Kfedtschenkoi Kaladp0088s0122
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
|
|---|---|---|---|---|---|---|
| Kfedtschenkoi_Kaladp0088s0122 [ Kaladp0088s0122] |
Scaffold_88 | 1248570 | 1250627 | v1.1 | Kalanchoe fedtschenkoi (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
|
|---|---|---|---|---|---|---|
| Kfedtschenkoi_Kaladp0088s0122.1 Kaladp0088s0122.1 |
Low | Yes | 1476 | OG0019644 | Get ORF Coding potential... Type: noncoding Potential: -1.178 Folding energies... MFEI: -28.367 AMFE: -0.731 GC content %: 38.821 | |
| Kfedtschenkoi_Kaladp0088s0122.2 Kaladp0088s0122.2 |
Low | Yes | 1543 | OG0019644 | Get ORF Coding potential... Type: noncoding Potential: -1.250 Folding energies... MFEI: -28.354 AMFE: -0.735 GC content %: 38.561 | |
| Kfedtschenkoi_Kaladp0088s0122.3 Kaladp0088s0122.3 |
Low | Yes | 1328 | OG0019644 | Get ORF Coding potential... Type: noncoding Potential: -1.232 Folding energies... MFEI: -29.089 AMFE: -0.734 GC content %: 39.608 |
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 |
|---|---|---|---|---|
| Kfedtschenkoi_Kaladp0088s0122.1 | Rfam | 14.6 | MIR159 | 8.1e-36 |
| Kfedtschenkoi_Kaladp0088s0122.2 | Rfam | 14.6 | MIR159 | 8.5e-36 |
| Kfedtschenkoi_Kaladp0088s0122.3 | Rfam | 14.6 | MIR159 | 7.3e-36 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
