Gene
Zmays GRMZM2G034174
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_GRMZM2G034174 GRMZM2G034174 |
1 | 164974147 | 164977022 | 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_GRMZM2G034174_T01 GRMZM2G034174_T01 PAC:31011415 |
Low | No | 2171 | Get ORF Coding potential... Type: noncoding Potential: -0.367 Folding energies... MFEI: -26.628 AMFE: -0.620 GC content %: 42.976 | |
| Zmays_GRMZM2G034174_T02 GRMZM2G034174_T02 PAC:31011414 |
Low | No | 1345 | Get ORF Coding potential... Type: noncoding Potential: -0.330 Folding energies... MFEI: -24.840 AMFE: -0.556 GC content %: 44.684 | |
| Zmays_GRMZM2G034174_T03 GRMZM2G034174_T03 PAC:31011413 |
Low | No | 1345 | Get ORF Coding potential... Type: noncoding Potential: -0.330 Folding energies... MFEI: -24.840 AMFE: -0.556 GC content %: 44.684 | |
| Zmays_GRMZM2G034174_T04 GRMZM2G034174_T04 PAC:31011412 |
Low | No | 2134 | Get ORF Coding potential... Type: noncoding Potential: -0.366 Folding energies... MFEI: -26.851 AMFE: -0.628 GC content %: 42.737 | |
| Zmays_GRMZM2G034174_T05 GRMZM2G034174_T05 PAC:31011416 |
High | No | 704 | Get ORF Coding potential... Type: noncoding Potential: -1.030 Folding energies... MFEI: -25.213 AMFE: -0.497 GC content %: 50.710 |
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_GRMZM2G034174_T01 | RepBase (RepeatMasker) | 2014-01-31 | SINE2-1a_SBi | |
| Zmays_GRMZM2G034174_T04 | RepBase (RepeatMasker) | 2014-01-31 | SINE2-1a_SBi | |
| Zmays_GRMZM2G034174_T01 | SwissProt | 2015-06-01 | Q5Z6B1 | 7.0e-14 |
| Zmays_GRMZM2G034174_T02 | SwissProt | 2015-06-01 | Q5Z6B1 | 3.0e-14 |
| Zmays_GRMZM2G034174_T03 | SwissProt | 2015-06-01 | Q5Z6B1 | 3.0e-14 |
| Zmays_GRMZM2G034174_T04 | SwissProt | 2015-06-01 | Q5Z6B1 | 6.0e-14 |
Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).
