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_002G147200 [ B456_002G147200]	2	27308031	27313867	v6	Gossypium raimondii (Ensembl Plants 51)	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	Orthologous group	Sequence	Details
Graimondii_KJB14868 KJB14868	Low	Yes	5329	OG0034586		Get ORF Coding potential... Type: noncoding Potential: -0.336 Folding energies... MFEI: -24.029 AMFE: -0.743 GC content %: 32.351
Graimondii_KJB14870 KJB14870	Low	Yes	5321	OG0034586		Get ORF Coding potential... Type: noncoding Potential: -0.209 Folding energies... MFEI: -24.086 AMFE: -0.746 GC content %: 32.306

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_KJB14870	Rfam	14.6	mir-1226	2.8e-4
Graimondii_KJB14868	RepBase (RepeatMasker)	2014-01-31	LTR/Gypsy
Graimondii_KJB14870	RepBase (RepeatMasker)	2014-01-31	LTR/Gypsy
Graimondii_KJB14868	SwissProt	2021-04-01	Q9C551	3.13e-26
Graimondii_KJB14870	SwissProt	2021-04-01	Q6YS30	5.85e-32
Graimondii_KJB14868	Rfam	14.6	mir-1226	2.8e-4

Gene models

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