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
Omeridionalis_OMERI05G02260 [ OMERI05G02260]	5	2065672	2068259	v1.3	Oryza meridionalis (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
Omeridionalis_OMERI05G02260.1 OMERI05G02260.1	High	No	982	OG0054230		Get ORF Coding potential... Type: noncoding Potential: -0.945 Folding energies... MFEI: -29.817 AMFE: -0.675 GC content %: 44.196
Omeridionalis_OMERI05G02260.2 OMERI05G02260.2	High	No	204	OG0257166		Get ORF Coding potential... Type: noncoding Potential: -0.697 Folding energies... MFEI: -34.118 AMFE: -0.552 GC content %: 61.765
Omeridionalis_OMERI05G02260.3 OMERI05G02260.3	Low	No	2180	OG0257167		Get ORF Coding potential... Type: noncoding Potential: -1.081 Folding energies... MFEI: -31.018 AMFE: -0.678 GC content %: 45.780

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
Omeridionalis_OMERI05G02260.3	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm; Satellite

Gene models

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