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
Graimondii_B456_010G066200 [ B456_010G066200]	10	8499620	8502639	v6	Gossypium raimondii (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
Graimondii_KJB64814 KJB64814	High	No	1086	OG0179761		Get ORF Coding potential... Type: noncoding Potential: -0.925 Folding energies... MFEI: -21.713 AMFE: -0.585 GC content %: 37.109
Graimondii_KJB64815 KJB64815	High	No	973	OG0003147		Get ORF Coding potential... Type: noncoding Potential: -0.868 Folding energies... MFEI: -25.560 AMFE: -0.669 GC content %: 38.232
Graimondii_KJB64816 KJB64816	Low	No	1073	OG0003147		Get ORF Coding potential... Type: noncoding Potential: -0.881 Folding energies... MFEI: -25.676 AMFE: -0.672 GC content %: 38.211

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
Graimondii_KJB64816	RepBase (RepeatMasker)	2014-01-31	LTR/Gypsy

Gene models

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