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_Bradi5g04854 Bradi5g04854	Bd5	6297702	6301144	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_Bradi5g04854.1 Bradi5g04854.1 PAC:32811104	Low	No	3032		Get ORF Coding potential... Type: noncoding Potential: -1.214 Folding energies... MFEI: -28.915 AMFE: -0.685 GC content %: 42.183
Bdistachyon_Bradi5g04854.2 Bradi5g04854.2 PAC:32811105	Low	No	2849		Get ORF Coding potential... Type: noncoding Potential: -1.207 Folding energies... MFEI: -29.080 AMFE: -0.680 GC content %: 42.752
Bdistachyon_Bradi5g04854.3 Bradi5g04854.3 PAC:32811106	High	No	1905		Get ORF Coding potential... Type: noncoding Potential: -0.984 Folding energies... MFEI: -30.735 AMFE: -0.678 GC content %: 45.354
Bdistachyon_Bradi5g04854.4 Bradi5g04854.4 PAC:32811107	High	No	2772		Get ORF Coding potential... Type: noncoding Potential: -1.078 Folding energies... MFEI: -28.763 AMFE: -0.674 GC content %: 42.677
Bdistachyon_Bradi5g04854.5 Bradi5g04854.5 PAC:32811108	High	No	1945		Get ORF Coding potential... Type: noncoding Potential: -0.985 Folding energies... MFEI: -30.540 AMFE: -0.676 GC content %: 45.193
Bdistachyon_Bradi5g04854.6 Bradi5g04854.6 PAC:32811109	Low	Yes	1350		Get ORF Coding potential... Type: noncoding Potential: -0.952 Folding energies... MFEI: -34.267 AMFE: -0.682 GC content %: 50.222

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_Bradi5g04854.1	SwissProt	2015-06-01	Q9LR47	1.0e-9
Bdistachyon_Bradi5g04854.2	SwissProt	2015-06-01	Q9LR47	1.0e-9

Gene models

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