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_TRIDC5AG041210 [ TRIDC5AG041210]	5A	476864475	476884251	v1	Triticum dicoccoides (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
Tdicoccoides_TRIDC5AG041210.1 TRIDC5AG041210.1	High	No	803	OG0062269		Get ORF Coding potential... Type: noncoding Potential: -0.506 Folding energies... MFEI: -33.537 AMFE: -0.665 GC content %: 50.436
Tdicoccoides_TRIDC5AG041210.2 TRIDC5AG041210.2	High	No	585	OG0062269		Get ORF Coding potential... Type: noncoding Potential: -0.597 Folding energies... MFEI: -28.821 AMFE: -0.615 GC content %: 46.838
Tdicoccoides_TRIDC5AG041210.3 TRIDC5AG041210.3	Low	No	893	OG0009466		Get ORF Coding potential... Type: noncoding Potential: -0.569 Folding energies... MFEI: -33.998 AMFE: -0.654 GC content %: 51.960
Tdicoccoides_TRIDC5AG041210.4 TRIDC5AG041210.4	Low	No	904	OG0009466		Get ORF Coding potential... Type: noncoding Potential: -0.536 Folding energies... MFEI: -33.617 AMFE: -0.644 GC content %: 52.212
Tdicoccoides_TRIDC5AG041210.5 TRIDC5AG041210.5	Low	No	818	OG0009466		Get ORF Coding potential... Type: noncoding Potential: -0.550 Folding energies... MFEI: -32.090 AMFE: -0.650 GC content %: 49.389
Tdicoccoides_TRIDC5AG041210.6 TRIDC5AG041210.6	High	No	584	OG0009466		Get ORF Coding potential... Type: noncoding Potential: -0.842 Folding energies... MFEI: -26.353 AMFE: -0.583 GC content %: 45.205
Tdicoccoides_TRIDC5AG041210.7 TRIDC5AG041210.7	High	No	864	OG0009466		Get ORF Coding potential... Type: noncoding Potential: -0.530 Folding energies... MFEI: -32.812 AMFE: -0.637 GC content %: 51.505

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_TRIDC5AG041210.5	RepBase (RepeatMasker)	2014-01-31	LTR/ERV1
Tdicoccoides_TRIDC5AG041210.3	RepBase (RepeatMasker)	2014-01-31	LTR/ERV1
Tdicoccoides_TRIDC5AG041210.4	RepBase (RepeatMasker)	2014-01-31	LTR/ERV1

Gene models

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