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_1AL_2B62AA327 Traes_1AL_2B62AA327	ta_iwgsc_1al_v2_3948393	1776	9055	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_1AL_2B62AA327.16 Traes_1AL_2B62AA327.16 PAC:31929519	Low	No	1883		Get ORF Coding potential... Type: noncoding Potential: -1.042 Folding energies... MFEI: -30.080 AMFE: -0.622 GC content %: 48.327
Taestivum_Traes_1AL_2B62AA327.17 Traes_1AL_2B62AA327.17 PAC:31929520	High	No	1979		Get ORF Coding potential... Type: noncoding Potential: -1.049 Folding energies... MFEI: -27.463 AMFE: -0.639 GC content %: 42.951

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_1AL_2B62AA327.16	RepBase (RepeatMasker)	2014-01-31	REP1_SB

Gene models

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