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_3AS_CD1BB221B Traes_3AS_CD1BB221B	ta_iwgsc_3as_v1_3317910	48	7023	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_3AS_CD1BB221B.5 Traes_3AS_CD1BB221B.5 PAC:31838576	Low	No	273		Get ORF Coding potential... Type: noncoding Potential: -0.872 Folding energies... MFEI: -29.048 AMFE: -0.522 GC content %: 55.678
Taestivum_Traes_3AS_CD1BB221B.6 Traes_3AS_CD1BB221B.6 PAC:31838577	Low	No	270		Get ORF Coding potential... Type: noncoding Potential: -1.126 Folding energies... MFEI: -29.333 AMFE: -0.521 GC content %: 56.296

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_3AS_CD1BB221B.5	RepBase (RepeatMasker)	2014-01-31	LINE1-1_SBi
Taestivum_Traes_3AS_CD1BB221B.6	RepBase (RepeatMasker)	2014-01-31	LINE1-1_SBi

Gene models

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