Gene
Zmays GRMZM2G063942
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_GRMZM2G063942 GRMZM2G063942 |
5 | 79567553 | 79574592 | Phytozome | 6a | Zea_mays | Coding? Yes |
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_GRMZM2G063942_T04 GRMZM2G063942_T04 PAC:30992140 |
Low | No | 4242 | Get ORF Coding potential... Type: noncoding Potential: -0.713 Folding energies... MFEI: -28.232 AMFE: -0.658 GC content %: 42.881 | |
| Zmays_GRMZM2G063942_T05 GRMZM2G063942_T05 PAC:30992141 |
High | No | 485 | Get ORF Coding potential... Type: noncoding Potential: -1.031 Folding energies... MFEI: -25.155 AMFE: -0.578 GC content %: 43.505 | |
| Zmays_GRMZM2G063942_T06 GRMZM2G063942_T06 PAC:30992139 |
Low | No | 4556 | Get ORF Coding potential... Type: noncoding Potential: -0.656 Folding energies... MFEI: -27.851 AMFE: -0.653 GC content %: 42.625 | |
| Zmays_GRMZM2G063942_T08 GRMZM2G063942_T08 PAC:30992138 |
Low | No | 4242 | Get ORF Coding potential... Type: noncoding Potential: -0.713 Folding energies... MFEI: -28.232 AMFE: -0.658 GC content %: 42.881 |
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_GRMZM2G063942_T04 | RepBase (RepeatMasker) | 2014-01-31 | hAT-18_ZM | |
| Zmays_GRMZM2G063942_T06 | RepBase (RepeatMasker) | 2014-01-31 | hAT-18_ZM | |
| Zmays_GRMZM2G063942_T08 | RepBase (RepeatMasker) | 2014-01-31 | hAT-18_ZM |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
