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_AET0Gv20009200 [ AET0Gv20009200]	Super_scaffold_652	1402968	1542782	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_AET0Gv20009200.27 AET0Gv20009200.27	Low	No	926	OG0067540		Get ORF Coding potential... Type: noncoding Potential: -1.175 Folding energies... MFEI: -29.492 AMFE: -0.649 GC content %: 45.464
Atauschii_AET0Gv20009200.45 AET0Gv20009200.45	High	No	255	OG0067541		Get ORF Coding potential... Type: noncoding Potential: -1.296 Folding energies... MFEI: -21.098 AMFE: -0.522 GC content %: 40.392
Atauschii_AET0Gv20009200.46 AET0Gv20009200.46	High	No	579	OG0067542		Get ORF Coding potential... Type: noncoding Potential: -1.116 Folding energies... MFEI: -21.174 AMFE: -0.622 GC content %: 34.024
Atauschii_AET0Gv20009200.47 AET0Gv20009200.47	Low	No	860	OG0067543		Get ORF Coding potential... Type: noncoding Potential: -0.160 Folding energies... MFEI: -23.756 AMFE: -0.608 GC content %: 39.070
Atauschii_AET0Gv20009200.50 AET0Gv20009200.50	Low	No	349	OG0067544		Get ORF Coding potential... Type: noncoding Potential: -1.131 Folding energies... MFEI: -32.178 AMFE: -0.597 GC content %: 53.868

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_AET0Gv20009200.27	SwissProt	2021-04-01	Q6H8D6	3.53e-4
Atauschii_AET0Gv20009200.47	SwissProt	2021-04-01	Q9SXB5	2.08e-15
Atauschii_AET0Gv20009200.50	SwissProt	2021-04-01	Q39191	6.0e-4
Atauschii_AET0Gv20009200.27	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).