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
Graimondii_B456_007G362100 [ B456_007G362100]	7	59372016	59374701	v6	Gossypium raimondii (Ensembl Plants 51)	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
Graimondii_KJB39062 KJB39062	Low	No	1827	OG0000917		Get ORF Coding potential... Type: noncoding Potential: -0.713 Folding energies... MFEI: -24.740 AMFE: -0.690 GC content %: 35.851
Graimondii_KJB39063 KJB39063	Low	No	2686	OG0000917		Get ORF Coding potential... Type: noncoding Potential: -0.768 Folding energies... MFEI: -23.816 AMFE: -0.705 GC content %: 33.805
Graimondii_KJB39064 KJB39064	Low	No	2515	OG0000917		Get ORF Coding potential... Type: noncoding Potential: -0.759 Folding energies... MFEI: -23.988 AMFE: -0.705 GC content %: 34.036
Graimondii_KJB39065 KJB39065	High	No	342	OG0000917		Get ORF Coding potential... Type: noncoding Potential: -0.315 Folding energies... MFEI: -19.444 AMFE: -0.429 GC content %: 45.322
Graimondii_KJB39066 KJB39066	High	No	342	OG0000917		Get ORF Coding potential... Type: noncoding Potential: -0.315 Folding energies... MFEI: -19.444 AMFE: -0.429 GC content %: 45.322

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
Graimondii_KJB39062	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm; DNA/hAT-Ac; DNA/MULE-MuDR; Satellite
Graimondii_KJB39063	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm; DNA/hAT-Ac; DNA/MULE-MuDR; Satellite
Graimondii_KJB39064	RepBase (RepeatMasker)	2014-01-31	DNA/CMC-EnSpm; DNA/hAT-Ac; DNA/MULE-MuDR; Satellite

Gene models

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