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Pan-Gene Data In MaizeGDB
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Introduction

The pan-gene and gene family datasets presented in this data center were calculated by MaizeGDB staff. Details about the analyses are in the information section below and in each pan-gene record page.

Note that different pan-gene and gene family analyses will produce difference results, and that the accuracy of the results are impacted by assembly and annotation quality.

We welcome comments, error reports, and suggestions. Please use the .

Simple Search
This search form allows you to find pan-genes by locus symbol, gene model ID, transcript ID, or protein ID.


Submit (see example gene model query or locus query)


Advanced Search
Check the boxes next to the fields you want to search; if you just want to find records that have any value for that attribute, check the box and leave the criteria alone.


Search for pan-genes:
in the pan-gene analysis
that contain the gene model(s)
that are associated with a gene locus
that are associated with protein(s)
that are associated with a trait
that have at least members
that have fewer than members
that have members in at least % of annotations
that have members in no more than % of annotations
that contain members from annotations for these assemblies
that do not contain members from annotations for these assemblies
Submit Clear

    (upper limit on results is 2,000 records)


Downloads
All bulk pan-zea downloads


Download pan-gene exemplar sequence
Enter up to 50 gene models. Sequence for the exemplar gene models for the pan-genes these belong to will be downloaded.
Example dataset
Sequence type: CDS protein in the pan-gene analysis
Note that one gene model from each pan-gene is selected as the exemplar for that pan-gene, rather than calculating a consensus gene model.

Submit


Zea phylogenetic tree
Calculated with Orthofinder.
Third party tools for further exploration

Pair-wise comparison of two genomes: Comparative Genome Viewer (CGV) at NCBI
Explore structural variation among the NAM founders and the latest assembly of B73.


Explore NCBI B73 gene model annotation Genome Data Viewer (GDV) at NCBI Explore structural variation at the gene model level among the NAM founders and the latest assembly of B73.


About pan-gene data at MaizeGDB
The Zea mays pan-gene analysis was generated by MaizeGDB staff, using the Pandagma pipeline. Details of each analysis are presented on separate tabs on the pan-gene record pages.

Note that pan-gene analyses generated out by different software is likely to produce different results.

Number of annotations represented in analysis: 57. Table is cut off at pan genes of size 200.




Definitions
exemplar
The gene model selected as being the standard for a pan-gene. This approach for producing sequence representative of the pan-gene is often more accurate than creating a consensus sequence. As the methods for pan-gene analysis are undergoing rapid change, pan-genes are rarely stable across multiple analyses. Therefore, the exemplars are used to identify pan-genes rather than assigning pan-gene identifiers.
gene family
A gene family differs from a pan-gene in that a pan-gene analysis typically operates within a species, or a clade with chromosome-to-chromosome correspondence, and makes use of synteny comparisons when assigning members to a pan-gene. Gene families look farther back into evolution and rely more on sequence similarity.
gene locus
It is difficult to precisely describe a "gene". Here, a gene locus is interpreted to be a locus that has been associated with a phenotype or function.
pan-gene
We define a pan-gene is the collection of all gene models that appear to be the same thing, based on synteny and sequence similarity, along with any gene loci that have been associated with one or more gene models in the pan-gene.
pan-gene analysis
A pan-gene analysis looks at genome and annotation sequence, gene model coordinates...
pan-genome
There are multiple definitions of a pan-genome. We define a pan-genome to be all of the unique sequence across a set of genomes MaizeGDB does not, at this time, archive or provide this data, only the sequence data for each genome.
pan-genome analysis
A pan-genome analysis is any analysis that includes assembly, and often annotation information from multiple genomes to make inferences about what is the same, similar, and different across all genomes included.