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_AET6Gv20339100 [ AET6Gv20339100]	6D	108634406	108636124	v4	Aegilops tauschii (Ensembl Plants 51)	Coding? No

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_AET6Gv20339100.1 AET6Gv20339100.1	High	No	368	OG0078516		Get ORF Coding potential... Type: noncoding Potential: -0.892 Folding energies... MFEI: -27.310 AMFE: -0.620 GC content %: 44.022
Atauschii_AET6Gv20339100.2 AET6Gv20339100.2	High	No	376	OG0078517		Get ORF Coding potential... Type: noncoding Potential: -0.914 Folding energies... MFEI: -27.713 AMFE: -0.632 GC content %: 43.883
Atauschii_AET6Gv20339100.3 AET6Gv20339100.3	Low	No	890	OG0025872		Get ORF Coding potential... Type: noncoding Potential: -1.070 Folding energies... MFEI: -27.539 AMFE: -0.685 GC content %: 40.225
Atauschii_AET6Gv20339100.4 AET6Gv20339100.4	Low	No	661	OG0025872		Get ORF Coding potential... Type: noncoding Potential: -0.897 Folding energies... MFEI: -27.322 AMFE: -0.676 GC content %: 40.393

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_AET6Gv20339100.3	RepBase (RepeatMasker)	2014-01-31	LTR/Gypsy
Atauschii_AET6Gv20339100.4	RepBase (RepeatMasker)	2014-01-31	LTR/Gypsy

Gene models

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