Gene
Athaliana AT1G28395
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 | Source | Assembly | Species | Details
|
|---|---|---|---|---|---|---|---|
| Athaliana_AT1G28395 AT1G28395 |
Chr1 | 9969321 | 9971681 | Phytozome | TAIR10 | Arabidopsis_thaliana | 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 | Sequence | Details
|
|---|---|---|---|---|---|
| Athaliana_AT1G28395.1 AT1G28395.1 PAC:19658037 |
Low | No | 507 | Get ORF Coding potential... Type: noncoding Potential: -1.230 Folding energies... MFEI: -24.576 AMFE: -0.513 GC content %: 47.929 | |
| Athaliana_AT1G28395.2 AT1G28395.2 PAC:19658038 |
Low | No | 635 | Get ORF Coding potential... Type: noncoding Potential: -1.291 Folding energies... MFEI: -25.827 AMFE: -0.566 GC content %: 45.669 | |
| Athaliana_AT1G28395.3 AT1G28395.3 PAC:19658039 |
Low | No | 540 | Get ORF Coding potential... Type: noncoding Potential: -1.207 Folding energies... MFEI: -22.870 AMFE: -0.510 GC content %: 44.815 | |
| Athaliana_AT1G28395.4 AT1G28395.4 PAC:19658040 |
Low | No | 772 | Get ORF Coding potential... Type: noncoding Potential: -1.314 Folding energies... MFEI: -23.407 AMFE: -0.553 GC content %: 42.358 | |
| Athaliana_AT1G28395.5 AT1G28395.5 PAC:19658041 |
Low | No | 783 | Get ORF Coding potential... Type: noncoding Potential: -1.043 Folding energies... MFEI: -22.069 AMFE: -0.522 GC content %: 42.273 |
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_AT1G28395.5 | SwissProt | 2015-06-01 | Q93ZJ3 | 1.0e-9 |
| Athaliana_AT1G28395.1 | SwissProt | 2015-06-01 | Q93ZJ3 | 1.0e-10 |
| Athaliana_AT1G28395.2 | SwissProt | 2015-06-01 | Q93ZJ3 | 2.0e-10 |
| Athaliana_AT1G28395.3 | SwissProt | 2015-06-01 | Q93ZJ3 | 1.0e-10 |
| Athaliana_AT1G28395.4 | SwissProt | 2015-06-01 | Q93ZJ3 | 5.0e-9 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
