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_AET4Gv20566300 [ AET4Gv20566300]	4D	389837495	389847504	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_AET4Gv20566300.10 AET4Gv20566300.10	High	No	504	OG0016380		Get ORF Coding potential... Type: noncoding Potential: -1.143 Folding energies... MFEI: -28.571 AMFE: -0.615 GC content %: 46.429
Atauschii_AET4Gv20566300.11 AET4Gv20566300.11	High	No	326	OG0075114		Get ORF Coding potential... Type: noncoding Potential: -1.043 Folding energies... MFEI: -33.712 AMFE: -0.604 GC content %: 55.828
Atauschii_AET4Gv20566300.12 AET4Gv20566300.12	High	No	444	OG0075115		Get ORF Coding potential... Type: noncoding Potential: -1.086 Folding energies... MFEI: -28.739 AMFE: -0.638 GC content %: 45.045
Atauschii_AET4Gv20566300.13 AET4Gv20566300.13	High	No	442	OG0016380		Get ORF Coding potential... Type: noncoding Potential: -1.028 Folding energies... MFEI: -27.285 AMFE: -0.609 GC content %: 44.796
Atauschii_AET4Gv20566300.14 AET4Gv20566300.14	High	No	424	OG0006955		Get ORF Coding potential... Type: noncoding Potential: -1.107 Folding energies... MFEI: -25.920 AMFE: -0.575 GC content %: 45.047
Atauschii_AET4Gv20566300.15 AET4Gv20566300.15	High	No	408	OG0006955		Get ORF Coding potential... Type: noncoding Potential: -1.049 Folding energies... MFEI: -26.642 AMFE: -0.604 GC content %: 44.118
Atauschii_AET4Gv20566300.16 AET4Gv20566300.16	Low	No	1856	OG0075116		Get ORF Coding potential... Type: noncoding Potential: -1.252 Folding energies... MFEI: -26.099 AMFE: -0.736 GC content %: 35.453
Atauschii_AET4Gv20566300.4 AET4Gv20566300.4	High	No	1566	OG0016380		Get ORF Coding potential... Type: noncoding Potential: -1.105 Folding energies... MFEI: -28.627 AMFE: -0.652 GC content %: 43.934
Atauschii_AET4Gv20566300.5 AET4Gv20566300.5	High	No	1151	OG0025374		Get ORF Coding potential... Type: noncoding Potential: -1.077 Folding energies... MFEI: -29.435 AMFE: -0.634 GC content %: 46.394
Atauschii_AET4Gv20566300.6 AET4Gv20566300.6	Low	No	3047	OG0025374		Get ORF Coding potential... Type: noncoding Potential: -1.190 Folding energies... MFEI: -26.170 AMFE: -0.655 GC content %: 39.941
Atauschii_AET4Gv20566300.7 AET4Gv20566300.7	High	No	564	OG0006955		Get ORF Coding potential... Type: noncoding Potential: -1.025 Folding energies... MFEI: -32.784 AMFE: -0.653 GC content %: 50.177
Atauschii_AET4Gv20566300.8 AET4Gv20566300.8	High	No	506	OG0006955		Get ORF Coding potential... Type: noncoding Potential: -1.100 Folding energies... MFEI: -33.360 AMFE: -0.647 GC content %: 51.581
Atauschii_AET4Gv20566300.9 AET4Gv20566300.9	High	No	581	OG0006955		Get ORF Coding potential... Type: noncoding Potential: -1.170 Folding energies... MFEI: -28.967 AMFE: -0.628 GC content %: 46.127

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_AET4Gv20566300.16	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm
Atauschii_AET4Gv20566300.6	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm

Gene models

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