The homepage is displayed in the following Fig 1-1.

1. Main functions of the database are provided in menu bar form (boxed in red).

2. Other databases contributed by our group.

3. Cite information.

Fig 1-1 Home page

The Exact search page is displayed in Fig 2-1:

1. Carefully select a keyword type: Two choices are provided.

2. Enter a keyword corresponding to selected dataset.

3. Three categories provided to filter results: RNA Category, Species and Subcellular Localization.

4. Use NCBI Gene/Ensembl/miRBase/RNAcentral/circBase to normalize your input information.

Fig 2-1 Exact Search page

The Fuzzy search page is displayed in Fig 2-2:

1. Select the category of your keyword.

2. Enter a keyword corresponding to selected.

Fig 2-2 Fuzzy Search page

The Batch search page is displayed in Fig 2-3:

1. Select a type for your keywords.

2. Enter the keywords or upload a file.

Fig 2-3 Batch Search page

This tutorial is as follows.

1. First we have to choose the type of keyword. There are two keyword types in our search page. In this example, we choose RNA Symbol as the keyword type.

Fig 3-1 Choose the type of keyword

2. Next, we enter the keyword according to the keyword type selected in the previous step. In this example, we choose 'ACTB' as the keyword.

Fig 3-2 Enter the keyword

3. Then select the RNA category for the keyword you entered. In this example, we choose 'mRNA' as the category of the keyword 'ACTB'.

Fig 3-3 Select the RNA category for the keyword

4. Then select the species for the keyword you entered. In this example, we choose 'Homo sapiens' as the species of the keyword 'ACTB'.

Fig 3-4 Select the species for the keyword

5. Then select the subcellular localization for the keyword you entered. In this example, we choose 'Cytosol' as the localization of the keyword 'ACTB'.

Fig 3-5 Select the subcellular localization for the keyword

6. With all the filters above, we can click 'Search' to query the result.

Fig 3-6 Click 'Search' to query the result

In the result page, all entries are listed with basic information including RNA symbols, RNA categories, species, tissue/cell lines and localizations.

Fig 4-1:

1. Your current input conditions.

2. Total sum of results.

3. Download your search results.

4. Click to turn the page.

5. Click to link to detail page.

Fig 4-1 Result page

Firstly, you can get general information including RNALocate ID, RNA symbol, and localization in the detail page.

Second, you can also get the RNA information, localization information, homology information and other subcellular localization of each entry.

Thrid, the association of ncRNA disease information and RNA interaction information also been provided.

Fig 5-1:

1. Click Localization to see its basic description in Gene Ontology database.

2. Click GO button to see its subcellular localization from RNA-seq Dataset.

Fig 5-1 Detail page of Basic Information

Fig 5-2:

1. For RNA information, RNA name from literature, RNA ID, RNA category, Species and Alias of each entry.

2. Click RNA ID to see its basic description in NCBI Gene/Ensembl/miRBase/RNAcentral/circBase/exoRBase database.

3. Click GO button to see its sequence of the RNA (detail in Fig 5-3).

Fig 5-2 Detail page of RNA Information

Fig 5-3:

Fig 5-3 Detail page of Sequence

Fig 5-4:

1. The tissue or cell line, method and description of each entry.

2. Click pubmed ID to see description in detail.

Fig 5-4 Detail page of Localization Information

Fig 5-5:

1. The association of homology information has been provided.

2. Click Go to button to search in RNALocate.

Fig 5-5 Detail page of Homology Information

Fig 5-6:

1. The other subcellular localization of this RNA has been provided.

2. Click RNALocate ID to see detail information of this entry.

Fig 5-6 Detail page of Other Subcellular Localization

Fig 5-7:

Disease information of each ncRNA in our database were provided. Click Link can see more informations about them.

Fig 5-7 Detail page of ncRNA Disease Information

Fig 5-8:

Interactions of each RNA in our database were provided. Click GO to can search more informations about them.

Fig 5-8 Detail page of RNA Interaction Information

The RNA-seq dataset search page is displayed in Fig 6-1:

Fig 6-1:

Use Ensembl Gene name or Gene stable ID as a keyword to search.

Fig 6-1

Firstly, you can get basic information about each RNA in the detail page.

Second, you can switch to the localization from literature mining search result page.

Third, you can see the subcellular localization of RNA in different RNA-seq dataset.

Fig 6-2:

1. Click Ensembl Gene Stable ID to see its description in Ensembl database.

2. Click GO button to search the localization of this RNA from literature mining.

Fig 6-2

Fig 6-3 (only in Mus musculus):

Plot: Subcellular localization (chromatin, cytoplasm and nucleoplasm) and expression of RNA under different conditions.

Table: Relative ratio of RNA expression in different location and condition, the larger of relative ratio, the more enriched RNA in this location and condition.

Note: The calculation method of relative ratio and the dataset number.

Fig 6-3

Fig 6-4:

Plot: Different subcellular localizations in individual cell type.

Table: Relative ratio of RNA expression in different locations, the larger of relative ratio, the more enriched RNA in this location.

Note: The calculation method of relative ratio and the dataset number.

Fig 6-4

Fig 6-5:

Plot: Subcellular localizations revealed by APEX-Seq.

Table: Relative ratio of RNA expression in different location and condition, the larger of relative ratio, the more enriched RNA in this location and condition.

Note: The calculation method of relative ratio and the dataset number.

Fig 6-5

Fig 6-6:

Plot: Single subcellular localization (nucleus) in different conditions.

Table: Relative ratio of RNA expression in different conditions, the larger of relative ratio, the more enriched RNA in this condition.

Note: The calculation method of relative ratio and the dataset number.

Fig 6-6

Fig 6-7:

Plot: Subcellular localizations of cytoplasm and nucleus in different cell lines.

Table: Relative C/N ratio of RNA expression in different cell lines, the larger of relative ratio, the more enriched RNA in the cytoplasm of this cell line.

Note: The calculation method of relative ratio and the dataset number.

Fig 6-7

In the browse by dataset page, we provide RNA-seq dataset that has localization information.

Fig 7-1:

1. Click download can get all RNA expression of the dataset.

2. Click more can see detail information for this dataset.

Fig 7-1 Browse page of RNA-seq Dataset

Fig 7-2:

Dataset number, species, cell line, pubmed ID and publish date were provided.

Fig 7-2 Detail information of RNA-seq Dataset

Fig 7-3:

Each sample ID, localization and condition were provided.

Fig 7-3 Sample information of RNA-seq Dataset

Fig 7-4:

Top 20 RNA expression of each sample were provided.

Fig 7-4 Sample gene expression of RNA-seq Dataset

Fig 7-5:

Top 50 RNA expression in each sample of GO enrichment result has been provided.

Fig 7-5 Sample gene GO enrichment of RNA-seq Dataset

Fig 8-1:

A deep-learning framework for multi-label mRNA subcellular localization prediction is provided.

1. Input mRNA sequence(s).

2. Click Run button.

Fig 8-1 Tool of DM3Loc

Fig 8-2:

The search results include predict subcellular localization and score.

Fig 8-2 Result of DM3Loc

Fig 8-3:

A tool for mRNA subcellular localization predict is provided.

1. Input mRNA sequence(s).

2. Click Run button.

Fig 8-3 Tool of iLoc-mRNA

Fig 8-4:

The search results include predict subcellular localization and score.

Fig 8-4 Result of iLoc-mRNA

Fig 8-5:

A tool for lncRNA subcellular localization predict is provided.

1. Input lncRNA sequence(s).

2. Click Run button.

Fig 8-5 Tool of iLoc-lncRNA

Fig 8-6:

The search results include predict subcellular localization and score.

Fig 8-6 Result of iLoc-lncRNA

Meaningful ID number is very important for data. Thus, we redefine the RNALocate ID number as follows:

RNALocate ID divided into two parts: letters and numbers.

Letters has two forms: RLID and RLID-D, the former means data from literature by manually reading, the latter means data from other databases.

Numbers are 8 digits: the first one represents subcellular localization (0-Intracellular region, 1-Extracellular region, 2-Others), the second represents RNA type (0-mRNA, 1-miRNA, 2-ncRNA, 3-snoRNA, 4-pseudo, 5-tRNA, 6-rRNA, 7-snRNA, 8-circRNA, 9-others), and the last 6 digits represents data entries.

Examples:

RLID:00016211: means the 16211th data entry of mRNA located in the Intracellular region from the literature.

RLID-D:18013509: means the 13509th data entry of circRNA located in the Extracellular region from other database.

Integration different RNA name conventions is challenging. To ensure maximal connectivity of data, we transform each RNA name found in the input sources to the appropriate naming convention.

1. For miRNA, we use miRBase ID and miRBase Accession.

2. For circRNA, we use circBase ID and exoRBase ID

3. For others, we use NCBI Gene Symbol, Entrez ID, Ensembl Gene Stable ID and RNAcentral identifier.

4. For species, we normalized organism names according to NCBI Taxonomy Database.

5. For subcellular localization, we use cellular component of Gene Ontology.