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_7AS_2D94ACEA3 Traes_7AS_2D94ACEA3	ta_iwgsc_7as_v1_4175519	3991	5793	Phytozome	v2.2	Triticum_aestivum	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
Taestivum_Traes_7AS_2D94ACEA3.1 Traes_7AS_2D94ACEA3.1 PAC:31907686	High	No	727		Get ORF Coding potential... Type: noncoding Potential: -0.863 Folding energies... MFEI: -31.733 AMFE: -0.677 GC content %: 46.905
Taestivum_Traes_7AS_2D94ACEA3.2 Traes_7AS_2D94ACEA3.2 PAC:31907685	Low	No	1453		Get ORF Coding potential... Type: noncoding Potential: -0.933 Folding energies... MFEI: -29.167 AMFE: -0.697 GC content %: 41.844
Taestivum_Traes_7AS_2D94ACEA3.3 Traes_7AS_2D94ACEA3.3 PAC:31907687	Low	No	826		Get ORF Coding potential... Type: noncoding Potential: -1.309 Folding energies... MFEI: -22.688 AMFE: -0.669 GC content %: 33.898

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_7AS_2D94ACEA3.2	RepBase (RepeatMasker)	2014-01-31	HADES_TA
Taestivum_Traes_7AS_2D94ACEA3.3	RepBase (RepeatMasker)	2014-01-31	HADES_TA

Gene models

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