The home page gives a brief about the resource and provides various search options with few examples each. The resource can be searched on the basis of chromosome, genomic loci, nearest gene, biotypes or the transcript IDs. Statistical information of the datasets has been provided alongwith a description of the schema used for classification of the transcripts into four different categories.

Search Result

Searching with either of the query options the user is directed to the list of transcripts satisfying the query. It details the genomic information corresponding to each transcript that includes the chromosome, start position, stop position, strand, corresponding class to which the transcript belongs, nearest gene and its length, distance of the transcript from the nearest gene and the author who has reported the transcript. The complete transcript information can be seen by selecting the transcript ID.

Result Page

The result page starts with a brief description in context to the genomic location of the transcript. This section informs the transcript name, type into which the transcript has been classified, genomic location of the transcript and the gene nearest to the transcript. This is followed by a diagrammatic representation of the exonic regions within the transcript. The genomic co-ordinates of the exons can be known by hovering over each exon.

Transcript names have been provided based on the nonmenclature conventions described as follows:

Transcript Description	Nonmenclature	Examples
Intronic transcripts	{Gene name}ia{numeral}	elavl4ia, arfgap1ia1, rnf150aia1
Overlapping Transcripts	{Gene name}oa{numeral}	irx6aos1, irx6aos2, irx6aos3
Promoter Associated Transcripts	{Gene name}pa{numeral}	chn1pa, si:dkey-281i8.1pa, dhrs9pa2
lincRNA highly expressed in blood	rakt{numeral}	rakt1, rakt2, rakt3
lincRNA highly expressed in brain	mstx{numeral}	mstx1, mstx2, mstx3
lincRNA highly expressed in heart	hrid{numeral}	hrid1, hrid2, hrid3
lincRNA highly expressed in kidney	vrkk{numeral}	vrkk1, vrkk2, vrkk3
lincRNA highly expressed in liver	ykrt{numeral}	ykrt1, ykrt2, ykrt3
lincRNA having negligible expression, no detectable expression or no specific expression pattern	lnc{numeral}_{Nearest gene name}	lnc_ccne1, lnc2_aktip, lnc2_psmc3
lincRNA with no specific expression pattern and no nearest gene detected	lnc{numeral}	lnc1, lnc2, lnc3

The classification of transcripts has been done based on the following criteria:

Type	Description	Example
Intronic	Transcripts that fall completely within the intron of a gene	ZF_LNC000319
lincRNA	Transcripts found to be falling within two genes	ZF_LNC002002
Overlapping	Transcripts having an overlap of atleast 1bp with a protein coding exon	ZF_LNC000167
Promoter Associated	Transcripts having an overlap of atleast 1bp with the promoter 5kb upstream of the TSS of a protein coding gene	ZF_LNC002139

Genome Browser

The entire genome can be explored with unparalled speed through the genome browser embedded on the result page. Various feature tracks have been provided to visualize localised annotations on each of the transcript.



	Feature	Description	Curation
1.	Reference Sequence	The track reports the genomic sequence of Zebrafish	Reference sequence for Zv9 assembly reported by RefSeq is used.
2.	lncRNA	The track represents 2,267 transcripts with the nonmenclature as described above.	Derived from the studies by Ulitsky et. al. (2011), Pauli et. al. (2012) and Kaushik et.al. (2013).
3.	Exons	The track represents the exonic regions within the transcripts.	The exonic co-ordinates are used after merging the transcript information provided by the three studies taken into consideration using cuffmerge.
4.	Nearest Gene	This track shows the gene nearest to each of the predicted lncRNA.	The information has been retrieved by parsing the ENSEMBL gene list for Zebrafish lncRNA to detect the coordinates of genes nearest to the predicted lncRNA.
5.	Ensembl Genes	The track depicts the genomic location of all the genes reported for Zebrafish till date.	The ENSEMBL gene list for danRer7 Zv9 assembly has been used.
6.	Variations	The track represents all the variations reported for Zebrafish till date.	The list of variations reported for Zebrafish in ENSEMBL release-76 has been used.
7.	Expression Levels	29 tracks from the three studies depict the corresponding stage specific or tissue specific expression.	Alignment maps were generated for the sequencing reads available from each stage specific or tissue specific sample provided by the three studies on SRA.
8.	Histone Modification	20 tracks depict the epigenetic regulation of transcripts by reporting the position of histone modification marks (H3K27ac, H3K27me3, H3K36me3, H3K4me1, and H3K4me3) predicted by different stage specific studies.	Chip-Seq data was retrieved from all the stage specific studies available on SRA.







Expression Information

Expression levels across 10 developmental time points and 5 adult tissues are calculated using Cuffdiff and represented graphically with log10 FPKM values plotted across different stages. More than 10 fold expression levels are reported in the graph. For less than 10 fold expression a statment "Negligible Expression across 15 developmental stages" is shown and in case of 0 FPKM values detected for all the stages - "No Detectable Expression across 15 developmental stages" is shown. log10FPKM values can be known by hovering over the bars corresponding to each stage.




Mutant Information

Retroviral insertions from publically available datasets have been systematically mapped to the exons of each lncRNA transcript. This information can be used for understanding the biological mechanisms and phenotypes associated with particular lncRNA. The table reports genomic location of the mutation with its ZFIN id which is linked to ZFIN, an online biogical database for Zebrafish.




Predicted Open Reading Frames

Open Reading Frames for each of the exon within the transcript were predicted and reported in the database with their corresponding coordinates and sequences.




Variant Information

This section reports all the variations that lie within the exonic region of the transcript. The table provides information about variant position along with its respective reference nucleotide, alternate nucleotide and rsID linked to dbSNP.