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_Pp3c17_4600 Pp3c17_4600	Chr17	3692091	3694917	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_Pp3c17_4600V3.1 Pp3c17_4600V3.1 PAC:32906637	Low	Yes	363		Get ORF Coding potential... Type: noncoding Potential: -0.933 Folding energies... MFEI: -42.342 AMFE: -0.718 GC content %: 58.953
Ppatens_Pp3c17_4600V3.2 Pp3c17_4600V3.2 PAC:32906638	Low	Yes	1539		Get ORF Coding potential... Type: noncoding Potential: -1.115 Folding energies... MFEI: -29.981 AMFE: -0.650 GC content %: 46.134

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_Pp3c17_4600V3.1	RepBase (RepeatMasker)	2014-01-31	MuDR1_ZM
Ppatens_Pp3c17_4600V3.2	Rfam	11.0	mir-166	2.2e-12

Gene models

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