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
Ppatens_Pp3c4_29419 Pp3c4_29419	Chr04	20437453	20440782	Phytozome	v3.3	Physcomitrella_patens	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
Ppatens_Pp3c4_29419V3.1 Pp3c4_29419V3.1 PAC:32920521	High	No	2348		Get ORF Coding potential... Type: noncoding Potential: -0.409 Folding energies... MFEI: -27.445 AMFE: -0.673 GC content %: 40.801
Ppatens_Pp3c4_29419V3.2 Pp3c4_29419V3.2 PAC:32920522	High	No	2471		Get ORF Coding potential... Type: noncoding Potential: -0.441 Folding energies... MFEI: -27.730 AMFE: -0.672 GC content %: 41.279
Ppatens_Pp3c4_29419V3.3 Pp3c4_29419V3.3 PAC:32920520	High	No	2215		Get ORF Coding potential... Type: noncoding Potential: -0.354 Folding energies... MFEI: -26.659 AMFE: -0.664 GC content %: 40.135
Ppatens_Pp3c4_29419V3.4 Pp3c4_29419V3.4 PAC:32920523	Low	No	2229		Get ORF Coding potential... Type: noncoding Potential: -0.349 Folding energies... MFEI: -26.855 AMFE: -0.665 GC content %: 40.377

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
Ppatens_Pp3c4_29419V3.4	SwissProt	2015-06-01	Q9VIU7	8.0e-5

Gene models

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