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_Bradi4g19863 Bradi4g19863	Bd4	22740770	22744274	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_Bradi4g19863.1 Bradi4g19863.1 PAC:32791050	Low	No	987		Get ORF Coding potential... Type: noncoding Potential: -1.179 Folding energies... MFEI: -23.840 AMFE: -0.497 GC content %: 47.923
Bdistachyon_Bradi4g19863.2 Bradi4g19863.2 PAC:32791051	Low	No	882		Get ORF Coding potential... Type: noncoding Potential: -1.193 Folding energies... MFEI: -23.390 AMFE: -0.484 GC content %: 48.299
Bdistachyon_Bradi4g19863.3 Bradi4g19863.3 PAC:32791052	Low	No	945		Get ORF Coding potential... Type: noncoding Potential: -1.201 Folding energies... MFEI: -24.466 AMFE: -0.505 GC content %: 48.466

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_Bradi4g19863.1	RepBase (RepeatMasker)	2014-01-31	Gypsy-25_BD-I
Bdistachyon_Bradi4g19863.2	RepBase (RepeatMasker)	2014-01-31	Gypsy-25_BD-I
Bdistachyon_Bradi4g19863.3	RepBase (RepeatMasker)	2014-01-31	Gypsy-25_BD-I

Gene models

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