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_7BL_39F8E5293 Traes_7BL_39F8E5293	ta_iwgsc_7bl_v1_6519207	1	1931	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_7BL_39F8E5293.1 Traes_7BL_39F8E5293.1 PAC:31811853	High	No	534		Get ORF Coding potential... Type: noncoding Potential: -1.019 Folding energies... MFEI: -39.981 AMFE: -0.700 GC content %: 57.116
Taestivum_Traes_7BL_39F8E5293.2 Traes_7BL_39F8E5293.2 PAC:31811851	High	No	780		Get ORF Coding potential... Type: noncoding Potential: -0.932 Folding energies... MFEI: -33.705 AMFE: -0.659 GC content %: 51.154
Taestivum_Traes_7BL_39F8E5293.3 Traes_7BL_39F8E5293.3 PAC:31811852	Low	No	1929		Get ORF Coding potential... Type: noncoding Potential: -1.080 Folding energies... MFEI: -31.503 AMFE: -0.694 GC content %: 45.412

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_7BL_39F8E5293.3	RepBase (RepeatMasker)	2014-01-31	Gypsy-27_BRa-I

Gene models

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