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	Source	Assembly	Species	Details
Bdistachyon_Bradi2g18576 Bradi2g18576	Bd2	16497837	16500382	Phytozome	v3.1	Brachypodium_distachyon	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	Sequence	Details
Bdistachyon_Bradi2g18576.1 Bradi2g18576.1 PAC:32773055	Low	Yes	2355		Get ORF Coding potential... Type: noncoding Potential: -1.360 Folding energies... MFEI: -30.998 AMFE: -0.707 GC content %: 43.822
Bdistachyon_Bradi2g18576.2 Bradi2g18576.2 PAC:32773056	Low	Yes	2182		Get ORF Coding potential... Type: noncoding Potential: -1.350 Folding energies... MFEI: -30.802 AMFE: -0.710 GC content %: 43.355

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
Bdistachyon_Bradi2g18576.2	RepBase (RepeatMasker)	2014-01-31	TREP216
Bdistachyon_Bradi2g18576.1	Rfam	11.0	MIR1122	6.5e-11
Bdistachyon_Bradi2g18576.2	Rfam	11.0	MIR1122	6.1e-11
Bdistachyon_Bradi2g18576.1	RepBase (RepeatMasker)	2014-01-31	TREP216

Gene models

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