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_AET1Gv20750400 [ AET1Gv20750400]	1D	417622631	417635777	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_AET1Gv20750400.1 AET1Gv20750400.1	Low	Yes	2189	OG0069028		Get ORF Coding potential... Type: noncoding Potential: -1.266 Folding energies... MFEI: -31.078 AMFE: -0.765 GC content %: 40.612
Atauschii_AET1Gv20750400.10 AET1Gv20750400.10	High	No	2272	OG0009753		Get ORF Coding potential... Type: noncoding Potential: -1.226 Folding energies... MFEI: -25.682 AMFE: -0.596 GC content %: 43.090
Atauschii_AET1Gv20750400.13 AET1Gv20750400.13	High	No	2343	OG0009753		Get ORF Coding potential... Type: noncoding Potential: -0.840 Folding energies... MFEI: -26.509 AMFE: -0.605 GC content %: 43.833
Atauschii_AET1Gv20750400.17 AET1Gv20750400.17	High	No	980	OG0009753		Get ORF Coding potential... Type: noncoding Potential: -0.635 Folding energies... MFEI: -28.163 AMFE: -0.604 GC content %: 46.633
Atauschii_AET1Gv20750400.18 AET1Gv20750400.18	High	No	974	OG0009753		Get ORF Coding potential... Type: noncoding Potential: -0.634 Folding energies... MFEI: -28.480 AMFE: -0.608 GC content %: 46.817

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_AET1Gv20750400.1	Rfam	14.6	MIR1122	4.6e-15
Atauschii_AET1Gv20750400.1	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).