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_7BAB586EC Traes_7BS_7BAB586EC	ta_iwgsc_7bs_v1_690141	1809	6820	Phytozome	v2.2	Triticum_aestivum	Coding? Yes

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_7BAB586EC.4 Traes_7BS_7BAB586EC.4 PAC:31950565	Low	No	365		Get ORF Coding potential... Type: noncoding Potential: -1.081 Folding energies... MFEI: -29.644 AMFE: -0.672 GC content %: 44.110
Taestivum_Traes_7BS_7BAB586EC.5 Traes_7BS_7BAB586EC.5 PAC:31950564	High	No	963		Get ORF Coding potential... Type: noncoding Potential: -1.121 Folding energies... MFEI: -23.873 AMFE: -0.600 GC content %: 39.772
Taestivum_Traes_7BS_7BAB586EC.6 Traes_7BS_7BAB586EC.6 PAC:31950566	High	No	620		Get ORF Coding potential... Type: noncoding Potential: -0.999 Folding energies... MFEI: -19.790 AMFE: -0.601 GC content %: 32.903
Taestivum_Traes_7BS_7BAB586EC.7 Traes_7BS_7BAB586EC.7 PAC:31950567	High	No	768		Get ORF Coding potential... Type: noncoding Potential: -1.342 Folding energies... MFEI: -19.622 AMFE: -0.520 GC content %: 37.760

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_7BAB586EC.4	RepBase (RepeatMasker)	2014-01-31	EnSpm-1_TA

Gene models

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