# Slide URLs for the MGC Workshop. March 16, 2023 # InterPro Domain search of NAC-domain containing proteins # slide https://maize-pangenome.gramene.org/?filters={%22status%22:%22init%22,%22operation%22:%22AND%22,%22negate%22:false,%22marked%22:false,%22leftIdx%22:0,%22rightIdx%22:3,%22children%22:[{%22fq_field%22:%22domains__ancestors%22,%22fq_value%22:%223441%22,%22name%22:%22NAC-dom%22,%22category%22:%22InterPro:%20Domain%22,%22leftIdx%22:1,%22rightIdx%22:2,%22negate%22:false,%22showMenu%22:false,%22marked%22:true}],%22showMarked%22:true,%22showMenu%22:false,%22moveCopyMode%22:%22%22,%22searchOffset%22:0,%22rows%22:20}&genomes= # Search for NAC078 # the maize ortholog Zm00001eb038920 is the ~4th result on the search page https://maize-pangenome.gramene.org/?filters={%22status%22:%22init%22,%22rows%22:20,%22operation%22:%22AND%22,%22negate%22:false,%22leftIdx%22:0,%22rightIdx%22:3,%22children%22:[{%22fq_field%22:%22homology__all_orthologs%22,%22fq_value%22:%22AT5G04410%22,%22name%22:%22Orthologs%20of%20NAC078%22,%22category%22:%22Gene%20Tree%22,%22leftIdx%22:1,%22rightIdx%22:2,%22negate%22:false,%22marked%22:false}],%22searchOffset%22:0}&genomes= # Gene Tree | Orthologs of NAC078 Maize Zm00001eb038920 # slides x-x https://maize-pangenome.gramene.org/?filters={%22status%22:%22init%22,%22rows%22:20,%22operation%22:%22AND%22,%22negate%22:false,%22leftIdx%22:0,%22rightIdx%22:3,%22children%22:[{%22fq_field%22:%22homology__all_orthologs%22,%22fq_value%22:%22Zm00001eb038920%22,%22name%22:%22Orthologs%20of%20Zm00001eb038920%22,%22category%22:%22Gene%20Tree%22,%22leftIdx%22:1,%22rightIdx%22:2,%22negate%22:false,%22marked%22:false}],%22searchOffset%22:0}&genomes= # Curation page for NAC078 Zm00001eb038920 http://curate.gramene.org/admin/curationUI/maize_v3/?since=4479&gene=Zm00001eb038920 # Ensembl Treeview page https://maize-pangenome-ensembl.gramene.org/Zea_maysb73/Gene/Compara_Tree?g=Zm00001eb038920;r=1:207741827-207746876 # Reactome Pathway Slide mrpa5 https://maize-pangenome.gramene.org/?filters={%22status%22:%22init%22,%22operation%22:%22AND%22,%22negate%22:false,%22marked%22:false,%22leftIdx%22:0,%22rightIdx%22:3,%22children%22:[{%22fq_field%22:%22id%22,%22fq_value%22:%22Zm00001eb070400%22,%22name%22:%22Zm00001eb070400%22,%22category%22:%22Genes%22,%22leftIdx%22:1,%22rightIdx%22:2,%22negate%22:false,%22showMenu%22:false,%22marked%22:true}],%22showMarked%22:true,%22showMenu%22:false,%22moveCopyMode%22:%22%22,%22searchOffset%22:0,%22rows%22:20}&genomes= # Papers Slide br2 https://maize-pangenome.gramene.org/?filters={%22status%22:%22init%22,%22operation%22:%22AND%22,%22negate%22:false,%22marked%22:false,%22leftIdx%22:0,%22rightIdx%22:3,%22children%22:[{%22fq_field%22:%22id%22,%22fq_value%22:%22Zm00001eb038710%22,%22name%22:%22Zm00001eb038710%22,%22category%22:%22Genes%22,%22leftIdx%22:1,%22rightIdx%22:2,%22negate%22:false,%22showMenu%22:false,%22marked%22:true}],%22showMarked%22:true,%22showMenu%22:false,%22moveCopyMode%22:%22%22,%22searchOffset%22:0,%22rows%22:20}&genomes= # Ensembl Browser View of NAC078 Zm00001eb038920 https://maize-pangenome-ensembl.gramene.org/Zea_maysb73/Gene/Summary?g=Zm00001eb038920;r=1:207741827-207746876 # Ensembl Browser Ontology slide NAC078 Zm00001eb038920 https://maize-pangenome-ensembl.gramene.org/Zea_maysb73/Gene/Ontologies/biological_process?g=Zm00001eb038920;r=1:207741827-207746876 # Ensembl Browser Sequence slide NAC078 Zm00001eb038920 https://maize-pangenome-ensembl.gramene.org/Zea_maysb73/Gene/Sequence?g=Zm00001eb038920;r=1:207741827-207746876 # Ensembl Browser Splice Variant slide NAC078 Zm00001eb038920 https://maize-pangenome-ensembl.gramene.org/Zea_maysb73/Gene/Splice?g=Zm00001eb038920;r=1:207741827-207746876 # Ensembl Browser Region in Detail slide NAC078 Zm00001eb038920 https://maize-pangenome-ensembl.gramene.org/Zea_maysb73/Location/View?db=core;g=Zm00001eb038920;r=1:207741827-207746876 # Ensembl Browser Variant Image slide NAC078 Zm00001eb038920 https://maize-pangenome-ensembl.gramene.org/Zea_maysb73/Gene/Variation_Gene/Image?g=Zm00001eb038920;r=1:207741827-207746876 # Ensembl Browser Variant Table slide NAC078 Zm00001eb038920 https://maize-pangenome-ensembl.gramene.org/Zea_maysb73/Gene/Variation_Gene/Table?g=Zm00001eb038920;r=1:207741827-207746876 # Ensembl Browser Variant Exploration slide NAC078 Zm00001eb038920 https://maize-pangenome-ensembl.gramene.org/Zea_maysb73/Variation/Explore?db=core;g=Zm00001eb038920;r=1:207741827-207746876;v=PZE01202539642;vdb=variation;vf=10282390 # Ensembl Browser Variant Detail slide PZE01202539642 (NAC078 Zm00001eb038920) https://maize-pangenome-ensembl.gramene.org/Zea_maysb73/Variation/Explore?db=core;g=Zm00001eb038920;r=1:207741827-207746876;v=PZE01202539642;vdb=variation;vf=10282390 # Ensembl Browser Variant Genotype slide PZE01202539642 (NAC078 Zm00001eb038920) https://maize-pangenome-ensembl.gramene.org/Zea_maysb73/Variation/Sample?db=core;g=Zm00001eb038920;r=1:207741827-207746876;v=PZE01202539642;vdb=variation;vf=10282390 # Ensembl Browser Variant Genotype slide PZE01202539642 (NAC078 Zm00001eb038920) https://maize-pangenome-ensembl.gramene.org/Zea_maysb73/Variation/Population?db=core;g=Zm00001eb038920;r=1:207741827-207746876;v=PZE01202539642;vdb=variation;vf=10282390