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
Ahalleri_Araha.46415s0003 Araha.46415s0003	Scaffold46415	13855	14987	Phytozome		[[Species:|]]"Species:" cannot be used as a page name in this wiki.	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
Ahalleri_Araha.46415s0003.1 Araha.46415s0003.1 PAC:28838323	Low	Yes	1038		Get ORF Coding potential... Type: noncoding Potential: -1.324 Folding energies... MFEI: -22.649 AMFE: -0.662 GC content %: 34.200
Ahalleri_Araha.46415s0003.2 Araha.46415s0003.2 PAC:28838322	Low	Yes	978		Get ORF Coding potential... Type: noncoding Potential: -1.320 Folding energies... MFEI: -21.493 AMFE: -0.626 GC content %: 34.356

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
Ahalleri_Araha.46415s0003.1	Rfam	11.0	mir-166	6.5e-23
Ahalleri_Araha.46415s0003.2	Rfam	11.0	mir-166	6.2e-23

Gene models

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