Zmays Zm00001d010213
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 | Assembly | Species | Details
|
|---|---|---|---|---|---|---|
| Zmays_Zm00001d010213 [ Zm00001d010213] |
8 | 104356766 | 104359468 | v4 | Zea mays (Phytozome 13) | 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 | Orthologous group | Sequence | Details
|
|---|---|---|---|---|---|---|
| Zmays_Zm00001d010213_T003 Zm00001d010213_T003 |
Low | Yes | 1392 | [1] | Get ORF Coding potential... Type: noncoding Potential: -0.247 Folding energies... MFEI: -27.708 AMFE: -0.653 GC content %: 42.457 | |
| Zmays_Zm00001d010213_T004 Zm00001d010213_T004 |
High | No | 832 | [2] | Get ORF Coding potential... Type: noncoding Potential: -1.168 Folding energies... MFEI: -28.450 AMFE: -0.663 GC content %: 42.909 | |
| Zmays_Zm00001d010213_T005 Zm00001d010213_T005 |
Low | No | 1017 | [3] | Get ORF Coding potential... Type: noncoding Potential: -0.340 Folding energies... MFEI: -28.545 AMFE: -0.675 GC content %: 42.281 |
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_Zm00001d010213_T003 | SwissProt | 2021-04-01 | Q15427 | 7.33e-5 |
| Zmays_Zm00001d010213_T005 | SwissProt | 2021-04-01 | Q15427 | 6.68e-4 |
| Zmays_Zm00001d010213_T003 | Rfam | 14.6 | MIR1122 | 4.5e-5 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
