Gene
Zmays GRMZM2G011721
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_GRMZM2G011721 GRMZM2G011721 |
4 | 209395552 | 209398384 | 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_GRMZM2G011721_T01 GRMZM2G011721_T01 PAC:31049289 |
Low | No | 1546 | Get ORF Coding potential... Type: noncoding Potential: -1.065 Folding energies... MFEI: -25.614 AMFE: -0.545 GC content %: 46.960 | |
| Zmays_GRMZM2G011721_T02 GRMZM2G011721_T02 PAC:31049290 |
High | No | 1000 | Get ORF Coding potential... Type: noncoding Potential: -1.004 Folding energies... MFEI: -26.830 AMFE: -0.497 GC content %: 54.000 | |
| Zmays_GRMZM2G011721_T03 GRMZM2G011721_T03 PAC:31049288 |
Low | Yes | 1033 | Get ORF Coding potential... Type: noncoding Potential: -0.900 Folding energies... MFEI: -25.392 AMFE: -0.731 GC content %: 34.753 |
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_GRMZM2G011721_T03 | Rfam | 11.0 | mir-1829 | 0.0031 |
| Zmays_GRMZM2G011721_T01 | RepBase (RepeatMasker) | 2014-01-31 | CENSATC4_ZM | |
| Zmays_GRMZM2G011721_T03 | RepBase (RepeatMasker) | 2014-01-31 | CENSATC4_ZM |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
