Gene
Zmays GRMZM2G100813
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_GRMZM2G100813 GRMZM2G100813 |
5 | 213019651 | 213022240 | 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_GRMZM2G100813_T01 GRMZM2G100813_T01 PAC:30990618 |
Low | No | 1850 | Get ORF Coding potential... Type: noncoding Potential: -1.224 Folding energies... MFEI: -28.346 AMFE: -0.658 GC content %: 43.081 | |
| Zmays_GRMZM2G100813_T02 GRMZM2G100813_T02 PAC:30990617 |
High | No | 585 | Get ORF Coding potential... Type: noncoding Potential: -1.281 Folding energies... MFEI: -33.128 AMFE: -0.621 GC content %: 53.333 | |
| Zmays_GRMZM2G100813_T03 GRMZM2G100813_T03 PAC:30990616 |
High | No | 590 | Get ORF Coding potential... Type: noncoding Potential: -1.283 Folding energies... MFEI: -32.847 AMFE: -0.617 GC content %: 53.220 | |
| Zmays_GRMZM2G100813_T04 GRMZM2G100813_T04 PAC:30990615 |
High | No | 758 | Get ORF Coding potential... Type: noncoding Potential: -1.455 Folding energies... MFEI: -30.554 AMFE: -0.626 GC content %: 48.813 |
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_GRMZM2G100813_T01 | RepBase (RepeatMasker) | 2014-01-31 | SZ-54A_LTR |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
