Gene
Athaliana AT1G11850
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_AT1G11850 AT1G11850 |
Chr1 | 3999199 | 3999876 | 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_AT1G11850.1 AT1G11850.1 PAC:19655565 |
Low | No | 582 | Get ORF Coding potential... Type: noncoding Potential: -0.637 Folding energies... MFEI: -27.732 AMFE: -0.633 GC content %: 43.814 | |
| Athaliana_AT1G11850.2 AT1G11850.2 PAC:19655563 |
Low | No | 675 | Get ORF Coding potential... Type: noncoding Potential: -0.477 Folding energies... MFEI: -27.422 AMFE: -0.623 GC content %: 44.000 | |
| Athaliana_AT1G11850.3 AT1G11850.3 PAC:19655566 |
Low | No | 504 | Get ORF Coding potential... Type: noncoding Potential: -0.705 Folding energies... MFEI: -25.516 AMFE: -0.637 GC content %: 40.079 | |
| Athaliana_AT1G11850.4 AT1G11850.4 PAC:19655564 |
Low | No | 591 | Get ORF Coding potential... Type: noncoding Potential: -0.604 Folding energies... MFEI: -27.682 AMFE: -0.624 GC content %: 44.332 |
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_AT1G11850.3 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy-44_BD-LTR | |
| Athaliana_AT1G11850.4 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy-44_BD-LTR | |
| Athaliana_AT1G11850.1 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy-44_BD-LTR | |
| Athaliana_AT1G11850.2 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy-44_BD-LTR |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
