Gene
Atrichopoda evm 27.TU.AmTr v1.0 scaffold00001.305
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
|
|---|---|---|---|---|---|---|---|
| Atrichopoda_evm_27.TU.AmTr_v1.0_scaffold00001.305 evm_27.TU.AmTr_v1.0_scaffold00001.305 |
AmTr_v1.0_scaffold00001 | 6137952 | 6140330 | Phytozome | v1.0 | Amborella_trichopoda | 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
|
|---|---|---|---|---|---|
| Atrichopoda_evm_27.model.AmTr_v1.0_scaffold00001.305 evm_27.model.AmTr_v1.0_scaffold00001.305 PAC:31550950 |
Low | No | 231 | Get ORF Coding potential... Type: noncoding Potential: -1.591 Folding energies... MFEI: -26.797 AMFE: -0.548 GC content %: 48.918 |
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 |
|---|---|---|---|---|
| Atrichopoda_evm_27.model.AmTr_v1.0_scaffold00001.305 | RepBase (RepeatMasker) | 2014-01-31 | Copia-127_SB-I |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
