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
Tpratense_Tp57577_TGAC_v2_gene23923 [ Tp57577_TGAC_v2_gene23923]	Tp57577_TGAC_v2_scaf_9506	498	1940	v2	Trifolium pratense (Phytozome 13)	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
Tpratense_Tp57577_TGAC_v2_mRNA24747 Tp57577_TGAC_v2_mRNA24747	Low	No	975	OG0059797		Get ORF Coding potential... Type: noncoding Potential: -0.869 Folding energies... MFEI: -24.903 AMFE: -0.647 GC content %: 38.462
Tpratense_Tp57577_TGAC_v2_mRNA24748 Tp57577_TGAC_v2_mRNA24748	Low	No	904	OG0059797		Get ORF Coding potential... Type: noncoding Potential: -0.860 Folding energies... MFEI: -25.553 AMFE: -0.649 GC content %: 39.381

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
Tpratense_Tp57577_TGAC_v2_mRNA24748	RepBase (RepeatMasker)	2014-01-31	LTR/Gypsy; Satellite
Tpratense_Tp57577_TGAC_v2_mRNA24747	RepBase (RepeatMasker)	2014-01-31	LTR/Gypsy; Satellite

Gene models

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