Zmays Zm00001d025456

From GreeNC


Gene information
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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

Zmays_Zm00001d025456
[ Zm00001d025456]
10 119082076 119083221 v4 Zea mays (Phytozome 13)
Coding?
No


Transcript features
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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

Zmays_Zm00001d025456_T001
Zm00001d025456_T001
Low No 612 [1]
Coding potential...
Type: noncoding Potential: -1.400
Folding energies...
MFEI: -22.042 AMFE: -0.630
GC content
%: 34.967
Zmays_Zm00001d025456_T002
Zm00001d025456_T002
Low No 569 [2]
Coding potential...
Type: noncoding Potential: -1.040
Folding energies...
MFEI: -22.285 AMFE: -0.660
GC content
%: 33.743
Zmays_Zm00001d025456_T003
Zm00001d025456_T003
Low No 456 [3]
Coding potential...
Type: noncoding Potential: -0.976
Folding energies...
MFEI: -22.127 AMFE: -0.635
GC content
%: 34.868


Matches to external databases
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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
Zmays_Zm00001d025456_T001  RepBase (RepeatMasker) 0000-00-00 RC/Helitron
Zmays_Zm00001d025456_T002  RepBase (RepeatMasker) 0000-00-00 RC/Helitron
Zmays_Zm00001d025456_T003  RepBase (RepeatMasker) 0000-00-00 RC/Helitron


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

Zmays_Zm00001d025456.png