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_gene557 [ Tp57577_TGAC_v2_gene557]	Tp57577_TGAC_v2_scaf_1800	5669	10208	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_mRNA558 Tp57577_TGAC_v2_mRNA558	Low	No	1458	OG0059838		Get ORF Coding potential... Type: noncoding Potential: -0.715 Folding energies... MFEI: -20.802 AMFE: -0.569 GC content %: 36.557
Tpratense_Tp57577_TGAC_v2_mRNA559 Tp57577_TGAC_v2_mRNA559	Low	No	1226	OG0059838		Get ORF Coding potential... Type: noncoding Potential: -0.449 Folding energies... MFEI: -20.677 AMFE: -0.563 GC content %: 36.705

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_mRNA558	SwissProt	2021-04-01	Q0WPH8	5.81e-9
Tpratense_Tp57577_TGAC_v2_mRNA559	SwissProt	2021-04-01	Q0WPH8	7.99e-9

Gene models

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