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_TRIDC5AG028740 [ TRIDC5AG028740]	5A	367906613	367910161	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_TRIDC5AG028740.2 TRIDC5AG028740.2	Low	No	521	OG0010058		Get ORF Coding potential... Type: noncoding Potential: -0.289 Folding energies... MFEI: -35.278 AMFE: -0.638 GC content %: 55.278
Tdicoccoides_TRIDC5AG028740.3 TRIDC5AG028740.3	Low	No	706	OG0010058		Get ORF Coding potential... Type: noncoding Potential: -0.047 Folding energies... MFEI: -33.980 AMFE: -0.638 GC content %: 53.258
Tdicoccoides_TRIDC5AG028740.4 TRIDC5AG028740.4	Low	No	654	OG0062241		Get ORF Coding potential... Type: noncoding Potential: -0.078 Folding energies... MFEI: -29.541 AMFE: -0.644 GC content %: 45.872
Tdicoccoides_TRIDC5AG028740.5 TRIDC5AG028740.5	Low	No	615	OG0062241		Get ORF Coding potential... Type: noncoding Potential: -0.841 Folding energies... MFEI: -29.236 AMFE: -0.633 GC content %: 46.179
Tdicoccoides_TRIDC5AG028740.6 TRIDC5AG028740.6	High	No	1145	OG0362106		Get ORF Coding potential... Type: noncoding Potential: -1.267 Folding energies... MFEI: -26.253 AMFE: -0.661 GC content %: 39.738

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_TRIDC5AG028740.2	SwissProt	2021-04-01	Q5BPM6	7.67e-8
Tdicoccoides_TRIDC5AG028740.3	SwissProt	2021-04-01	Q5BPM6	2.49e-15
Tdicoccoides_TRIDC5AG028740.4	SwissProt	2021-04-01	O80588	5.83e-13
Tdicoccoides_TRIDC5AG028740.5	SwissProt	2021-04-01	Q5BPM6	1.49e-7

Gene models

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