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_AET0Gv20154800 [ AET0Gv20154800]	jcf7190000162732	46774	54272	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_AET0Gv20154800.3 AET0Gv20154800.3	Low	Yes	1013	OG0024197		Get ORF Coding potential... Type: noncoding Potential: -0.696 Folding energies... MFEI: -28.756 AMFE: -0.613 GC content %: 46.890
Atauschii_AET0Gv20154800.5 AET0Gv20154800.5	High	No	801	OG0024197		Get ORF Coding potential... Type: noncoding Potential: -0.996 Folding energies... MFEI: -29.988 AMFE: -0.649 GC content %: 46.192
Atauschii_AET0Gv20154800.7 AET0Gv20154800.7	Low	Yes	599	OG0067668		Get ORF Coding potential... Type: noncoding Potential: -0.933 Folding energies... MFEI: -33.306 AMFE: -0.683 GC content %: 48.748

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_AET0Gv20154800.3	Rfam	14.6	mir-671	0.0033
Atauschii_AET0Gv20154800.7	Rfam	14.6	mir-671	0.0019

Gene models

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