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_Bradi3g11930 Bradi3g11930	Bd3	10458373	10464488	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_Bradi3g11930.1 Bradi3g11930.1 PAC:32821090	High	No	501		Get ORF Coding potential... Type: noncoding Potential: -1.042 Folding energies... MFEI: -24.471 AMFE: -0.483 GC content %: 50.699
Bdistachyon_Bradi3g11930.2 Bradi3g11930.2 PAC:32821092	High	No	638		Get ORF Coding potential... Type: noncoding Potential: -1.096 Folding energies... MFEI: -24.436 AMFE: -0.484 GC content %: 50.470
Bdistachyon_Bradi3g11930.3 Bradi3g11930.3 PAC:32821088	Low	Yes	777		Get ORF Coding potential... Type: noncoding Potential: -1.134 Folding energies... MFEI: -27.529 AMFE: -0.606 GC content %: 45.431
Bdistachyon_Bradi3g11930.4 Bradi3g11930.4 PAC:32821089	High	No	676		Get ORF Coding potential... Type: noncoding Potential: -1.108 Folding energies... MFEI: -27.086 AMFE: -0.531 GC content %: 51.036
Bdistachyon_Bradi3g11930.5 Bradi3g11930.5 PAC:32821091	High	No	639		Get ORF Coding potential... Type: noncoding Potential: -1.097 Folding energies... MFEI: -23.928 AMFE: -0.508 GC content %: 47.105

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_Bradi3g11930.3	Rfam	11.0	MIR1122	2.1e-14
Bdistachyon_Bradi3g11930.3	RepBase (RepeatMasker)	2014-01-31	ICARUS_TM

Gene models

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