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_3AL_226FA49B6 Traes_3AL_226FA49B6	ta_iwgsc_3al_v1_4287893	1	1795	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_3AL_226FA49B6.2 Traes_3AL_226FA49B6.2 PAC:31785077	Low	No	1351		Get ORF Coding potential... Type: noncoding Potential: -1.188 Folding energies... MFEI: -23.212 AMFE: -0.539 GC content %: 43.079
Taestivum_Traes_3AL_226FA49B6.3 Traes_3AL_226FA49B6.3 PAC:31785079	Low	No	1438		Get ORF Coding potential... Type: noncoding Potential: -0.328 Folding energies... MFEI: -26.892 AMFE: -0.585 GC content %: 45.967
Taestivum_Traes_3AL_226FA49B6.4 Traes_3AL_226FA49B6.4 PAC:31785078	Low	No	898		Get ORF Coding potential... Type: noncoding Potential: -0.922 Folding energies... MFEI: -30.290 AMFE: -0.553 GC content %: 54.788
Taestivum_Traes_3AL_226FA49B6.5 Traes_3AL_226FA49B6.5 PAC:31785080	Low	No	541		Get ORF Coding potential... Type: noncoding Potential: -0.113 Folding energies... MFEI: -34.769 AMFE: -0.586 GC content %: 59.335

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_3AL_226FA49B6.2	RepBase (RepeatMasker)	2014-01-31	hAT-N18_SBi
Taestivum_Traes_3AL_226FA49B6.4	RepBase (RepeatMasker)	2014-01-31	hAT-N18_SBi

Gene models

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