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
Orufipogon_ORUFI05G04410 [ ORUFI05G04410]	5	3293323	3304006	w1943	Oryza rufipogon (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
Orufipogon_ORUFI05G04410.1 ORUFI05G04410.1	Low	Yes	1143	OG0003470		Get ORF Coding potential... Type: noncoding Potential: -1.570 Folding energies... MFEI: -39.948 AMFE: -0.702 GC content %: 56.868
Orufipogon_ORUFI05G04410.2 ORUFI05G04410.2	Low	Yes	1131	OG0003470		Get ORF Coding potential... Type: noncoding Potential: -1.570 Folding energies... MFEI: -40.301 AMFE: -0.707 GC content %: 57.029

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
Orufipogon_ORUFI05G04410.2	Rfam	14.6	MIR408	1.0e-3
Orufipogon_ORUFI05G04410.1	RepBase (RepeatMasker)	2014-01-31	DNA; DNA/hAT-Ac; DNA/Maverick
Orufipogon_ORUFI05G04410.2	RepBase (RepeatMasker)	2014-01-31	DNA; DNA/hAT-Ac; DNA/Maverick
Orufipogon_ORUFI05G04410.1	Rfam	14.6	MIR408	1.0e-3

Gene models

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