Gene
Zmays GRMZM2G119513
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_GRMZM2G119513 GRMZM2G119513 |
7 | 137650880 | 137654097 | 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_GRMZM2G119513_T01 GRMZM2G119513_T01 PAC:30998128 |
High | No | 904 | Get ORF Coding potential... Type: noncoding Potential: -0.928 Folding energies... MFEI: -32.876 AMFE: -0.624 GC content %: 52.655 | |
| Zmays_GRMZM2G119513_T02 GRMZM2G119513_T02 PAC:30998130 |
Low | No | 1137 | Get ORF Coding potential... Type: noncoding Potential: -1.034 Folding energies... MFEI: -30.378 AMFE: -0.658 GC content %: 46.174 | |
| Zmays_GRMZM2G119513_T03 GRMZM2G119513_T03 PAC:30998129 |
Low | No | 749 | Get ORF Coding potential... Type: noncoding Potential: -0.962 Folding energies... MFEI: -30.534 AMFE: -0.615 GC content %: 49.666 | |
| Zmays_GRMZM2G119513_T04 GRMZM2G119513_T04 PAC:30998131 |
Low | No | 471 | Get ORF Coding potential... Type: noncoding Potential: -1.202 Folding energies... MFEI: -21.741 AMFE: -0.528 GC content %: 41.189 |
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_GRMZM2G119513_T03 | RepBase (RepeatMasker) | 2014-01-31 | STOWAWAY14_SB | |
| Zmays_GRMZM2G119513_T04 | RepBase (RepeatMasker) | 2014-01-31 | Copia12-ZM_I-int | |
| Zmays_GRMZM2G119513_T02 | RepBase (RepeatMasker) | 2014-01-31 | STOWAWAY14_SB |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
