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_AET2Gv20263100 [ AET2Gv20263100]	2D	79776917	79782100	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_AET2Gv20263100.10 AET2Gv20263100.10	High	No	538	OG0004661		Get ORF Coding potential... Type: noncoding Potential: -1.388 Folding energies... MFEI: -28.941 AMFE: -0.592 GC content %: 48.885
Atauschii_AET2Gv20263100.11 AET2Gv20263100.11	High	No	844	OG0004661		Get ORF Coding potential... Type: noncoding Potential: -1.429 Folding energies... MFEI: -25.415 AMFE: -0.586 GC content %: 43.365
Atauschii_AET2Gv20263100.8 AET2Gv20263100.8	Low	Yes	3602	OG0004661		Get ORF Coding potential... Type: noncoding Potential: -1.050 Folding energies... MFEI: -27.651 AMFE: -0.680 GC content %: 40.672
Atauschii_AET2Gv20263100.9 AET2Gv20263100.9	High	No	649	OG0004661		Get ORF Coding potential... Type: noncoding Potential: -1.183 Folding energies... MFEI: -26.810 AMFE: -0.580 GC content %: 46.225

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_AET2Gv20263100.8	Rfam	14.6	MIR1122	2.7e-17
Atauschii_AET2Gv20263100.8	RepBase (RepeatMasker)	2014-01-31	DNA; DNA/TcMar-Stowaway

Gene models

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