Zmays Zm00001d005858

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_Zm00001d005858
[ Zm00001d005858]
2 190973608 190979528 v4 Zea mays (Phytozome 13)
Coding?
Yes


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_Zm00001d005858_T002
Zm00001d005858_T002
Low No 5725 [1]
Coding potential...
Type: noncoding Potential: -1.142
Folding energies...
MFEI: -28.482 AMFE: -0.667
GC content
%: 42.672
Zmays_Zm00001d005858_T003
Zm00001d005858_T003
Low No 605 [2]
Coding potential...
Type: noncoding Potential: -0.971
Folding energies...
MFEI: -33.355 AMFE: -0.664
GC content
%: 50.248
Zmays_Zm00001d005858_T004
Zm00001d005858_T004
Low No 4238 [3]
Coding potential...
Type: noncoding Potential: -1.040
Folding energies...
MFEI: -29.658 AMFE: -0.661
GC content
%: 44.856
Zmays_Zm00001d005858_T005
Zm00001d005858_T005
High No 668 [4]
Coding potential...
Type: noncoding Potential: -0.853
Folding energies...
MFEI: -30.479 AMFE: -0.642
GC content
%: 47.455


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_Zm00001d005858_T004  RepBase (RepeatMasker) 0000-00-00 LINE/Tad1
Zmays_Zm00001d005858_T003  SwissProt 2021-04-01 Q54T60 5.52e-4
Zmays_Zm00001d005858_T002  RepBase (RepeatMasker) 0000-00-00 LINE/Tad1
Zmays_Zm00001d005858_T003  RepBase (RepeatMasker) 0000-00-00 LINE/Tad1


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_Zm00001d005858.png