Gene
Ahalleri Araha.6046s0002
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
|
|---|---|---|---|---|---|---|---|
| Ahalleri_Araha.6046s0002 Araha.6046s0002 |
Scaffold6046 | 9686 | 12263 | Phytozome | [[Species:|]]"Species:" cannot be used as a page name in this wiki. | 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
|
|---|---|---|---|---|---|
| Ahalleri_Araha.6046s0002.1 Araha.6046s0002.1 PAC:28850245 |
Low | Yes | 1139 | Get ORF Coding potential... Type: noncoding Potential: -1.228 Folding energies... MFEI: -22.616 AMFE: -0.661 GC content %: 34.241 | |
| Ahalleri_Araha.6046s0002.2 Araha.6046s0002.2 PAC:28850242 |
Low | Yes | 758 | Get ORF Coding potential... Type: noncoding Potential: -1.169 Folding energies... MFEI: -22.190 AMFE: -0.612 GC content %: 36.280 | |
| Ahalleri_Araha.6046s0002.3 Araha.6046s0002.3 PAC:28850243 |
Low | Yes | 1069 | Get ORF Coding potential... Type: noncoding Potential: -1.213 Folding energies... MFEI: -23.386 AMFE: -0.672 GC content %: 34.799 | |
| Ahalleri_Araha.6046s0002.4 Araha.6046s0002.4 PAC:28850241 |
Low | Yes | 680 | Get ORF Coding potential... Type: noncoding Potential: -1.153 Folding energies... MFEI: -21.574 AMFE: -0.604 GC content %: 35.735 | |
| Ahalleri_Araha.6046s0002.5 Araha.6046s0002.5 PAC:28850244 |
Low | Yes | 991 | Get ORF Coding potential... Type: noncoding Potential: -1.204 Folding energies... MFEI: -23.350 AMFE: -0.681 GC content %: 34.309 | |
| Ahalleri_Araha.6046s0002.6 Araha.6046s0002.6 PAC:28850246 |
Low | Yes | 828 | Get ORF Coding potential... Type: noncoding Potential: -1.196 Folding energies... MFEI: -20.918 AMFE: -0.591 GC content %: 35.386 |
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 |
|---|---|---|---|---|
| Ahalleri_Araha.6046s0002.1 | Rfam | 11.0 | mir-156 | 3.8e-18 |
| Ahalleri_Araha.6046s0002.2 | Rfam | 11.0 | mir-156 | 2.5e-18 |
| Ahalleri_Araha.6046s0002.3 | Rfam | 11.0 | mir-156 | 3.5e-18 |
| Ahalleri_Araha.6046s0002.4 | Rfam | 11.0 | mir-156 | 2.2e-18 |
| Ahalleri_Araha.6046s0002.5 | Rfam | 11.0 | mir-156 | 3.3e-18 |
| Ahalleri_Araha.6046s0002.6 | Rfam | 11.0 | mir-156 | 2.7e-18 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
