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_7BS_FD31F2A2E Traes_7BS_FD31F2A2E	ta_iwgsc_7bs_v1_3000324	3	2282	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_7BS_FD31F2A2E.1 Traes_7BS_FD31F2A2E.1 PAC:31739285	Low	No	896		Get ORF Coding potential... Type: noncoding Potential: -0.073 Folding energies... MFEI: -30.558 AMFE: -0.637 GC content %: 47.991
Taestivum_Traes_7BS_FD31F2A2E.2 Traes_7BS_FD31F2A2E.2 PAC:31739283	Low	No	2101		Get ORF Coding potential... Type: noncoding Potential: -0.156 Folding energies... MFEI: -28.334 AMFE: -0.653 GC content %: 43.408
Taestivum_Traes_7BS_FD31F2A2E.3 Traes_7BS_FD31F2A2E.3 PAC:31739284	Low	No	962		Get ORF Coding potential... Type: noncoding Potential: -0.021 Folding energies... MFEI: -31.019 AMFE: -0.649 GC content %: 47.817
Taestivum_Traes_7BS_FD31F2A2E.4 Traes_7BS_FD31F2A2E.4 PAC:31739286	Low	No	1286		Get ORF Coding potential... Type: noncoding Potential: -0.500 Folding energies... MFEI: -27.784 AMFE: -0.663 GC content %: 41.913
Taestivum_Traes_7BS_FD31F2A2E.5 Traes_7BS_FD31F2A2E.5 PAC:31739287	Low	No	674		Get ORF Coding potential... Type: noncoding Potential: -0.468 Folding energies... MFEI: -27.181 AMFE: -0.632 GC content %: 43.027

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_7BS_FD31F2A2E.2	RepBase (RepeatMasker)	2014-01-31	Copia-42_Mad-I
Taestivum_Traes_7BS_FD31F2A2E.4	RepBase (RepeatMasker)	2014-01-31	Copia-42_Mad-I

Gene models

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