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_AET4Gv20024000 [ AET4Gv20024000]	4D	5488669	5492177	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_AET4Gv20024000.3 AET4Gv20024000.3	High	No	504	OG0074178		Get ORF Coding potential... Type: noncoding Potential: -0.454 Folding energies... MFEI: -31.210 AMFE: -0.645 GC content %: 48.413
Atauschii_AET4Gv20024000.5 AET4Gv20024000.5	Low	No	898	OG0009969		Get ORF Coding potential... Type: noncoding Potential: -0.793 Folding energies... MFEI: -27.539 AMFE: -0.644 GC content %: 42.762
Atauschii_AET4Gv20024000.6 AET4Gv20024000.6	Low	No	887	OG0009969		Get ORF Coding potential... Type: noncoding Potential: -1.203 Folding energies... MFEI: -26.280 AMFE: -0.642 GC content %: 40.924
Atauschii_AET4Gv20024000.7 AET4Gv20024000.7	High	No	729	OG0009969		Get ORF Coding potential... Type: noncoding Potential: -1.306 Folding energies... MFEI: -25.926 AMFE: -0.634 GC content %: 40.878

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_AET4Gv20024000.6	SwissProt	2021-04-01	B1XIZ3	1.68e-8
Atauschii_AET4Gv20024000.5	SwissProt	2021-04-01	A7GSK0	7.5e-10

Gene models

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