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	Assembly	Species	Details
Bvulgaris_BVRB_001900 [ BVRB_001900]	0056.scaffold00205	165932	166807	v1.2	Beta vulgaris (Phytozome 13)	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	Orthologous group	Sequence	Details
Bvulgaris_KMS96118 KMS96118	Low	No	703	OG0027794		Get ORF Coding potential... Type: noncoding Potential: -1.075 Folding energies... MFEI: -22.418 AMFE: -0.606 GC content %: 36.984
Bvulgaris_KMS96119 KMS96119	Low	No	503	OG0027794		Get ORF Coding potential... Type: noncoding Potential: -1.343 Folding energies... MFEI: -21.372 AMFE: -0.575 GC content %: 37.177

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
Bvulgaris_KMS96119	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm; DNA/PIF-Harbinger
Bvulgaris_KMS96118	SwissProt	2021-04-01	Q8BR93	5.47e-10
Bvulgaris_KMS96118	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm; DNA/PIF-Harbinger

Gene models

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