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
Bdistachyon_Bradi5g06730 Bradi5g06730	Bd5	8900838	8901769	Phytozome	v3.1	Brachypodium_distachyon	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
Bdistachyon_Bradi5g06730.1 Bradi5g06730.1 PAC:32811451	Low	Yes	853		Get ORF Coding potential... Type: noncoding Potential: -1.003 Folding energies... MFEI: -28.992 AMFE: -0.773 GC content %: 37.515
Bdistachyon_Bradi5g06730.2 Bradi5g06730.2 PAC:32811450	Low	Yes	932		Get ORF Coding potential... Type: noncoding Potential: -0.532 Folding energies... MFEI: -28.691 AMFE: -0.766 GC content %: 37.446

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
Bdistachyon_Bradi5g06730.1	RepBase (RepeatMasker)	2014-01-31	TREP216
Bdistachyon_Bradi5g06730.2	RepBase (RepeatMasker)	2014-01-31	TREP216
Bdistachyon_Bradi5g06730.2	SwissProt	2015-06-01	Q9SYX2	2.0e-4
Bdistachyon_Bradi5g06730.1	Rfam	11.0	MIR1122	7.0e-13
Bdistachyon_Bradi5g06730.2	Rfam	11.0	MIR1122	7.6e-13

Gene models

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