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_AET1Gv20140600 [ AET1Gv20140600]	1D	40618309	40620067	v4	Aegilops tauschii (Ensembl Plants 51)	Coding? No

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_AET1Gv20140600.1 AET1Gv20140600.1	Low	No	1286	OG0006768		Get ORF Coding potential... Type: noncoding Potential: -1.308 Folding energies... MFEI: -26.314 AMFE: -0.602 GC content %: 43.701
Atauschii_AET1Gv20140600.2 AET1Gv20140600.2	High	No	921	OG0006768		Get ORF Coding potential... Type: noncoding Potential: -0.976 Folding energies... MFEI: -36.287 AMFE: -0.689 GC content %: 52.660
Atauschii_AET1Gv20140600.3 AET1Gv20140600.3	Low	No	1086	OG0006768		Get ORF Coding potential... Type: noncoding Potential: -0.981 Folding energies... MFEI: -25.737 AMFE: -0.575 GC content %: 44.751
Atauschii_AET1Gv20140600.4 AET1Gv20140600.4	High	No	465	OG0067877		Get ORF Coding potential... Type: noncoding Potential: -1.065 Folding energies... MFEI: -23.892 AMFE: -0.534 GC content %: 44.731
Atauschii_AET1Gv20140600.5 AET1Gv20140600.5	High	No	208	OG0067878		Get ORF Coding potential... Type: noncoding Potential: -1.238 Folding energies... MFEI: -21.875 AMFE: -0.403 GC content %: 54.327

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_AET1Gv20140600.1	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm
Atauschii_AET1Gv20140600.3	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).