In this database, we described the tissue-specific NAGNAG alternative splicing events in Arabidopsis.
The explantation of the database content is as follows:
| Options | Example | Description |
|---|---|---|
| nagID | ath-nagnag100-AT1G11592 | A unique identifier describing the NAGNAG motif |
| locus | chr1:3895845-3895848_- | the two splicing sites of the NAGNAG motif |
| chr | chr1 | chromosome information |
| strand | - | strand information |
| geneID | AT1G11592 | TAIR ID that hosts the NAGNAG motif |
| site1 | 3895845 | the first NAGNAG splicing site |
| site 2 | 3895848 | the second NAGNAG splicing site |
| tissue | mixedTissue | tissue information |
| annotated NAGNAG acceptor | yes | whether or not this NAGNAG motif has been reported in TAIR10 |
| site1_splicingLink | 3895845-3895935 | the upstream and downstream splicing sites for the first NAGNAG splicing event |
| site1_exonBoundary | yes | whether or not the first NAGNAG splicing site overlaps with the reported exon boundary |
| site2_splicingLink | 3895848-3895935 | the upstream and downstream splicing sites for the second NAGNAG splicing event |
| site2_exonBoundary | yes | whether or not the second NAGNAG splicing site overlaps with the reported exon boundary |
| ratio_min | -1.253 | minimum value of the expression ratio betwen two splicing sites. Positive value means the expression of the first splicing site is higher than that of second splicing site. Nagative value means the expression of the second splicing site is higher than that of the first splicing site. |
| ratio_q1 | -0.182 | Q1 of the expression ratio between two splicing sites |
| ratio_median | 0.144 | median value of the expression ratio between two splicing sites |
| ratio_mean | 0.177 | mean value of the expression ratio between two splicing sites |
| ratio_q3 | 0.56 | Q3 of the expression ratio between two splicing sites |
| ratio_max | 1.705 | Maximum value of the expression ratio between two splicing sites |
| nag_frequency | 14/435 | the frequency of this NAGNAG splicing event. For this motif, we identified it in 14 out of 435 RNA-Seq data sets. |
| transcriptName | Parent=AT3G46210.6 | the transcript hosting this NAGNAG motif |
| locusType | 3UTR | the genome annotation of alternative splicing site, including 5UTR, exon, and 3UTR. It comes from the R package: nagnag. |
| frame | -,0,1,2 | the reading frame at the alternative splicing site |
| nagSpliceDiff | -,0,1,2 | the splicing difference of two isoforms at the NAGNAG splicing site. |
| nagType | nagnag+, nagnag++ | the splicing type, including "nagnag+", or "nagnag++". "nagnag+" means that the NAGNAG splicing site is the only difference between two isoforms. "nagnag++" means that there are more difference between two isoforms including NAGNAG splicing site. |
| firstSeq | MCYSLSIQSSIDFHNRNALKIHCMNNMVA | the upstream sequence before NAGNAG splicing site |
| lastSeq | the downstream sequence after NAGNAG splicing site, including NAGNAG splicing site | AA* |