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_FD09F04FA Traes_7BS_FD09F04FA	ta_iwgsc_7bs_v1_3127962	1332	5087	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_FD09F04FA.15 Traes_7BS_FD09F04FA.15 PAC:32001003	High	No	1538		Get ORF Coding potential... Type: noncoding Potential: -0.248 Folding energies... MFEI: -27.035 AMFE: -0.648 GC content %: 41.743
Taestivum_Traes_7BS_FD09F04FA.16 Traes_7BS_FD09F04FA.16 PAC:32001004	High	No	1450		Get ORF Coding potential... Type: noncoding Potential: -0.144 Folding energies... MFEI: -27.593 AMFE: -0.648 GC content %: 42.552
Taestivum_Traes_7BS_FD09F04FA.17 Traes_7BS_FD09F04FA.17 PAC:32001005	High	No	1446		Get ORF Coding potential... Type: noncoding Potential: -0.785 Folding energies... MFEI: -26.459 AMFE: -0.626 GC content %: 42.254
Taestivum_Traes_7BS_FD09F04FA.18 Traes_7BS_FD09F04FA.18 PAC:32001006	Low	Yes	1046		Get ORF Coding potential... Type: noncoding Potential: -0.580 Folding energies... MFEI: -27.228 AMFE: -0.636 GC content %: 42.830
Taestivum_Traes_7BS_FD09F04FA.19 Traes_7BS_FD09F04FA.19 PAC:32001007	High	No	1687		Get ORF Coding potential... Type: noncoding Potential: -0.703 Folding energies... MFEI: -27.119 AMFE: -0.643 GC content %: 42.146

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_FD09F04FA.18	Rfam	11.0	mir-44	0.0079

Gene models

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