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_AET3Gv20606100 [ AET3Gv20606100]	3D	355054582	355079747	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_AET3Gv20606100.47 AET3Gv20606100.47	Low	No	413	OG0072934		Get ORF Coding potential... Type: noncoding Potential: -0.869 Folding energies... MFEI: -35.496 AMFE: -0.603 GC content %: 58.838
Atauschii_AET3Gv20606100.48 AET3Gv20606100.48	Low	No	602	OG0072935		Get ORF Coding potential... Type: noncoding Potential: -1.037 Folding energies... MFEI: -39.086 AMFE: -0.634 GC content %: 61.628
Atauschii_AET3Gv20606100.49 AET3Gv20606100.49	High	No	318	OG0072936		Get ORF Coding potential... Type: noncoding Potential: -1.159 Folding energies... MFEI: -34.057 AMFE: -0.541 GC content %: 62.893
Atauschii_AET3Gv20606100.71 AET3Gv20606100.71	High	No	1342	OG0072937		Get ORF Coding potential... Type: noncoding Potential: -1.117 Folding energies... MFEI: -23.979 AMFE: -0.606 GC content %: 39.568
Atauschii_AET3Gv20606100.76 AET3Gv20606100.76	Low	No	885	OG0072938		Get ORF Coding potential... Type: coding Potential: 1.243 Folding energies... MFEI: -20.158 AMFE: -0.557 GC content %: 36.158

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_AET3Gv20606100.48	RepBase (RepeatMasker)	2014-01-31	LINE/L1
Atauschii_AET3Gv20606100.48	SwissProt	2021-04-01	P0C2F6	1.28e-4
Atauschii_AET3Gv20606100.47	RepBase (RepeatMasker)	2014-01-31	LINE/L1

Gene models

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