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_6BS_516A1040C Traes_6BS_516A1040C	ta_iwgsc_6bs_v1_3043098	3	566	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_6BS_516A1040C.1 Traes_6BS_516A1040C.1 PAC:31750438	High	No	234		Get ORF Coding potential... Type: noncoding Potential: -0.967 Folding energies... MFEI: -23.547 AMFE: -0.546 GC content %: 43.162
Taestivum_Traes_6BS_516A1040C.2 Traes_6BS_516A1040C.2 PAC:31750436	Low	No	300		Get ORF Coding potential... Type: noncoding Potential: -0.705 Folding energies... MFEI: -26.533 AMFE: -0.637 GC content %: 41.667
Taestivum_Traes_6BS_516A1040C.3 Traes_6BS_516A1040C.3 PAC:31750437	High	No	234		Get ORF Coding potential... Type: noncoding Potential: -0.871 Folding energies... MFEI: -27.991 AMFE: -0.636 GC content %: 44.017
Taestivum_Traes_6BS_516A1040C.4 Traes_6BS_516A1040C.4 PAC:31750439	High	No	207		Get ORF Coding potential... Type: noncoding Potential: -1.196 Folding energies... MFEI: -23.720 AMFE: -0.571 GC content %: 41.546

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_6BS_516A1040C.2	RepBase (RepeatMasker)	2014-01-31	L1-8_SBi

Gene models

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