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_6BL_4159688FC Traes_6BL_4159688FC	ta_iwgsc_6bl_v1_4269873	2	3643	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_6BL_4159688FC.1 Traes_6BL_4159688FC.1 PAC:31815615	High	No	1966		Get ORF Coding potential... Type: noncoding Potential: -0.608 Folding energies... MFEI: -27.462 AMFE: -0.683 GC content %: 40.183
Taestivum_Traes_6BL_4159688FC.2 Traes_6BL_4159688FC.2 PAC:31815614	High	No	1194		Get ORF Coding potential... Type: noncoding Potential: -0.546 Folding energies... MFEI: -28.995 AMFE: -0.654 GC content %: 44.305
Taestivum_Traes_6BL_4159688FC.3 Traes_6BL_4159688FC.3 PAC:31815617	Low	No	1409		Get ORF Coding potential... Type: noncoding Potential: -1.192 Folding energies... MFEI: -25.912 AMFE: -0.670 GC content %: 38.680
Taestivum_Traes_6BL_4159688FC.4 Traes_6BL_4159688FC.4 PAC:31815616	Low	No	616		Get ORF Coding potential... Type: noncoding Potential: -1.090 Folding energies... MFEI: -22.468 AMFE: -0.586 GC content %: 38.312

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_6BL_4159688FC.3	RepBase (RepeatMasker)	2014-01-31	ATHOS_TM
Taestivum_Traes_6BL_4159688FC.4	RepBase (RepeatMasker)	2014-01-31	ATHOS_TM

Gene models

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