Gene
Zmays GRMZM2G178517
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_GRMZM2G178517 GRMZM2G178517 |
5 | 188512723 | 188518155 | Phytozome | 6a | Zea_mays | Coding? Yes |
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_GRMZM2G178517_T05 GRMZM2G178517_T05 PAC:30987732 |
Low | No | 1337 | Get ORF Coding potential... Type: noncoding Potential: -1.227 Folding energies... MFEI: -32.064 AMFE: -0.634 GC content %: 50.561 | |
| Zmays_GRMZM2G178517_T06 GRMZM2G178517_T06 PAC:30987731 |
Low | No | 1095 | Get ORF Coding potential... Type: noncoding Potential: -1.425 Folding energies... MFEI: -29.562 AMFE: -0.633 GC content %: 46.667 | |
| Zmays_GRMZM2G178517_T07 GRMZM2G178517_T07 PAC:30987730 |
High | No | 705 | Get ORF Coding potential... Type: noncoding Potential: -1.252 Folding energies... MFEI: -36.128 AMFE: -0.565 GC content %: 63.972 |
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_GRMZM2G178517_T05 | SwissProt | 2015-06-01 | Q6H849 | 5.0e-7 |
| Zmays_GRMZM2G178517_T05 | RepBase (RepeatMasker) | 2014-01-31 | ENSPM-9_ZM | |
| Zmays_GRMZM2G178517_T06 | RepBase (RepeatMasker) | 2014-01-31 | ENSPM-9_ZM |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
