Zmays Zm00001d024612

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_Zm00001d024612
[ Zm00001d024612]
10 80319653 80328964 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_Zm00001d024612_T021
Zm00001d024612_T021
Low No 5317 [1]
Coding potential...
Type: noncoding Potential: -0.004
Folding energies...
MFEI: -26.904 AMFE: -0.645
GC content
%: 41.734
Zmays_Zm00001d024612_T038
Zm00001d024612_T038
Low No 5727 [2]
Coding potential...
Type: noncoding Potential: -0.293
Folding energies...
MFEI: -26.551 AMFE: -0.650
GC content
%: 40.877
Zmays_Zm00001d024612_T044
Zm00001d024612_T044
Low No 4558 [3]
Coding potential...
Type: noncoding Potential: -0.157
Folding energies...
MFEI: -27.214 AMFE: -0.652
GC content
%: 41.729
Zmays_Zm00001d024612_T045
Zm00001d024612_T045
Low No 4812 [4]
Coding potential...
Type: noncoding Potential: -0.072
Folding energies...
MFEI: -27.255 AMFE: -0.654
GC content
%: 41.687
Zmays_Zm00001d024612_T052
Zm00001d024612_T052
Low No 5255 [5]
Coding potential...
Type: noncoding Potential: -0.108
Folding energies...
MFEI: -26.839 AMFE: -0.657
GC content
%: 40.856
Zmays_Zm00001d024612_T055
Zm00001d024612_T055
Low No 4740 [6]
Coding potential...
Type: noncoding Potential: -0.022
Folding energies...
MFEI: -27.291 AMFE: -0.657
GC content
%: 41.540
Zmays_Zm00001d024612_T059
Zm00001d024612_T059
Low No 4484 [7]
Coding potential...
Type: noncoding Potential: -0.178
Folding energies...
MFEI: -26.719 AMFE: -0.656
GC content
%: 40.700
Zmays_Zm00001d024612_T063
Zm00001d024612_T063
Low No 5331 [8]
Coding potential...
Type: noncoding Potential: -0.005
Folding energies...
MFEI: -26.762 AMFE: -0.655
GC content
%: 40.874
Zmays_Zm00001d024612_T066
Zm00001d024612_T066
Low No 3761 [9]
Coding potential...
Type: noncoding Potential: -0.247
Folding energies...
MFEI: -26.169 AMFE: -0.655
GC content
%: 39.963
Zmays_Zm00001d024612_T067
Zm00001d024612_T067
Low No 3488 [10]
Coding potential...
Type: noncoding Potential: -0.227
Folding energies...
MFEI: -25.536 AMFE: -0.659
GC content
%: 38.733
Zmays_Zm00001d024612_T069
Zm00001d024612_T069
Low No 566 [11]
Coding potential...
Type: noncoding Potential: -0.138
Folding energies...
MFEI: -23.180 AMFE: -0.566
GC content
%: 40.989


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_Zm00001d024612_T066  SwissProt 2021-04-01 F4K2A1 1.16e-9
Zmays_Zm00001d024612_T045  SwissProt 2021-04-01 Q8LJW3 2.16e-17
Zmays_Zm00001d024612_T066  RepBase (RepeatMasker) 0000-00-00 SINE/tRNA
Zmays_Zm00001d024612_T045  RepBase (RepeatMasker) 0000-00-00 SINE/tRNA
Zmays_Zm00001d024612_T067  SwissProt 2021-04-01 F4K2A1 1.05e-9
Zmays_Zm00001d024612_T052  SwissProt 2021-04-01 F4K2A1 5.84e-10
Zmays_Zm00001d024612_T067  RepBase (RepeatMasker) 0000-00-00 SINE/tRNA
Zmays_Zm00001d024612_T052  RepBase (RepeatMasker) 0000-00-00 LTR
Zmays_Zm00001d024612_T069  SwissProt 2021-04-01 Q9SDG8 1.61e-11
Zmays_Zm00001d024612_T055  SwissProt 2021-04-01 Q8LJW3 2.08e-17
... further results
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_Zm00001d024612.png