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_Bradi2g34156 Bradi2g34156	Bd2	33980402	33985520	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_Bradi2g34156.1 Bradi2g34156.1 PAC:32773125	Low	Yes	851		Get ORF Coding potential... Type: noncoding Potential: -1.060 Folding energies... MFEI: -32.409 AMFE: -0.668 GC content %: 48.531
Bdistachyon_Bradi2g34156.2 Bradi2g34156.2 PAC:32773124	High	No	1064		Get ORF Coding potential... Type: noncoding Potential: -1.108 Folding energies... MFEI: -27.810 AMFE: -0.623 GC content %: 44.643

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_Bradi2g34156.1	Rfam	11.0	MIR1122	2.6e-11
Bdistachyon_Bradi2g34156.1	miRBase	21.0	bdi-miR5175a	0.018

Gene models

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