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_AET2Gv20621700 [ AET2Gv20621700]	2D	341160636	341165584	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_AET2Gv20621700.10 AET2Gv20621700.10	High	No	214	OG0070580		Get ORF Coding potential... Type: noncoding Potential: -1.241 Folding energies... MFEI: -21.916 AMFE: -0.504 GC content %: 43.458
Atauschii_AET2Gv20621700.11 AET2Gv20621700.11	Low	Yes	797	OG0009811		Get ORF Coding potential... Type: noncoding Potential: -1.216 Folding energies... MFEI: -34.279 AMFE: -0.770 GC content %: 44.542
Atauschii_AET2Gv20621700.12 AET2Gv20621700.12	Low	Yes	695	OG0009811		Get ORF Coding potential... Type: noncoding Potential: -1.188 Folding energies... MFEI: -35.554 AMFE: -0.789 GC content %: 45.036

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_AET2Gv20621700.11	Rfam	14.6	MIR1122	2.5e-7
Atauschii_AET2Gv20621700.12	Rfam	14.6	MIR1122	2.2e-7
Atauschii_AET2Gv20621700.11	RepBase (RepeatMasker)	2014-01-31	DNA
Atauschii_AET2Gv20621700.12	RepBase (RepeatMasker)	2014-01-31	DNA

Gene models

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