Gene

Atrichopoda evm 27.TU.AmTr v1.0 scaffold00001.120

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 Source Assembly Species Details

Atrichopoda_evm_27.TU.AmTr_v1.0_scaffold00001.120
evm_27.TU.AmTr_v1.0_scaffold00001.120
AmTr_v1.0_scaffold00001 2034042 2034746 Phytozome v1.0 Amborella_trichopoda
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 Sequence Details

Atrichopoda_evm_27.model.AmTr_v1.0_scaffold00001.120
evm_27.model.AmTr_v1.0_scaffold00001.120
PAC:31551439
Low No 285
Coding potential...
Type: noncoding Potential: -0.492
Folding energies...
MFEI: -28.912 AMFE: -0.589
GC content
%: 49.123


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
Atrichopoda_evm_27.model.AmTr_v1.0_scaffold00001.120  SwissProt 2015-06-01 Q9FRI5 9.0e-15


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).

evm_27.TU.AmTr_v1.0_scaffold00001.120.png