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_7DL_30AEE2CF6 Traes_7DL_30AEE2CF6	ta_iwgsc_7dl_v1_3395141	11488	14779	Phytozome	v2.2	Triticum_aestivum	Coding? No

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_7DL_30AEE2CF6.1 Traes_7DL_30AEE2CF6.1 PAC:31906615	Low	No	695		Get ORF Coding potential... Type: noncoding Potential: -1.000 Folding energies... MFEI: -31.482 AMFE: -0.629 GC content %: 50.072
Taestivum_Traes_7DL_30AEE2CF6.2 Traes_7DL_30AEE2CF6.2 PAC:31906611	Low	No	587		Get ORF Coding potential... Type: noncoding Potential: -0.979 Folding energies... MFEI: -31.124 AMFE: -0.639 GC content %: 48.722
Taestivum_Traes_7DL_30AEE2CF6.3 Traes_7DL_30AEE2CF6.3 PAC:31906612	Low	No	660		Get ORF Coding potential... Type: noncoding Potential: -0.994 Folding energies... MFEI: -31.424 AMFE: -0.625 GC content %: 50.303
Taestivum_Traes_7DL_30AEE2CF6.4 Traes_7DL_30AEE2CF6.4 PAC:31906613	Low	No	649		Get ORF Coding potential... Type: noncoding Potential: -0.992 Folding energies... MFEI: -31.217 AMFE: -0.616 GC content %: 50.693
Taestivum_Traes_7DL_30AEE2CF6.5 Traes_7DL_30AEE2CF6.5 PAC:31906614	Low	No	962		Get ORF Coding potential... Type: noncoding Potential: -1.037 Folding energies... MFEI: -31.788 AMFE: -0.651 GC content %: 48.857

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_7DL_30AEE2CF6.1	RepBase (RepeatMasker)	2014-01-31	EnSpm-N1_HV
Taestivum_Traes_7DL_30AEE2CF6.2	RepBase (RepeatMasker)	2014-01-31	EnSpm-N1_HV
Taestivum_Traes_7DL_30AEE2CF6.3	RepBase (RepeatMasker)	2014-01-31	EnSpm-N1_HV
Taestivum_Traes_7DL_30AEE2CF6.4	RepBase (RepeatMasker)	2014-01-31	EnSpm-N1_HV

Gene models

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