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
Oglumipatula_OGLUM01G11530 [ OGLUM01G11530]	1	10138357	10144090	v1.5	Oryza glumipatula (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
Oglumipatula_OGLUM01G11530.1 OGLUM01G11530.1	Low	No	945	OG0002661		Get ORF Coding potential... Type: noncoding Potential: -0.626 Folding energies... MFEI: -30.042 AMFE: -0.671 GC content %: 44.762
Oglumipatula_OGLUM01G11530.2 OGLUM01G11530.2	Low	No	1079	OG0002661		Get ORF Coding potential... Type: noncoding Potential: -0.535 Folding energies... MFEI: -29.323 AMFE: -0.675 GC content %: 43.466

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
Oglumipatula_OGLUM01G11530.1	RepBase (RepeatMasker)	2014-01-31	LINE/Jockey; LTR/ERV1; LTR/Pao
Oglumipatula_OGLUM01G11530.2	RepBase (RepeatMasker)	2014-01-31	LINE/Jockey; LTR/ERV1; LTR/Pao

Gene models

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