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
Tdicoccoides_TRIDC6BG037840 [ TRIDC6BG037840]	6B	388658140	388660629	v1	Triticum dicoccoides (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
Tdicoccoides_TRIDC6BG037840.10 TRIDC6BG037840.10	High	No	452	OG0365415		Get ORF Coding potential... Type: noncoding Potential: -0.904 Folding energies... MFEI: -50.553 AMFE: -0.737 GC content %: 68.584
Tdicoccoides_TRIDC6BG037840.2 TRIDC6BG037840.2	Low	Yes	1365	OG0015428		Get ORF Coding potential... Type: noncoding Potential: -1.018 Folding energies... MFEI: -32.225 AMFE: -0.682 GC content %: 47.253
Tdicoccoides_TRIDC6BG037840.4 TRIDC6BG037840.4	Low	Yes	1315	OG0015428		Get ORF Coding potential... Type: noncoding Potential: -0.789 Folding energies... MFEI: -36.259 AMFE: -0.702 GC content %: 51.635
Tdicoccoides_TRIDC6BG037840.5 TRIDC6BG037840.5	Low	Yes	959	OG0015428		Get ORF Coding potential... Type: noncoding Potential: -1.347 Folding energies... MFEI: -28.308 AMFE: -0.670 GC content %: 42.231
Tdicoccoides_TRIDC6BG037840.7 TRIDC6BG037840.7	High	No	1198	OG0015428		Get ORF Coding potential... Type: noncoding Potential: -0.954 Folding energies... MFEI: -31.678 AMFE: -0.651 GC content %: 48.664

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
Tdicoccoides_TRIDC6BG037840.2	Rfam	14.6	MIR1122	2.9e-4
Tdicoccoides_TRIDC6BG037840.4	Rfam	14.6	MIR1122	2.8e-4
Tdicoccoides_TRIDC6BG037840.5	Rfam	14.6	MIR1122	2.1e-4

Gene models

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