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_AET2Gv20969200 [ AET2Gv20969200]	2D	546493601	546495436	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_AET2Gv20969200.2 AET2Gv20969200.2	Low	No	1027	OG0071264		Get ORF Coding potential... Type: noncoding Potential: -0.604 Folding energies... MFEI: -34.197 AMFE: -0.659 GC content %: 51.899
Atauschii_AET2Gv20969200.3 AET2Gv20969200.3	Low	Yes	1570	OG0071265		Get ORF Coding potential... Type: noncoding Potential: -0.897 Folding energies... MFEI: -31.459 AMFE: -0.663 GC content %: 47.452

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_AET2Gv20969200.3	Rfam	14.6	MIR1122	3.3e-7
Atauschii_AET2Gv20969200.2	RepBase (RepeatMasker)	2014-01-31	DNA; DNA/PIF-Harbinger
Atauschii_AET2Gv20969200.3	RepBase (RepeatMasker)	2014-01-31	DNA/PIF-Harbinger; 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).