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_6BS_594AA477A Traes_6BS_594AA477A	ta_iwgsc_6bs_v1_3013203	178	2719	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_6BS_594AA477A.4 Traes_6BS_594AA477A.4 PAC:31941760	Low	No	852		Get ORF Coding potential... Type: noncoding Potential: -1.008 Folding energies... MFEI: -26.033 AMFE: -0.593 GC content %: 43.897
Taestivum_Traes_6BS_594AA477A.5 Traes_6BS_594AA477A.5 PAC:31941761	Low	No	846		Get ORF Coding potential... Type: noncoding Potential: -1.069 Folding energies... MFEI: -25.898 AMFE: -0.592 GC content %: 43.735
Taestivum_Traes_6BS_594AA477A.6 Traes_6BS_594AA477A.6 PAC:31941762	Low	No	903		Get ORF Coding potential... Type: noncoding Potential: -1.036 Folding energies... MFEI: -26.069 AMFE: -0.610 GC content %: 42.746

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_6BS_594AA477A.6	RepBase (RepeatMasker)	2014-01-31	Copia-96_ST-I

Gene models

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