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_gene25695 [ Tp57577_TGAC_v2_gene25695]	Tp57577_TGAC_v2_scaf_169	180896	182190	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_mRNA26573 Tp57577_TGAC_v2_mRNA26573	Low	No	1005	OG0059800		Get ORF Coding potential... Type: noncoding Potential: -0.854 Folding energies... MFEI: -24.637 AMFE: -0.643 GC content %: 38.308
Tpratense_Tp57577_TGAC_v2_mRNA26574 Tp57577_TGAC_v2_mRNA26574	Low	No	1163	OG0059800		Get ORF Coding potential... Type: noncoding Potential: -0.973 Folding energies... MFEI: -24.660 AMFE: -0.667 GC content %: 36.973

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_mRNA26573	RepBase (RepeatMasker)	2014-01-31	LTR/ERV1
Tpratense_Tp57577_TGAC_v2_mRNA26574	RepBase (RepeatMasker)	2014-01-31	LTR/ERV1

Gene models

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