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Gene Name:
JGI's name for the predicted gene of Populus trichocarpa. If the gene was predicted by another center, the name is the one assigned by that center
Gene Model:
A gene model represents the mRNA transcript of a gene and therefore contains information about features of the transcript such as exon-intron boundaries, splice sites, UTRs, etc.
Protein ID:
The unique protein serial number of Populus trichocarpa.
TF Family:
The family the gene belongs to.
Chromosome:
The linkage group of the gene locates in.
Gene Structure:
The gene structure picture is used to demonstrate the exons distribution along the gene. The gene length is the entire length, including exons and introns.
Annotation:
Relative GO or UniGene information was selected and listed.
Protein Sequence Features:
Graphic view. Relative information as supported evidences from InterPro, UniPro, RefSeq, and TransFac was selected.
Nucleic Location Signal:
Nucleic location signals were scanned using PredictNLS.
Homology:
List the homological peer(s) from Arobidopsis or two subspecies of Asian cultivated rice ( Oryza sativa ssp. japonica and Oryza sativa ssp. indica).
Sequence:
List the CDS sequence and protein sequence. One can download the sequence or do the BLAST search.
Details:
List the relative information as supported evidences from EMBL, InterPro, UniPro, RefSeq, and TransFac
Family Multi-alignment and Phylogenetic Tree:
If the family has more than 1 gene model, we supplied DNA binding domain multi-alignment for families characterized by HMMer scan DNA binding domain and supplied whole protein sequence multi-alignment for families identified by BLAST. The multi alignment are generated by ClusterW and the displayed colorful alignment is modified by CHROMA (CHromatic Representation Of Multiple Alignments).
If the family has more than 3 gene models. We constructed phylogenetic tree based on the DNA-binding domain or whole protein sequences by Neighbor-Joining method with 100 times bootstrap in PHYLIP3.0.
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