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
Atrichopoda_evm_27.TU.AmTr_v1.0_scaffold00007.150 evm_27.TU.AmTr_v1.0_scaffold00007.150	AmTr_v1.0_scaffold00007	3192127	3192402	Phytozome	v1.0	Amborella_trichopoda	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
Atrichopoda_evm_27.model.AmTr_v1.0_scaffold00007.150 evm_27.model.AmTr_v1.0_scaffold00007.150 PAC:31557563	Low	No	276		Get ORF Coding potential... Type: noncoding Potential: -0.151 Folding energies... MFEI: -29.819 AMFE: -0.549 GC content %: 54.348

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
Atrichopoda_evm_27.model.AmTr_v1.0_scaffold00007.150	SwissProt	2015-06-01	O64864	3.0e-22

Gene models

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