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_AET2Gv20405400 [ AET2Gv20405400]	2D	154410809	154417860	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_AET2Gv20405400.12 AET2Gv20405400.12	Low	No	966	OG0024636		Get ORF Coding potential... Type: noncoding Potential: -0.512 Folding energies... MFEI: -26.408 AMFE: -0.643 GC content %: 41.097
Atauschii_AET2Gv20405400.14 AET2Gv20405400.14	High	No	730	OG0024636		Get ORF Coding potential... Type: noncoding Potential: -0.876 Folding energies... MFEI: -28.260 AMFE: -0.635 GC content %: 44.521
Atauschii_AET2Gv20405400.17 AET2Gv20405400.17	Low	No	382	OG0070251		Get ORF Coding potential... Type: noncoding Potential: -0.817 Folding energies... MFEI: -30.209 AMFE: -0.638 GC content %: 47.382
Atauschii_AET2Gv20405400.18 AET2Gv20405400.18	High	No	250	OG0070252		Get ORF Coding potential... Type: noncoding Potential: -1.198 Folding energies... MFEI: -30.040 AMFE: -0.429 GC content %: 70.000

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_AET2Gv20405400.12	SwissProt	2021-04-01	O05235	7.44e-6
Atauschii_AET2Gv20405400.17	SwissProt	2021-04-01	P34913	1.44e-10

Gene models

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