Gene
Zmays GRMZM2G063945
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_GRMZM2G063945 GRMZM2G063945 |
5 | 161119271 | 161123537 | 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_GRMZM2G063945_T01 GRMZM2G063945_T01 PAC:30987560 |
High | No | 703 | Get ORF Coding potential... Type: noncoding Potential: -1.218 Folding energies... MFEI: -32.688 AMFE: -0.644 GC content %: 50.782 | |
| Zmays_GRMZM2G063945_T02 GRMZM2G063945_T02 PAC:30987559 |
Low | No | 3961 | Get ORF Coding potential... Type: noncoding Potential: -1.318 Folding energies... MFEI: -30.169 AMFE: -0.690 GC content %: 43.701 | |
| Zmays_GRMZM2G063945_T03 GRMZM2G063945_T03 PAC:30987557 |
High | No | 770 | Get ORF Coding potential... Type: noncoding Potential: -0.968 Folding energies... MFEI: -32.909 AMFE: -0.651 GC content %: 50.519 | |
| Zmays_GRMZM2G063945_T04 GRMZM2G063945_T04 PAC:30987558 |
Low | No | 3367 | Get ORF Coding potential... Type: noncoding Potential: -1.254 Folding energies... MFEI: -27.680 AMFE: -0.692 GC content %: 40.006 |
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_GRMZM2G063945_T02 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy-154_ZM-I | |
| Zmays_GRMZM2G063945_T04 | RepBase (RepeatMasker) | 2014-01-31 | Gypsy-154_ZM-I |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
