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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.


Number of annotations: 57
Assembly Annotation Gene model count  Min length  Max length  Ave length  % placed in pan-genes
B73 RefGen_v3  5b+ 37828 84 25046 1619.9 81
Zm-B73-REFERENCE-GRAMENE-4.0  Zm00001d.2 49202 9 15804 1053.7 60.3
Zm-B73-REFERENCE-NAM-5.0  Zm00001eb.1 39756 153 16278 1102.1 76.7
Zm-W22-REFERENCE-NRGENE-2.0  Zm00004b.1 40690 6 16281 1141.3 82.2
Zm-PH207-REFERENCE_NS-UIUC_UMN-1.0  Zm00008a.1 40557 9 14844 1061.4 76
Zm-EP1-REFERENCE-TUM-1.0  Zm00010a.1 46105 30 16278 1025.2 73
Zm-F7-REFERENCE-TUM-1.0  Zm00011a.1 48370 30 16278 999.6 69.9
Zm-Mo17-REFERENCE-CAU-2.0  Zm00014ba.1 42580 75 15201 1094.2 76
Zm-SK-REFERENCE-YAN-1.0  Zm00015a.1 43271 120 16278 1179.3 75
Zm-DK105-REFERENCE-TUM-1.0  Zm00016a.1 48140 30 16278 998.2 71.1
Zm-PE0075-REFERENCE-TUM-1.0  Zm00017a.1 48306 30 16278 998 71.5
Zm-B97-REFERENCE-NAM-1.0  Zm00018ab.1 40368 135 16278 1077.9 76.2
Zm-CML52-REFERENCE-NAM-1.0  Zm00019ab.1 40473 126 16278 1087.6 74.3
Zm-CML69-REFERENCE-NAM-1.0  Zm00020ab.1 40272 120 16278 1062.3 75.3
Zm-CML103-REFERENCE-NAM-1.0  Zm00021ab.1 40013 93 16278 1080.6 76.6
Zm-CML228-REFERENCE-NAM-1.0  Zm00022ab.1 41577 45 16278 1076 73.4
Zm-CML247-REFERENCE-NAM-1.0  Zm00023ab.1 40383 84 15201 1082.4 76
Zm-CML277-REFERENCE-NAM-1.0  Zm00024ab.1 40325 105 16278 1077.7 75.8
Zm-CML322-REFERENCE-NAM-1.0  Zm00025ab.1 41122 105 16278 1067 74.9
Zm-CML333-REFERENCE-NAM-1.0  Zm00026ab.1 40428 72 16278 1080.3 75.9
Zm-HP301-REFERENCE-NAM-1.0  Zm00027ab.1 39785 69 16278 1085.4 77
Zm-Il14H-REFERENCE-NAM-1.0  Zm00028ab.1 40290 69 16278 1074.6 75.8
Zm-Ki3-REFERENCE-NAM-1.0  Zm00029ab.1 41059 138 16278 1071.8 75.2
Zm-Ki11-REFERENCE-NAM-1.0  Zm00030ab.1 39868 156 16278 1087.1 77.1
Zm-Ky21-REFERENCE-NAM-1.0  Zm00031ab.1 40778 123 16278 1070 76
Zm-M37W-REFERENCE-NAM-1.0  Zm00032ab.1 40905 138 16278 1071.6 75.7
Zm-M162W-REFERENCE-NAM-1.0  Zm00033ab.1 41486 105 16278 1062.2 74.4
Zm-Mo18W-REFERENCE-NAM-1.0  Zm00034ab.1 41204 75 16278 1061.1 74.9
Zm-Ms71-REFERENCE-NAM-1.0  Zm00035ab.1 41247 69 16278 1074.6 74.7
Zm-NC350-REFERENCE-NAM-1.0  Zm00036ab.1 40484 153 16278 1082.6 76.1
Zm-NC358-REFERENCE-NAM-1.0  Zm00037ab.1 39787 117 16278 1086.2 77.5
Zm-Oh7B-REFERENCE-NAM-1.0  Zm00038ab.1 40334 105 16278 1078 76.3
Zm-Oh43-REFERENCE-NAM-1.0  Zm00039ab.1 39973 156 16278 1082.7 77.1
Zm-P39-REFERENCE-NAM-1.0  Zm00040ab.1 41478 99 16278 1059.2 73.7
Zm-Tx303-REFERENCE-NAM-1.0  Zm00041ab.1 41164 132 16278 1065.5 75.2
Zm-Tzi8-REFERENCE-NAM-1.0  Zm00042ab.1 41593 27 16278 1066 73.8
Zm-Ia453-REFERENCE-FL-1.0  Zm00045a.1 38368 48 19343 1635.7 74
Zm-K0326Y-REFERENCE-SIPPE-1.0  Zm00054a.1 38238 156 15465 1126 75.5
Zm-A188-REFERENCE-KSU-1.0  Zm00056aa.1 40747 93 16392 1089.7 79.3
Zm-A632-REFERENCE-CAAS_FIL-1.0  Zm00092aa.1 45287 150 16269 1122 78.2
Zm-Chang-7_2-REFERENCE-CAAS_FIL-1.0  Zm00093aa.1 42500 150 15201 1140.9 79.3
Zm-Dan340-REFERENCE-CAAS_FIL-1.0  Zm00094aa.1 43718 150 16278 1124 77
Zm-Huangzaosi-REFERENCE-CAAS_FIL-1.0  Zm00095aa.1 44771 6 16278 1125.8 78
Zm-Jing724-REFERENCE-CAAS_FIL-1.0  Zm00096aa.1 46311 62 16278 1111.9 76.3
Zm-Jing92-REFERENCE-CAAS_FIL-1.0  Zm00097aa.1 45537 150 16278 1120.2 78.3
Zm-PH207-REFERENCE-CAAS_FIL-1.0  Zm00099aa.1 45809 150 16278 1104.9 77.2
Zm-S37-REFERENCE-CAAS_FIL-1.0  Zm00100aa.1 44719 150 16302 1124.6 76.9
Zm-Xu178-REFERENCE-CAAS_FIL-1.0  Zm00101aa.1 44191 150 16278 1119.8 77.2
Zm-Ye478-REFERENCE-CAAS_FIL-1.0  Zm00102aa.1 44791 150 16278 1120.8 77.5
Zm-Zheng58-REFERENCE-CAAS_FIL-1.0  Zm00103aa.1 44845 150 16269 1121 78.1
Zm-CML457-REFERENCE-HiLo-1.0  Zm00106aa.1 40104 9 16278 973.3 75.4
Zm-CML459-REFERENCE-HiLo-1.0  Zm00107aa.1 39298 15 16278 1114.3 82.6
Zm-CML530-REFERENCE-HiLo-1.0  Zm00108aa.1 42075 12 16278 1183.1 78.5
Zm-PT-REFERENCE-HiLo-1.0  Zm00109aa.1 40357 51 16278 1213.5 79.7
Zm-TAB-REFERENCE-HiLo-1.0  Zm00110aa.1 48487 66 16278 1180.9 76.8
Zm-ZAP-REFERENCE-HiLo-1.0  Zm00110aa.1 48487 66 16278 1180.9 76.8
Zm-ZAP-REFERENCE-HiLo-1.0  Zm00111aa.1 44482 24 16278 1034.3 71.3
Zm-TAB-REFERENCE-HiLo-1.0  Zm00111aa.1 44482 24 16278 1034.3 71.3
Zm-PDJ-REFERENCE-HiLo-1.0  Zm00112aa.1 52317 51 16809 1132.1 68.3



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, and synteny to calculate likely sets of gene models from multiple genomes that appear to be serving the same role.
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.