Athaliana AT2G43780
From GreeNC
This table contains information about coordinates, assembly and annotation regarding the lncRNA-transcribing gene. In details, it shows whether this this gene transcribes any protein-coding transcript.
| Gene alias / name | Chrom. | Start | End | Assembly | Species | Details
|
|---|---|---|---|---|---|---|
| Athaliana_AT2G43780 AT2G43780 |
Chr2 | 18136108 | 18137803 | v11 | Arabidopsis thaliana (Phytozome 13) | Coding? No |
This table shows how a lncRNA has been classified (high/low confidence) or whether it has been classified as pre-miRNA (go to FAQ for classification criteria). Besides, it displays the lncRNA length and sequence as well as information about the ORF, the coding potential calculated by the Coding Potential Calculator (CPC), and the folding energies calculated by RNAfold.
| Transcript alias / name | Confidence | Pre-miRNA | Length | Orthologous group | Sequence | Details
|
|---|---|---|---|---|---|---|
| Athaliana_AT2G43780.1 AT2G43780.1 |
High | No | 813 | OG0009669 | Get ORF Coding potential... Type: noncoding Potential: -0.983 Folding energies... MFEI: -24.748 AMFE: -0.583 GC content %: 42.435 | |
| Athaliana_AT2G43780.2 AT2G43780.2 |
Low | No | 917 | OG0009669 | Get ORF Coding potential... Type: noncoding Potential: -1.007 Folding energies... MFEI: -25.016 AMFE: -0.650 GC content %: 38.495 | |
| Athaliana_AT2G43780.3 AT2G43780.3 |
High | No | 780 | OG0009669 | Get ORF Coding potential... Type: noncoding Potential: -0.975 Folding energies... MFEI: -25.064 AMFE: -0.598 GC content %: 41.923 | |
| Athaliana_AT2G43780.4 AT2G43780.4 |
Low | No | 891 | OG0009669 | Get ORF Coding potential... Type: noncoding Potential: -0.760 Folding energies... MFEI: -23.906 AMFE: -0.623 GC content %: 38.384 |
The lncRNAs from GreeNC have been analysed against the following databases: SwissProt, miRBase, Rfam, RepBase (RepeatMasker), NONCODE, and lncRNAdb. This table displays any association with these databases.
| Transcript alias | Database | Version | Hit | Evalue |
|---|---|---|---|---|
| Athaliana_AT2G43780.4 | RepBase (RepeatMasker) | 2014-01-31 | DNA/PIF-Harbinger | |
| Athaliana_AT2G43780.2 | RepBase (RepeatMasker) | 2014-01-31 | DNA/PIF-Harbinger |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
