Gene
Zmays GRMZM2G396483
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
|
|---|---|---|---|---|---|---|---|
| Zmays_GRMZM2G396483 GRMZM2G396483 |
1 | 84072323 | 84077716 | Phytozome | 6a | Zea_mays | 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
|
|---|---|---|---|---|---|
| Zmays_GRMZM2G396483_T01 GRMZM2G396483_T01 PAC:31013607 |
High | No | 884 | Get ORF Coding potential... Type: noncoding Potential: -0.985 Folding energies... MFEI: -25.566 AMFE: -0.501 GC content %: 51.018 | |
| Zmays_GRMZM2G396483_T02 GRMZM2G396483_T02 PAC:31013605 |
Low | Yes | 1426 | Get ORF Coding potential... Type: noncoding Potential: -1.156 Folding energies... MFEI: -34.376 AMFE: -0.678 GC content %: 50.701 | |
| Zmays_GRMZM2G396483_T03 GRMZM2G396483_T03 PAC:31013606 |
Low | Yes | 1480 | Get ORF Coding potential... Type: noncoding Potential: -1.171 Folding energies... MFEI: -34.189 AMFE: -0.664 GC content %: 51.486 | |
| Zmays_GRMZM2G396483_T04 GRMZM2G396483_T04 PAC:31013604 |
High | No | 486 | Get ORF Coding potential... Type: noncoding Potential: -1.013 Folding energies... MFEI: -29.753 AMFE: -0.476 GC content %: 62.551 | |
| Zmays_GRMZM2G396483_T05 GRMZM2G396483_T05 PAC:31013611 |
Low | No | 2149 | Get ORF Coding potential... Type: noncoding Potential: -1.096 Folding energies... MFEI: -26.375 AMFE: -0.581 GC content %: 45.370 | |
| Zmays_GRMZM2G396483_T06 GRMZM2G396483_T06 PAC:31013610 |
Low | No | 2149 | Get ORF Coding potential... Type: noncoding Potential: -1.096 Folding energies... MFEI: -26.375 AMFE: -0.581 GC content %: 45.370 | |
| Zmays_GRMZM2G396483_T07 GRMZM2G396483_T07 PAC:31013609 |
Low | No | 2350 | Get ORF Coding potential... Type: noncoding Potential: -1.014 Folding energies... MFEI: -25.213 AMFE: -0.640 GC content %: 39.404 | |
| Zmays_GRMZM2G396483_T08 GRMZM2G396483_T08 PAC:31013608 |
Low | No | 1389 | Get ORF Coding potential... Type: noncoding Potential: -1.044 Folding energies... MFEI: -24.276 AMFE: -0.619 GC content %: 39.237 |
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 |
|---|---|---|---|---|
| Zmays_GRMZM2G396483_T07 | RepBase (RepeatMasker) | 2014-01-31 | Helitron2_ZM | |
| Zmays_GRMZM2G396483_T08 | RepBase (RepeatMasker) | 2014-01-31 | Helitron2_ZM | |
| Zmays_GRMZM2G396483_T02 | RepBase (RepeatMasker) | 2014-01-31 | TE-3-1_ZM | |
| Zmays_GRMZM2G396483_T03 | RepBase (RepeatMasker) | 2014-01-31 | TE-3-1_ZM | |
| Zmays_GRMZM2G396483_T05 | RepBase (RepeatMasker) | 2014-01-31 | Helitron2_ZM | |
| Zmays_GRMZM2G396483_T06 | RepBase (RepeatMasker) | 2014-01-31 | Helitron2_ZM |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
