Gene
Zmays GRMZM5G861100
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_GRMZM5G861100 GRMZM5G861100 |
1 | 188092775 | 188096470 | 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_GRMZM5G861100_T01 GRMZM5G861100_T01 PAC:31010925 |
Low | No | 2913 | Get ORF Coding potential... Type: noncoding Potential: -1.215 Folding energies... MFEI: -22.774 AMFE: -0.569 GC content %: 40.027 | |
| Zmays_GRMZM5G861100_T02 GRMZM5G861100_T02 PAC:31010927 |
Low | No | 2728 | Get ORF Coding potential... Type: noncoding Potential: -1.213 Folding energies... MFEI: -23.138 AMFE: -0.567 GC content %: 40.836 | |
| Zmays_GRMZM5G861100_T03 GRMZM5G861100_T03 PAC:31010926 |
Low | No | 2955 | Get ORF Coding potential... Type: noncoding Potential: -1.215 Folding energies... MFEI: -23.455 AMFE: -0.582 GC content %: 40.271 |
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_GRMZM5G861100_T01 | RepBase (RepeatMasker) | 2014-01-31 | Helitron-5_ZM | |
| Zmays_GRMZM5G861100_T02 | RepBase (RepeatMasker) | 2014-01-31 | hAT-25_ZM | |
| Zmays_GRMZM5G861100_T03 | RepBase (RepeatMasker) | 2014-01-31 | hAT-25_ZM |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
