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_2BL_A7CCE64F5 Traes_2BL_A7CCE64F5	ta_iwgsc_2bl_v1_8010332	10055	13374	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_2BL_A7CCE64F5.1 Traes_2BL_A7CCE64F5.1 PAC:31883597	High	No	1353		Get ORF Coding potential... Type: noncoding Potential: -0.801 Folding energies... MFEI: -26.260 AMFE: -0.614 GC content %: 42.794
Taestivum_Traes_2BL_A7CCE64F5.3 Traes_2BL_A7CCE64F5.3 PAC:31883596	Low	No	682		Get ORF Coding potential... Type: noncoding Potential: -0.678 Folding energies... MFEI: -25.645 AMFE: -0.597 GC content %: 42.962
Taestivum_Traes_2BL_A7CCE64F5.4 Traes_2BL_A7CCE64F5.4 PAC:31883598	High	No	513		Get ORF Coding potential... Type: noncoding Potential: -0.636 Folding energies... MFEI: -24.639 AMFE: -0.569 GC content %: 43.275
Taestivum_Traes_2BL_A7CCE64F5.5 Traes_2BL_A7CCE64F5.5 PAC:31883599	Low	No	589		Get ORF Coding potential... Type: noncoding Potential: -0.710 Folding energies... MFEI: -25.739 AMFE: -0.604 GC content %: 42.615

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_2BL_A7CCE64F5.3	RepBase (RepeatMasker)	2014-01-31	Gypsy46-ZM_I-int
Taestivum_Traes_2BL_A7CCE64F5.5	RepBase (RepeatMasker)	2014-01-31	Gypsy46-ZM_I-int

Gene models

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