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_AET2Gv20054000 [ AET2Gv20054000]	2D	12434928	12438696	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_AET2Gv20054000.1 AET2Gv20054000.1	High	No	981	OG0009773		Get ORF Coding potential... Type: noncoding Potential: -0.706 Folding energies... MFEI: -29.266 AMFE: -0.647 GC content %: 45.260
Atauschii_AET2Gv20054000.13 AET2Gv20054000.13	High	No	376	OG0001141		Get ORF Coding potential... Type: noncoding Potential: -0.826 Folding energies... MFEI: -28.351 AMFE: -0.558 GC content %: 50.798
Atauschii_AET2Gv20054000.14 AET2Gv20054000.14	High	No	389	OG0001141		Get ORF Coding potential... Type: noncoding Potential: -0.631 Folding energies... MFEI: -32.211 AMFE: -0.626 GC content %: 51.414
Atauschii_AET2Gv20054000.3 AET2Gv20054000.3	High	No	532	OG0009773		Get ORF Coding potential... Type: noncoding Potential: -0.908 Folding energies... MFEI: -26.109 AMFE: -0.604 GC content %: 43.233
Atauschii_AET2Gv20054000.4 AET2Gv20054000.4	Low	No	614	OG0009773		Get ORF Coding potential... Type: noncoding Potential: -0.947 Folding energies... MFEI: -25.586 AMFE: -0.586 GC content %: 43.648
Atauschii_AET2Gv20054000.7 AET2Gv20054000.7	High	No	622	OG0009773		Get ORF Coding potential... Type: noncoding Potential: -0.840 Folding energies... MFEI: -29.164 AMFE: -0.626 GC content %: 46.624

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_AET2Gv20054000.4	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm

Gene models

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