Gene

Stuberosum PGSC0003DMG403001341

From GreeNC


Gene information
Help.png

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

Stuberosum_PGSC0003DMG403001341
PGSC0003DMG403001341
chr02 67220033 67223604 Phytozome v3.4 Solanum_tuberosum
Coding?
Yes


Transcript features
Help.png

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

Stuberosum_PGSC0003DMT400003392
PGSC0003DMT400003392
PAC:24426897
Low No 3242
Coding potential...
Type: noncoding Potential: -0.730
Folding energies...
MFEI: -24.479 AMFE: -0.653
GC content
%: 37.477
Stuberosum_PGSC0003DMT400003393
PGSC0003DMT400003393
PAC:24426898
Low No 3376
Coding potential...
Type: noncoding Potential: -0.855
Folding energies...
MFEI: -24.843 AMFE: -0.661
GC content
%: 37.589


Matches to external databases
Help.png

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
Stuberosum_PGSC0003DMT400003392  RepBase (RepeatMasker) 2014-01-31 TS
Stuberosum_PGSC0003DMT400003393  RepBase (RepeatMasker) 2014-01-31 TS


Gene models
Help.png

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

PGSC0003DMG403001341.png