Gene
Mtruncatula Medtr4g078770
From GreeNC
Gene information
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
|
|---|---|---|---|---|---|---|---|
| Mtruncatula_Medtr4g078770 Medtr4g078770 |
chr4 | 30438923 | 30441250 | Phytozome | Mt4.0v1 | Medicago_truncatula | Coding? No |
Transcript features
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
|
|---|---|---|---|---|---|
| Mtruncatula_Medtr4g078770.1 Medtr4g078770.1 PAC:31106989 |
Low | No | 984 | Get ORF Coding potential... Type: noncoding Potential: -0.922 Folding energies... MFEI: -22.307 AMFE: -0.582 GC content %: 38.313 | |
| Mtruncatula_Medtr4g078770.10 Medtr4g078770.10 PAC:31106985 |
Low | No | 829 | Get ORF Coding potential... Type: noncoding Potential: -0.847 Folding energies... MFEI: -21.303 AMFE: -0.550 GC content %: 38.721 | |
| Mtruncatula_Medtr4g078770.11 Medtr4g078770.11 PAC:31106990 |
Low | No | 646 | Get ORF Coding potential... Type: noncoding Potential: -0.832 Folding energies... MFEI: -20.619 AMFE: -0.508 GC content %: 40.557 | |
| Mtruncatula_Medtr4g078770.12 Medtr4g078770.12 PAC:31106986 |
Low | No | 1391 | Get ORF Coding potential... Type: noncoding Potential: -1.019 Folding energies... MFEI: -22.725 AMFE: -0.609 GC content %: 37.311 | |
| Mtruncatula_Medtr4g078770.13 Medtr4g078770.13 PAC:31106993 |
Low | No | 1724 | Get ORF Coding potential... Type: noncoding Potential: -1.066 Folding energies... MFEI: -22.111 AMFE: -0.604 GC content %: 36.601 | |
| Mtruncatula_Medtr4g078770.14 Medtr4g078770.14 PAC:31106992 |
Low | No | 908 | Get ORF Coding potential... Type: noncoding Potential: -0.945 Folding energies... MFEI: -23.359 AMFE: -0.596 GC content %: 39.207 | |
| Mtruncatula_Medtr4g078770.15 Medtr4g078770.15 PAC:31106996 |
Low | No | 1315 | Get ORF Coding potential... Type: noncoding Potential: -1.022 Folding energies... MFEI: -22.943 AMFE: -0.606 GC content %: 37.871 | |
| Mtruncatula_Medtr4g078770.16 Medtr4g078770.16 PAC:31106983 |
Low | No | 668 | Get ORF Coding potential... Type: noncoding Potential: -0.850 Folding energies... MFEI: -21.168 AMFE: -0.520 GC content %: 40.719 | |
| Mtruncatula_Medtr4g078770.17 Medtr4g078770.17 PAC:31106984 |
Low | No | 699 | Get ORF Coding potential... Type: noncoding Potential: -0.802 Folding energies... MFEI: -21.845 AMFE: -0.547 GC content %: 39.914 | |
| Mtruncatula_Medtr4g078770.2 Medtr4g078770.2 PAC:31106988 |
Low | No | 1434 | Get ORF Coding potential... Type: noncoding Potential: -1.037 Folding energies... MFEI: -23.033 AMFE: -0.616 GC content %: 37.378 | |
| Mtruncatula_Medtr4g078770.3 Medtr4g078770.3 PAC:31106997 |
Low | No | 632 | Get ORF Coding potential... Type: noncoding Potential: -0.851 Folding energies... MFEI: -21.060 AMFE: -0.499 GC content %: 42.247 | |
| Mtruncatula_Medtr4g078770.4 Medtr4g078770.4 PAC:31106994 |
Low | No | 880 | Get ORF Coding potential... Type: noncoding Potential: -0.938 Folding energies... MFEI: -21.693 AMFE: -0.561 GC content %: 38.636 | |
| Mtruncatula_Medtr4g078770.5 Medtr4g078770.5 PAC:31106999 |
Low | No | 919 | Get ORF Coding potential... Type: noncoding Potential: -0.946 Folding energies... MFEI: -22.775 AMFE: -0.578 GC content %: 39.391 | |
| Mtruncatula_Medtr4g078770.6 Medtr4g078770.6 PAC:31106991 |
Low | No | 865 | Get ORF Coding potential... Type: noncoding Potential: -0.892 Folding energies... MFEI: -23.040 AMFE: -0.588 GC content %: 39.191 | |
| Mtruncatula_Medtr4g078770.7 Medtr4g078770.7 PAC:31106987 |
Low | No | 1272 | Get ORF Coding potential... Type: noncoding Potential: -1.003 Folding energies... MFEI: -22.634 AMFE: -0.599 GC content %: 37.814 | |
| Mtruncatula_Medtr4g078770.8 Medtr4g078770.8 PAC:31106995 |
Low | No | 1605 | Get ORF Coding potential... Type: noncoding Potential: -1.056 Folding energies... MFEI: -22.131 AMFE: -0.599 GC content %: 36.947 | |
| Mtruncatula_Medtr4g078770.9 Medtr4g078770.9 PAC:31106998 |
Low | No | 1038 | Get ORF Coding potential... Type: noncoding Potential: -0.973 Folding energies... MFEI: -22.245 AMFE: -0.577 GC content %: 38.536 |
Matches to external databases
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 |
|---|---|---|---|---|
| Mtruncatula_Medtr4g078770.5 | SwissProt | 2015-06-01 | Q93ZJ3 | 1.0e-6 |
| Mtruncatula_Medtr4g078770.16 | SwissProt | 2015-06-01 | Q93ZJ3 | 4.0e-7 |
| Mtruncatula_Medtr4g078770.11 | SwissProt | 2015-06-01 | Q93ZJ3 | 4.0e-7 |
| Mtruncatula_Medtr4g078770.6 | SwissProt | 2015-06-01 | Q93ZJ3 | 9.0e-7 |
| Mtruncatula_Medtr4g078770.17 | SwissProt | 2015-06-01 | Q93ZJ3 | 7.0e-8 |
| Mtruncatula_Medtr4g078770.12 | SwissProt | 2015-06-01 | Q93ZJ3 | 2.0e-6 |
| Mtruncatula_Medtr4g078770.7 | SwissProt | 2015-06-01 | Q93ZJ3 | 2.0e-6 |
| Mtruncatula_Medtr4g078770.2 | SwissProt | 2015-06-01 | Q93ZJ3 | 3.0e-6 |
| Mtruncatula_Medtr4g078770.13 | SwissProt | 2015-06-01 | Q93ZJ3 | 3.0e-6 |
| Mtruncatula_Medtr4g078770.8 | SwissProt | 2015-06-01 | Q93ZJ3 | 3.0e-6 |
... further results
Gene models
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
