Gene
Csativus Cucsa.383480
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
|
|---|---|---|---|---|---|---|---|
| Csativus_Cucsa.383480 Cucsa.383480 |
scaffold03882 | 491630 | 495563 | Phytozome | v1.0 | Cucumis_sativus | 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
|
|---|---|---|---|---|---|
| Csativus_Cucsa.383480.1 Cucsa.383480.1 PAC:16982375 |
Low | Yes | 941 | Get ORF Coding potential... Type: noncoding Potential: -0.672 Folding energies... MFEI: -28.672 AMFE: -0.619 GC content %: 46.334 | |
| Csativus_Cucsa.383480.2 Cucsa.383480.2 PAC:16982376 |
Low | Yes | 1004 | Get ORF Coding potential... Type: noncoding Potential: -0.689 Folding energies... MFEI: -29.064 AMFE: -0.628 GC content %: 46.315 | |
| Csativus_Cucsa.383480.3 Cucsa.383480.3 PAC:16982377 |
Low | Yes | 994 | Get ORF Coding potential... Type: noncoding Potential: -0.686 Folding energies... MFEI: -29.376 AMFE: -0.633 GC content %: 46.378 | |
| Csativus_Cucsa.383480.4 Cucsa.383480.4 PAC:16982378 |
High | No | 1404 | Get ORF Coding potential... Type: noncoding Potential: -0.520 Folding energies... MFEI: -26.161 AMFE: -0.662 GC content %: 39.530 | |
| Csativus_Cucsa.383480.5 Cucsa.383480.5 PAC:16982379 |
Low | Yes | 1155 | Get ORF Coding potential... Type: noncoding Potential: -0.724 Folding energies... MFEI: -27.887 AMFE: -0.633 GC content %: 44.069 | |
| Csativus_Cucsa.383480.6 Cucsa.383480.6 PAC:16982380 |
Low | Yes | 1052 | Get ORF Coding potential... Type: noncoding Potential: -0.701 Folding energies... MFEI: -29.068 AMFE: -0.634 GC content %: 45.817 | |
| Csativus_Cucsa.383480.7 Cucsa.383480.7 PAC:16982381 |
Low | Yes | 1145 | Get ORF Coding potential... Type: noncoding Potential: -0.722 Folding energies... MFEI: -28.148 AMFE: -0.638 GC content %: 44.105 |
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 |
|---|---|---|---|---|
| Csativus_Cucsa.383480.5 | Rfam | 11.0 | mir-128 | 0.0049 |
| Csativus_Cucsa.383480.6 | Rfam | 11.0 | mir-128 | 0.0045 |
| Csativus_Cucsa.383480.7 | Rfam | 11.0 | mir-128 | 0.0049 |
| Csativus_Cucsa.383480.1 | Rfam | 11.0 | mir-128 | 0.004 |
| Csativus_Cucsa.383480.2 | Rfam | 11.0 | mir-128 | 0.0043 |
| Csativus_Cucsa.383480.3 | Rfam | 11.0 | mir-128 | 0.0042 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
