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	Source	Assembly	Species	Details
Osativa_LOC_Os07g46710 LOC_Os07g46710	Chr7	27922242	27924658	Phytozome	v7.0	Oryza_sativa_Japonica_Group	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	Sequence	Details
Osativa_LOC_Os07g46710.1 LOC_Os07g46710.1 PAC:24109890	Low	No	836		Get ORF Coding potential... Type: noncoding Potential: -0.270 Folding energies... MFEI: -26.053 AMFE: -0.573 GC content %: 45.455
Osativa_LOC_Os07g46710.2 LOC_Os07g46710.2 PAC:24109891	High	No	876		Get ORF Coding potential... Type: noncoding Potential: -0.276 Folding energies... MFEI: -25.457 AMFE: -0.553 GC content %: 46.005
Osativa_LOC_Os07g46710.3 LOC_Os07g46710.3 PAC:24109892	High	No	809		Get ORF Coding potential... Type: noncoding Potential: -0.267 Folding energies... MFEI: -25.909 AMFE: -0.597 GC content %: 43.387

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
Osativa_LOC_Os07g46710.1	RepBase (RepeatMasker)	2014-01-31	SINE9_OS

Gene models

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