GreeNC

Gene information

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
Atauschii_AET1Gv20475500 [ AET1Gv20475500]	1D	263096190	263101824	v4	Aegilops tauschii (Ensembl Plants 51)	Coding? Yes

Transcript features

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
Atauschii_AET1Gv20475500.12 AET1Gv20475500.12	High	No	393	OG0068467		Get ORF Coding potential... Type: noncoding Potential: -0.498 Folding energies... MFEI: -27.659 AMFE: -0.621 GC content %: 44.529
Atauschii_AET1Gv20475500.13 AET1Gv20475500.13	High	No	907	OG0068468		Get ORF Coding potential... Type: noncoding Potential: -0.791 Folding energies... MFEI: -40.948 AMFE: -0.703 GC content %: 58.214
Atauschii_AET1Gv20475500.2 AET1Gv20475500.2	Low	No	1505	OG0009731		Get ORF Coding potential... Type: noncoding Potential: -0.964 Folding energies... MFEI: -26.718 AMFE: -0.654 GC content %: 40.864
Atauschii_AET1Gv20475500.5 AET1Gv20475500.5	Low	No	1184	OG0009731		Get ORF Coding potential... Type: noncoding Potential: -1.040 Folding energies... MFEI: -27.280 AMFE: -0.662 GC content %: 41.216
Atauschii_AET1Gv20475500.9 AET1Gv20475500.9	High	No	1321	OG0009731		Get ORF Coding potential... Type: noncoding Potential: -0.670 Folding energies... MFEI: -26.752 AMFE: -0.651 GC content %: 41.105

Matches to external databases

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
Atauschii_AET1Gv20475500.2	RepBase (RepeatMasker)	2014-01-31	LTR/Copia
Atauschii_AET1Gv20475500.5	RepBase (RepeatMasker)	2014-01-31	LTR/Copia

Gene models

Transcripts can be colored as magenta (coding transcripts), green (high confidence lncRNAs), cyan (low confidence lncRNAs), or salmon (other ncRNAs).