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_FFAEA1E22 Traes_7BL_FFAEA1E22	ta_iwgsc_7bl_v1_6693641	4357	8968	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_7BL_FFAEA1E22.10 Traes_7BL_FFAEA1E22.10 PAC:31796520	Low	No	891		Get ORF Coding potential... Type: noncoding Potential: -0.991 Folding energies... MFEI: -28.563 AMFE: -0.656 GC content %: 43.547
Taestivum_Traes_7BL_FFAEA1E22.11 Traes_7BL_FFAEA1E22.11 PAC:31796526	High	No	1183		Get ORF Coding potential... Type: noncoding Potential: -1.223 Folding energies... MFEI: -24.041 AMFE: -0.666 GC content %: 36.095
Taestivum_Traes_7BL_FFAEA1E22.5 Traes_7BL_FFAEA1E22.5 PAC:31796521	Low	No	1796		Get ORF Coding potential... Type: noncoding Potential: -0.023 Folding energies... MFEI: -26.086 AMFE: -0.638 GC content %: 40.869

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_FFAEA1E22.5	RepBase (RepeatMasker)	2014-01-31	Copia-52_ZM-I

Gene models

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