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_AET4Gv20436900 [ AET4Gv20436900]	4D	295348880	295356036	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_AET4Gv20436900.10 AET4Gv20436900.10	High	No	327	OG0074868		Get ORF Coding potential... Type: noncoding Potential: -0.962 Folding energies... MFEI: -20.336 AMFE: -0.435 GC content %: 46.789
Atauschii_AET4Gv20436900.4 AET4Gv20436900.4	High	No	1362	OG0074869		Get ORF Coding potential... Type: noncoding Potential: -0.756 Folding energies... MFEI: -35.184 AMFE: -0.634 GC content %: 55.507
Atauschii_AET4Gv20436900.6 AET4Gv20436900.6	High	No	1190	OG0016347		Get ORF Coding potential... Type: noncoding Potential: -1.138 Folding energies... MFEI: -26.916 AMFE: -0.618 GC content %: 43.529
Atauschii_AET4Gv20436900.7 AET4Gv20436900.7	High	No	1270	OG0016347		Get ORF Coding potential... Type: noncoding Potential: -1.150 Folding energies... MFEI: -27.307 AMFE: -0.628 GC content %: 43.465
Atauschii_AET4Gv20436900.8 AET4Gv20436900.8	High	No	1699	OG0016347		Get ORF Coding potential... Type: noncoding Potential: -1.201 Folding energies... MFEI: -32.348 AMFE: -0.630 GC content %: 51.383
Atauschii_AET4Gv20436900.9 AET4Gv20436900.9	Low	No	509	OG0074870		Get ORF Coding potential... Type: noncoding Potential: -1.292 Folding energies... MFEI: -25.324 AMFE: -0.589 GC content %: 43.026

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_AET4Gv20436900.9	RepBase (RepeatMasker)	2014-01-31	DNA/hAT-Tag1; LTR/Gypsy

Gene models

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