP | Spermine-binding protein |
| SC | Stem cells |
| sem-v. | Seminal vesicle |
| ser. | Serum |
| sgs | Salivary gland secretion protein |
| sis | Simian sarcoma virus oncogene |
| sk-m. | Skeletal muscle |
| skel-m. | Skeletal muscle |
| smooth-m. | Smooth muscle |
| snRNA | Small nuclear RNA |
| snRNA | Small nuclear ribonucleoprotein |
| SOD | Superoxide dismutase |
| som | Somatic |
| spat-reg. | Spatially regulated |
| Spec | Strongylocentrotus purpureatus ectoderm enriched RNA |
| SPI | Serine protease inhibitor |
| sry | "serendipity" locus |
| SV40T | Tumor antigen of simian virus 40 (SV40) |
| SVS | Seminal vesicle secretory protein |
| synt. | Synthase |
| T3d' | T-cell antigen receptor-associated T3-complex delta chain |
| TAT | Tyrosine aminotransferase |
| TCDD | 2,3,7,8-Tetrachlorodibenzo-p-dioxin |
| TCGF | T-cell growth factor |
| TCR | T-cell receptor |
| TdT | Terminal deoxynucleotidyltransferase |
| test. | testis |
| TF | Transcription factor |
| TGA1a | TGACG-specific DNA-binding protein 1a |
| TGF-b' | Transforming growth factor beta |
| TH | Tyrosin hydroxylase |
| thyr. | Thyroxine |
| Thy-1.2 | Thy-1 (thymocyte) antigen/glycoprotein allotype 2 |
| TIF | Trans-inducing factor |
| TIM | Triosephosphate isomerase |
| tis. | Tissue |
| TM | Tropomyosin |
| tmr | "tumor morphology root" locus |
| TNF | Tumor necrosis factor |
| TnI | Troponin I (inhibitory subunit) |
| TnT | Troponin T (tropomyosin-binding subunit) |
| TO | Tryptophan oxygenase |
| TP1,TP2,. | Transition protein 1,2,. |
| TPA | 12-O-tetradecaonyl-phorbol-13-acetate |
| TPI | Triosephosphate isomerase |
| tr.,tr- | Transcript |
| TRF | T-cell replacing factor |
| TRH | Thyrotropin-releasing hormone |
| TS | Thymidylate sythetase |
| TSH | Thyroid stimulating hormone |
| T/t | Large/small T(tumor) antigen |
| Ubx | "ultrabithorax" locus |
| uPA | Urine plasminogen activator |
| URO-D | Uroporphyrinogen decarboxylase |
| Vg1 | Vegetal hemisphere-specific mRNA 1 |
| vir-inf. | Viral infection |
| VL30 | Retrovirus-like 30s RNA |
| VLDL | Very low density lipoprotein |
| V_NP | (Immunoglobulin heavy chain) variable region specific for 4-hydroxyl-3-nitrophenacetyl |
| VP5 | Virion protein 5 (HSV-1/2: =major capsid protein) |
| VSP | Virion stimulatory protein |
| vWf | von Willebrand factor |
| Zen | "zerknuellt" protein |
Last update November 2016