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_AET1Gv20154600 [ AET1Gv20154600]	1D	46545486	46588291	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_AET1Gv20154600.1 AET1Gv20154600.1	High	No	535	OG0004626		Get ORF Coding potential... Type: noncoding Potential: -0.771 Folding energies... MFEI: -28.654 AMFE: -0.626 GC content %: 45.794
Atauschii_AET1Gv20154600.2 AET1Gv20154600.2	High	No	596	OG0004626		Get ORF Coding potential... Type: noncoding Potential: -0.752 Folding energies... MFEI: -30.628 AMFE: -0.650 GC content %: 47.148
Atauschii_AET1Gv20154600.3 AET1Gv20154600.3	High	No	593	OG0004626		Get ORF Coding potential... Type: noncoding Potential: -0.779 Folding energies... MFEI: -29.781 AMFE: -0.645 GC content %: 46.206
Atauschii_AET1Gv20154600.4 AET1Gv20154600.4	High	No	463	OG0004626		Get ORF Coding potential... Type: noncoding Potential: -0.681 Folding energies... MFEI: -32.181 AMFE: -0.651 GC content %: 49.460
Atauschii_AET1Gv20154600.5 AET1Gv20154600.5	High	No	591	OG0000131		Get ORF Coding potential... Type: noncoding Potential: -0.763 Folding energies... MFEI: -29.391 AMFE: -0.648 GC content %: 45.347
Atauschii_AET1Gv20154600.6 AET1Gv20154600.6	Low	No	1379	OG0000131		Get ORF Coding potential... Type: noncoding Potential: -1.022 Folding energies... MFEI: -25.453 AMFE: -0.660 GC content %: 38.579

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_AET1Gv20154600.6	RepBase (RepeatMasker)	2014-01-31	SINE; Unknown

Gene models

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