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_AET4Gv20721200 [ AET4Gv20721200]	4D	473881068	473889710	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_AET4Gv20721200.17 AET4Gv20721200.17	Low	No	649	OG0075407		Get ORF Coding potential... Type: noncoding Potential: -0.270 Folding energies... MFEI: -23.374 AMFE: -0.583 GC content %: 40.062
Atauschii_AET4Gv20721200.21 AET4Gv20721200.21	Low	No	1381	OG0006964		Get ORF Coding potential... Type: noncoding Potential: -0.998 Folding energies... MFEI: -27.000 AMFE: -0.627 GC content %: 43.085
Atauschii_AET4Gv20721200.22 AET4Gv20721200.22	Low	No	1510	OG0006964		Get ORF Coding potential... Type: noncoding Potential: -0.838 Folding energies... MFEI: -25.925 AMFE: -0.610 GC content %: 42.517
Atauschii_AET4Gv20721200.23 AET4Gv20721200.23	High	No	307	OG0075408		Get ORF Coding potential... Type: noncoding Potential: -1.130 Folding energies... MFEI: -20.977 AMFE: -0.484 GC content %: 43.322
Atauschii_AET4Gv20721200.24 AET4Gv20721200.24	High	No	1519	OG0006964		Get ORF Coding potential... Type: noncoding Potential: -1.114 Folding energies... MFEI: -25.502 AMFE: -0.623 GC content %: 40.948

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_AET4Gv20721200.17	SwissProt	2021-04-01	Q94A27	6.72e-16
Atauschii_AET4Gv20721200.21	SwissProt	2021-04-01	Q7XZU1	1.34e-7
Atauschii_AET4Gv20721200.22	SwissProt	2021-04-01	Q7XZU1	1.26e-7

Gene models

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