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_2AS_859DE6040 Traes_2AS_859DE6040	ta_iwgsc_2as_v1_5303294	4	1291	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_2AS_859DE6040.1 Traes_2AS_859DE6040.1 PAC:31901676	Low	Yes	1220		Get ORF Coding potential... Type: noncoding Potential: -0.769 Folding energies... MFEI: -22.555 AMFE: -0.644 GC content %: 35.000
Taestivum_Traes_2AS_859DE6040.2 Traes_2AS_859DE6040.2 PAC:31901677	Low	Yes	674		Get ORF Coding potential... Type: noncoding Potential: -1.367 Folding energies... MFEI: -19.525 AMFE: -0.604 GC content %: 32.344

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_2AS_859DE6040.1	Rfam	11.0	MIR1122	0.0013
Taestivum_Traes_2AS_859DE6040.2	Rfam	11.0	MIR1122	7.3e-4
Taestivum_Traes_2AS_859DE6040.1	RepBase (RepeatMasker)	2014-01-31	ATHOS_HV
Taestivum_Traes_2AS_859DE6040.2	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).