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_AET2Gv20333100 [ AET2Gv20333100]	2D	112439293	112447228	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_AET2Gv20333100.12 AET2Gv20333100.12	High	No	638	OG0024611		Get ORF Coding potential... Type: noncoding Potential: -0.933 Folding energies... MFEI: -27.884 AMFE: -0.591 GC content %: 47.179
Atauschii_AET2Gv20333100.2 AET2Gv20333100.2	Low	Yes	2708	OG0070123		Get ORF Coding potential... Type: noncoding Potential: -1.069 Folding energies... MFEI: -29.889 AMFE: -0.736 GC content %: 40.620
Atauschii_AET2Gv20333100.20 AET2Gv20333100.20	High	No	370	OG0070124		Get ORF Coding potential... Type: noncoding Potential: -0.817 Folding energies... MFEI: -31.270 AMFE: -0.606 GC content %: 51.622
Atauschii_AET2Gv20333100.21 AET2Gv20333100.21	High	No	375	OG0070125		Get ORF Coding potential... Type: noncoding Potential: -0.868 Folding energies... MFEI: -33.173 AMFE: -0.604 GC content %: 54.933
Atauschii_AET2Gv20333100.8 AET2Gv20333100.8	High	No	328	OG0070126		Get ORF Coding potential... Type: noncoding Potential: -0.788 Folding energies... MFEI: -44.299 AMFE: -0.685 GC content %: 64.634

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_AET2Gv20333100.2	Rfam	14.6	MIR1122	1.7e-21
Atauschii_AET2Gv20333100.2	RepBase (RepeatMasker)	2014-01-31	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).