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
Taestivum_Traes_1BS_4073CE3DB Traes_1BS_4073CE3DB	ta_iwgsc_1bs_v1_1420918	15	6324	Phytozome	v2.2	Triticum_aestivum	Coding? Yes

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
Taestivum_Traes_1BS_4073CE3DB.17 Traes_1BS_4073CE3DB.17 PAC:31961150	Low	No	1318		Get ORF Coding potential... Type: noncoding Potential: -0.610 Folding energies... MFEI: -27.959 AMFE: -0.614 GC content %: 45.524
Taestivum_Traes_1BS_4073CE3DB.18 Traes_1BS_4073CE3DB.18 PAC:31961151	Low	No	1043		Get ORF Coding potential... Type: noncoding Potential: -0.778 Folding energies... MFEI: -28.178 AMFE: -0.668 GC content %: 42.186

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
Taestivum_Traes_1BS_4073CE3DB.17	RepBase (RepeatMasker)	2014-01-31	Gypsy-20_Mad-I

Gene models

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