Search help

Select search target

A 'search target' is a set of entries that a user would like to search.

In this form, you can designate one search target from pre-defined sets, previous search results and new sets made by the user.

Pre-defined sets
This database has 4 pre-defined set(s) as follows.
- All sequences
- FANTOM1 sequences (21,076 sequences)
- FANTOM2 sequences (60,770 sequences)
- FANTOM3 new sequences
In order to select a pre-defined set:
1. Select one radio button attached to a name of a set.
2. A selected search target will be switched automatically. If not changed, push the 'switch' button.
Previous search results
If you have already searched for entries in the database, you can search within a previously searched set.
In order to select a previous result:
1. When the previous results are hidden, click 'search within the previous results' label
2. Select one radio button.
3. A selected search target will be switched automatically. If not changed, push the 'switch' button.
New sets made by the user
You can make a new search target by specifying identifiers of entries or by combining among pre-defined sets and previous search results.
In order to make a new set:
1. Specifying identifiers of entries
  1. Click 'make new search target' label, and then input forms will be shown.
  2. Select a type of identifiers
  3. Input a name of the list (this field is optional)
  4. Input ID list. Identifiers should be separated with a space or ',' characters.
  5. Push the 'submit' button
2. Combining among pre-defined sets and previous results
  1. Click 'make new search target' label, and then input forms will be shown.
  2. Check boxes of two or more sets in listed pre-defined sets and previous results
  3. Select 'intersect' or 'union', which is a logical operation to combine the sets
  4. Push the 'submit' button
In both cases, the created set was recorded as a previous search result.

Library search

In this form, you can search for entries by libraries that their cDNA clones were derived from.

Push the 'Show library list' button. A list of library identifiers and names are shown.
Do (A) or (B).
A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

Keyword search for automated annotation

In this form, you can search for entries by keywords in automated annotations.

Input keywords.
Push the 'submit' button. A list of entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

ID random search

By pushing the 'submit' button, one randomly picked annotation page will be shown. It is chosen in the selected search target.

ID search

In this form, you can search for entries with their identifiers

Select a type of identifiers. You can search for entries with the following types:
- Clone ID
- (FANTOM 3) Sequence ID
- Rearray ID
- DDBJ Accession in HTC
- DDBJ Accessions in EST
- (FANTOM 2) Sequence ID
- (FANTOM 1) Sequence ID
- MGI Clone Accession
- MGI Marker Accession
You can also select 'Any ID types', which means that all ID types are tried.
Input an entry's ID
Push the 'submit' button

If only one entry is found, an annotation page of the entry will be shown.

Keyword search for curated annotation

In this form, you can search for entries by keywords in annotations of following qualifiers.

Chimeric clone note (clone_chimera_note)
Reverse clone note (clone_reverse_note)
CDS note (cds_note)
Transcript description (transcript_desc_name)
Transcript description symbol (transcript_desc_symbol)
Transcript description synonym (transcript_desc_synonym)
Transcript description category (transcript_desc_category)
Transcript description status (transcript_desc_status)
Transcript description note (transcript_desc_note)
Non-coding Transcript description note (nc_transcript_desc_note)
Gene Ontology (gene_ontology)
Gene Ontology rejected (gene_ontology_rejected)
Gene Ontology note (gene_ontology_note)

Check boxes for qualifiers to be searched.
If multiple qualifiers are selected, the system will retrieve entries containing keywords (satisfying conditions) in any of selected qualifiers.

note: GO IDs can be used as keywords (e.g. GO:0004364)
Input keywords.
Push the 'submit' button. A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

Basic keyword search

If you would like to search for entries that contain a specific word, you may write the word in the first text box.

For example: searches for entries that contain the word 'binding'.

Keyword searches are executed case-insensitively, which means that the keywords 'RNA' and 'rna' are regarded as the same.

'And' keyword search

If you write multiple words in the box, the system searches for entries that containing all words.

For example: searches for entries that contain 'actin' and 'binding'.

'Not' keyword search

If you wish to searches for entries that contain specific words and DON'T contain other specific words, you should attach the minus('-') character before the word not to be contained.

For example: searches for entries that contain 'actin' without containing 'interacting.

'Or' keyword search

If you would like to search for entries that one of specific words, you should write each word in each box.

For example:

or
searches for entries that contain 'insulin' or 'receptor'.

You can combine 'and', 'or' and 'not' searches.

Automated annotation category search

In this form, you can search for entries by annotation categories with automated annotations.

Push the 'show category list' button. A list of category names are shown.
Do (A) or (B).
A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

InterPro search

In this form, you can search for entries by identified InterPro motifs/domains/families/sites with a program package 'InterProScan'.

If you know the InterPro ID (e.g. IPR000001) that you wish to search,

Input InterPro ID.
Push the 'submit' button. A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

If you would like to see a list of all InterPro identifiers and descriptions,

Push the 'Show InterPro list' button. A list of InterPro identifiers are shown.
Do (A) or (B).
A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

Pfam search

In this form, you can search for entries by identified Pfam motifs/domains/families/sites with a detection program 'estwisedb' in the Wise2 package.

If you know the Pfam name (e.g. GP120) that you wish to search,

Input Pfam name. (This search is case sensitive)
Push the 'submit' button. A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

If you would like to see a list of all Pfam names and descriptions,

Push the 'Show Pfam list' button. A list of Pfam names are shown.
Do (A) or (B).
A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

Gene Ontology search

In this form, you can search for entries by automatically assigned Gene Ontology terms.

If you know the Gene Ontology ID (e.g. GO:0005634) that you wish to search,

Input Gene Ontology ID.
Push the 'submit' button. A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

If you would like to see a list of all Gene Ontology identifiers and terms,

Push the 'Show GO list' button. A list of Gene Ontology identifiers are shown.
Do (A) or (B).
A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

Rfam search

In this form, you can search for entries by identified Rfam motifs with Infernal.

If you know the Rfam ID (e.g. RF00032) that you wish to search,

Input Rfam ID.
Push the 'submit' button. A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

If you would like to see a list of all Rfam ID and descriptions,

Push the 'Show Rfam list' button. A list of Rfam ID is shown.
Do (A) or (B).
A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

miRNA search

In this form, you can search for entries by detected miRNA precursor.

Push the 'Show miRNA list' button. A list of miRNA names are shown.
Do (A) or (B).
A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

snoRNA search

In this form, you can search for entries by detected snoRNA.

Push the 'Show snoRNA list' button. A list of snoRNA names are shown.
Do (A) or (B).
A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

Repeat search

In this form, you can search for entries by identified repeat elements with the program 'RepeatMasker'.

Push the 'Show repeat list' button. A list of repeat names are shown.
Do (A) or (B).
A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

Membrane Orgnization Class search

In this form, you can search for entries by libraries that their cDNA clones were derived from.

Push the 'Show membrane organization class list' button. A list of Membrane Organization Classes are shown.
Do (A) or (B).
A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

DNA sequence length search

In this form, you can search for entries by DNA sequence lengths.

If you would like to search for entries whose lengths in a specific region,

Input lower bound of lengths. (0 if not specified)
Input upper bound of lengths. (unlimited if not specified).
Push the 'submit' button. A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

If you wish to see a distribution of lengths,

Push the 'Show distribution' button. A histogram of lengths are shown.
Click a region of lengths. A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

AA sequence length search

In this form, you can search for entries by amino acid sequence lengths.

If you would like to search for entries whose lengths in a specific region,

Input lower bound of lengths. (0 if not specified)
Input upper bound of lengths. (unlimited if not specified).
Push the 'submit' button. A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

If you wish to see a distribution of lengths,

Push the 'Show distribution' button. A histogram of lengths are shown.
Click a region of lengths. A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

Predicted CDS length search

In this form, you can search for entries by predicted CDS lengths.

If you would like to search for entries whose lengths in a specific region,

Select a CDS predicting method.
Input lower bound of lengths. (0 if not specified)
Input upper bound of lengths. (unlimited if not specified).
Push the 'submit' button. A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

If you wish to see a distribution of lengths,

Select a CDS predicting method. (Lower and upper bounds are ignored)
Push the 'Show distribution' button. A histogram of lengths are shown.
Click a region of lengths. A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

Mapped position search

In this form, you can search for entries by coordination in the genome.

Input chromosome number or 'Un'.
Input start base position to search
Input stop base position to search
Push the 'submit' button. A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

Cis-antisense category search

In this form, you can search for entries by cis-antisense category (Kiyosawa et al., 2003)

Push the 'show category list' button. A list of category names are shown.
Do (A) or (B).
A list of matched entries are shown.
Click an entry, and you can see an annotation page of the entry. You can additionally search for entries within them by clicking a 'search within the result' label.

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RIKEN (The Institute of Physical and Chemical Research) / NTT Software Corporation.