Dicty cDB is a publicly available gene information database comprising the primary sequence information obtained by EST analysis of Dictyostelium discoideum, which is known as a social amoeba, and a variery of additional secondary information. This database represents the results of the Dictyostelium cDNA Project in Japan for Dictyostelium discoideum.
| Data name | README |
| Description of data contents | HTML file to describe "Dicty_cDB" data. |
| File | README_e.html(English) |
| Data name | EST sequences and their annotation (amino acid sequence and results of homology search) |
| Description of data contents |
Sequences of cDNA clones of Dictyostelium discoideum and their annotations (amino acid sequence, homology search results (with target DBs: dicty EST-DB, DNA-DB and protein-DB)). Links to the Atlas database (http://dictycdb.biol.tsukuba.ac.jp/~tools/bin/ISH/index.html), which is the database of images depicting localization of clones in Dictyostelium discoideum, the National BioResource Project (http://www.nbrp.jp/) and the dictyBase (http://dictybase.org/) are provided. Link to the table of contigs containing EST sequences is also provided. For each clone, the following four categories are established: 5' EST sequence, 3' EST sequence, 5' EST-3'EST-ligated sequence and full-length cDNA sequence. If both 5' EST sequence and 3' EST sequence are available, the treatment to ligate the 5' EST sequence to the 3' EST sequence is peformed to generate a sequence connecting the two sequences with ten pieces of hyphen. If an overlapped region exists between the two sequences, the sequence obtained by overlapping is considered as a full-length sequence. For some clones that do not allow overlapping, the full-length is obtained by sequencing the gap region. F, Z, P and E are added to the end of the Clone ID to identify 5' EST sequence, 3' EST sequence, 5' EST-3'EST-ligated sequence and full-length cDNA sequence. For each clone, these sequences are stored on a single line. Among these sequences, one sequence is selected as the representative sequence by prioritizing full-length cDNA sequence, 5' EST-3'EST-ligated sequence, 5' EST sequence and 3' EST sequence in this order, and the BLAST-based homology search is performed. Search is performed by the blastn search against clone sequences of dicty_cDB, the DNA sequence in public database, and blastx search against the protein sequence in public database, and then the top 10 hit information is stored. CSV format text file. |
| File | dicty_cdb_clone.zip (181MB) |
| Data item | Description |
|---|---|
| IDs and Links | |
| Library | 14 different sequenced cDNA libraries (AF, AH, CF, CH, FC, FC-IC, FCL, SF, SH, SL, SS, VF, VH and VS) derived from five developmental stages. |
| Clone ID | ID of cDNA clone |
| Atlas ID | ID of Atlas database (http://dictycdb.biol.tsukuba.ac.jp/~tools/bin/ISH/index.html) and link to Atlas database |
| NBRP ID | ID of cDNA clone covering full-length ORF provided by the National BioResource Project (http://www.nbrp.jp/). The link to the "National BioResource Project (NBRP) Dictyostelium discoideum" gene database (http://nenkin.lab.nig.ac.jp/genes?locale=en) is provided in the TogoDB edition. |
| dictyBase ID | ID of Protein Coding Gene in dictyBase (http://dictybase.org/). The link to dictyBase is provided in the TogoDB edition. |
| Link to Contig | Link to contig containing EST (TogoDB edition only) |
| Representative Seq. and Annotation | |
| Representative seq. ID | ID of DNA sequence used in homology search. Among these sequences, one sequence is selected as the representative DNA sequence by prioritizing 1) full-length cDNA sequence, 2) 5' EST-3'EST-ligated sequence, 3) 5' EST sequence and 4) 3' EST sequence in this order. |
| Representative DNA sequence | Representative DNA sequence |
| sequence update | Last update of representative DNA sequence |
| Translated Amino Acid sequence | Amino acid sequence translated from representative DNA sequence |
| Translated Amino Acid sequence (All Frames) | Amino acid sequences resulting from translation in all six reading frames of DNA sequence |
| Homology vs CSM-cDNA | List of top 10 hits in blastn search against the clone sequence in dicty_cDB |
| own update | Last update of homology search against CSM (a set of clone sequences) |
| Homology vs DNA | List of top 10 hits in blastn search against DNA sequences in public database |
| dna update | Last update of homology search against DNA sequences in public database |
| Homology vs Protein | List of top 10 hits in blastx search against protein sequences in public database |
| protein update | Last update of homology search against protein sequences in public database |
| PSORT | The results of PSORT (http://psort.ims.u-tokyo.ac.jp/), which is a program to predict the subcellular localization of proteins. |
| Seqeunces | |
| 5' end seq. ID | ID of 5' EST sequence. "F" is added to the end of ID. |
| 5' end seq. | 5' EST sequence. FASTA format. |
| Length of 5' end seq. | Length of 5' EST sequence. |
| 3' end seq. ID | ID of 3' EST sequence. "Z" is added to the end of ID. |
| 3' end seq. | 3' EST sequence. FASTA format. |
| Length of 3' end seq. | Length of 3' EST sequence. |
| Connected seq. ID | ID of 5' EST-3' EST-ligated sequence. "P" is added to the end of ID. |
| Connected seq. | Sequence of 5' EST ligated to 3' EST by 10 gaps (-). |
| Length of connected seq. | ID of 5' EST-3' EST-ligated sequence. (Gap (-) are not counted.) |
| Full length Seq ID | ID of full-length cDNA. "E" is added to the end of ID. |
| Full length Seq. | Full-length cDNA sequence. FASTA format. |
| Length of full length seq. | Length of full-length cDNA. |
| Data name | Contig sequences and their annotation (amino acid sequence and results of homology search), and expression profile |
| Description of data contents |
Contig sequences of cDNA sequences of Dictyostelium discoideum and their annotation (amino acid sequence and results of homology search (with target DBs: contig sequence-DB, DNA-DB and protein-DB)). Contig sequences are obtained by assemblying 5' EST sequence, 3' EST sequence, 5' EST-3'EST-ligated sequence and full-length cDNA sequence by the assembly program Phrap (http://www.phrap.org/index.html). Link to the list of clones constituting the contig, the information on its mapping to the genome mapped to genome sequence and the list of top 10 hits in the results of homology search are provided. Also, the number of clones constituting the contig in each library is given for five developmental stages and 14 different libraries. Library-specific clones can be searched. The data are given in a CSV format text file. |
| File | dicty_cdb_contig.zip (91.6MB) |
| Data item | Description |
|---|---|
| Contig information | |
| Contig ID | ID of contig sequence |
| Contig update | Last update of sequence |
| Contig sequence | Contig sequence |
| Gap | Presence of gap (-) in contig. -If gap is included: gap included. -If gap is not included: no gap. |
| Contig length | Length of contig |
| Chromosome number (1..6, M) | Chromosome number of the chromosome to which the contig is mapped. If mapped, numbers 1 to 6 or M (mitochondria) will be used. |
| Chromosome length | Length of the chromosome to which the contig is mapped. |
| Start point | Start position of the contig mapped to the genome. |
| End point | End position of the contig mapped to the genome. |
| Strand (PLUS/MINUS) | Direction of the contig mapped to the genome (PLUS/MINUS) |
| Number of clones | Number of clones constituting the contig |
| Number of EST | Number of ESTs constituting the contig |
| Link to clone list | Link of all clones constituting contig to TogoDB edition. Link to the clone list is provided in the TogoDB edition only. |
| List of clone(s) | List of clones constituting contig. Link to each clone is provided in the TogoDB edition only. |
| Annotation | |
| Translated Amino Acid sequence | Representative amino acid sequence translated from DNA sequence. |
| Translated Amino Acid sequence (All Frames) | Amino acid sequences resulting from translation in all six reading frames of DNA sequence. |
| own update | Last update of blastn search against contig sequences in dicty_cDB. |
| Homology vs CSM-cDNA | List of top 10 hits in blastn search against contig sequences in dicty_cDB. |
| dna update | Last update of blastn search against DNA sequences in public database. |
| Homology vs DNA | List of top 10 hits in the results of blastn search against DNA sequences in public database. |
| protein update | Last update of blastx search against protein sequences in public database. |
| Homology vs Protein | List of top 10 hits in the results of blastx search against protein sequences in public database. |
| PSORT | The results of running PSORT(http://psort.ims.u-tokyo.ac.jp/), which is the program to predict the localization of proteins in the cell. |
| Expression profile | |
| VS (DIR, S) | Number of VS-derived clones constituting the contig |
| VH (FL, L) | Number of VH-derived clones constituting the contig |
| VF (FL, S) | Number of VF-derived clones constituting the contig |
| AH (FL, L) | Number of AH-derived clones constituting the contig |
| AF (FL, S) | Number of AF-derived clones constituting the contig |
| SL (DIR, L) | Number of SL-derived clones constituting the contig |
| SS (DIR, S) | Number of SS-derived clones constituting the contig |
| SH (FL, L) | Number of SH-derived clones constituting the contig |
| SF (FL, S) | Number of SF-derived clones constituting the contig |
| CH (FL, L) | Number of CH-derived clones constituting the contig |
| CF (FL, S) | Number of CF-derived clones constituting the contig |
| FCL (DIR, L) | Number of FCL-derived clones constituting the contig |
| FC (DIR, S) | Number of FC-derived clones constituting the contig |
| FC-IC (SUB) | Number of FC-IC-derived clones constituting the contig |
| Data name | cDNA library information |
| Description of data contents |
Description of cDNA libraries of Dictyostelium discoideum (Functional Genomics of the Social Amoebae, Dictyostelium discoideum, Hideko Urushihara, Mol. Cells, Vol. 13, No. 1, pp. 1-4, http://molcells.inforang.com/article_pdf/Ksmcb/13/Ksmcb13-1-1.pdf, http://dictycdb.biol.tsukuba.ac.jp/cDNAproject.html, http://lifesciencedb.jp/houkoku/pdf/001/c009.pdf) |
| File | dicty_cdb_lib.zip (1KB) |
| Data item | Description |
|---|---|
| cDNA library name | Names of cDNA libraries (AF, AH, CF, CH, FC, FC-IC, FCL, SF, SH, SL, SS, VF, VH and VS) |
| stages of the life cycle | Stages in the life cycle of Dictyostelium discoideum 1) vegetatively growing cells (Vegetative phase)(V) 2) asexually developing cells at the aggregating (Aggregation phase)(A) 3) slug cells (Slug phase)(S) 4) culminating stages (Morphogenetic phase)(C) 5) sexually fusion-competent KAX3 cells (Gamete phase) (F) |
| cDNA library construction method | How to construct cDNA library 1) Conventional oligo-d(T) primed, directional cDNA libraries (dir) 2) Full-length cDNA libraries (oligocapped method)(fl) 3) Gamete-specific subtraction library (sub) |
| cDNA library construction protocol | Link to the webpage describing the protocol for generating cDNA library |
| Size fractionation | Size fractionation of clone 1) Fractionation of long clone (long) 2) Fractionation of short clone (short) 3) No fractionation (no) |
| clone size | Clone size(kb) |
The Standard License specifies the license terms regarding the use of this database and the requirements you must follow in using this database.
The Additional License specifies those items that are exceptionally permitted even though they are generally prohibited in the Standard License.
The Standard License for this database is the license specified in the
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If you use data from this database, please be sure attribute this database as follows:
"Dicty_cDB, Copyright© 2009 Hideko Urushihara (University of Tsukuba) licensed under CC Attribution-Share Alike 2.1 Japan".
The summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found
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With regard to this database, you are licensed to:
under the Standard License, as long as you comply with the following conditions:
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2. When you conduct research by using this database, and describe the research results in an article or paper, you always need to cite this database, and specify the name and URL of this database in the article or paper.
3.You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the Standard License and the above Additional License.
Hideko Urushihara
Graduate School of Life and Environmental Sciences, Department of Biological Sciences, University of Tsukuba
1-1-1 Ten-noudai, Tsukuba, Ibaraki
305-8572
Tel: +81-29-853-4664
FAX: +81-29-853-6614
E-mail: hideko[at]biol[dot]tsukuba[dot]ac[dot]jp
You can freely provide links to all contents in this database. But, contents might be changed without notice.
| Date | Update contents |
| 2015/01/09 | The original website information was updated. |
| 2010/03/29 | Dicty_cDB English archive site is opened. |
| 2009/8 | Data is updated. |
| 1996/12 | Dicty_cDB(http://dictycdb.biol.tsukuba.ac.jp/cDNA/database.html) is released. |
Hideko Urushihara
Graduate School of Life and Environmental Sciences, Department of Biological Sciences, University of Tsukuba
1-1-1 Ten-noudai, Tsukuba, Ibaraki
305-8572
Tel: +81-29-853-4664
FAX: +81-29-853-6614
E-mail: hideko[at]biol[dot]tsukuba[dot]ac[dot]jp