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_7AL_26D9F73E3 Traes_7AL_26D9F73E3	ta_iwgsc_7al_v1_4551907	76	3302	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_7AL_26D9F73E3.1 Traes_7AL_26D9F73E3.1 PAC:32004553	Low	No	548		Get ORF Coding potential... Type: noncoding Potential: -0.783 Folding energies... MFEI: -24.781 AMFE: -0.585 GC content %: 42.336
Taestivum_Traes_7AL_26D9F73E3.2 Traes_7AL_26D9F73E3.2 PAC:32004552	Low	No	561		Get ORF Coding potential... Type: noncoding Potential: -0.890 Folding energies... MFEI: -21.925 AMFE: -0.539 GC content %: 40.642
Taestivum_Traes_7AL_26D9F73E3.3 Traes_7AL_26D9F73E3.3 PAC:32004554	Low	Yes	1250		Get ORF Coding potential... Type: noncoding Potential: -0.986 Folding energies... MFEI: -28.110 AMFE: -0.668 GC content %: 42.080

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_7AL_26D9F73E3.3	Rfam	11.0	MIR1122	5.6e-12
Taestivum_Traes_7AL_26D9F73E3.3	RepBase (RepeatMasker)	2014-01-31	ATHOS_HV

Gene models

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