Curated Maize V4 Gene Models

Curated Maize V4 Gene Models

The genes in this list were evaluated during a Pilot Community Curation Effort lead by the NSF-funded Gramene (IOS-1127112) and MaizeCode (IOS-1445025) projects. Ten graduate students and one post-doctoral fellow were invited to participate in the first of a series of Maize Annotation Jamborees; eight students continued with the curation efforts over a period of one year. Classical gene models and well-researched gene families were prioritized for inclusion in this effort. We used MAKER-P annotation metrics (Campbell et al, 2014) and the Gramene Gene Tree Visualizer (Olson et al, unpublished) to identify potential annotation errors, and the Apollo Annotation Editor (Dunn et al, 2019) to correct them.

To view the improved gene models in Gramene's genome browser, simply attach this GFF file as a Custom track from any Maize page, such as this Region in Detail. To attach or upload a custom track, click the Custom tracks button in the left side menu of the page and attach the GFF file by pasting its corresponding URL ( in the resulting window. Alternatively, if you have clicked on Configure this page, add data by navigating to the Personal Data tab in the configuration window and click on Custom tracks.

The improved models will be soon made available as a permanent track in the Ensembl Gramene browser and also registered at the Track Hub Registry. Click on the embedded links for additional instructions on "Adding Custom Tracks" and "Adding Track Hubs" to the Gramene Ensembl browser.

For additional information about the Maize Annotation Jamborees, please see the MaizeCode Outreach page.

Gene ID Genomic coordinates RefGenV4 Gene name Curated by
Zm00001d028963 1:53142425-53144911 protein kinase inhibitor1 H. Wu
Zm00001d029074 1:57250815-57254236 lesion22 M. K. Tello-Ruiz, S. Sapkota, F-M. Hsu
Zm00001d029577 1:77398644-77401233   C. F. Marco, M. Okoro
Zm00001d031073 1:175980669-175983357 origin recognition complex3 Z. Brenton, F-M. Hsu, M. Stitzer
Zm00001d031620 1:196372442-196380539 Zea mays MADS6 S. Sapkota, C. F. Marco
Zm00001d031871 1:204748411-204755635 brachytic2 C. F. Marco
Zm00001d032249 1:218790654-218795894 KANADI1 M. K. Tello-Ruiz
Zm00001d032922 1:243201405-243204865 indeterminate growth1 H. Wu, C. F. Marco
Zm00001d032969 1:245012635-245014564 bronze2 M. K. Tello-Ruiz, H. Wu
Zm00001d034087 1:283670581-283672729   M. Stitzer, F-M. Hsu, Z. Brenton, C. F. Marco
Zm00001d034635 1:298580972-298582430 chalcone flavanone isomerase1 C. F. Marco
Zm00001d001941 2:3201231-3204850 invertase cell wall4 M. K. Tello-Ruiz
Zm00001d001943 2:3240579-3242932   M. K. Tello-Ruiz
Zm00001d001944 2:3244741-3247431   M. K. Tello-Ruiz
Zm00001d001960 2:3559183-3560951 flavanone 3-hydroxylase1 S. Sapkota
Zm00001d002353 2:10743536-10746206 glossy2 P. Qiao, C. F. Marco
Zm00001d002449 2:12914091-12917068 Zea floricaula leafy2 P. Qiao
Zm00001d002830 2:24145621-24150188 invertase1 M. K. Tello-Ruiz
Zm00001d002982 2:28866474-28867724 aberrant phyllotaxy1 J. Zhan
Zm00001d003006 2:29275928-29278172 plasma membrane intrinsic protein2 H. Wu, C. F. Marco
Zm00001d003157 2:33981493-33984783 S-adenosyl methionine decarboxylase2 C. F. Marco
Zm00001d003533 2:47105187-47109372 tassel seed1 S. Sapkota, C. F. Marco
Zm00001d003776 2:58876332-58879327 miniature seed1 M. K. Tello-Ruiz
Zm00001d003804 2:59926707-59928357 phosphatidylethanolamine-binding protein4 R. S. Khangura
Zm00001d003913 2:66964007-66969688 high chlorophyll fluorescence106 S. Sapkota, C. F. Marco
Zm00001d005890 2:191852046-191853897 alpha amylase3 S. Sapkota
Zm00001d006082 2:197602488-197606112 PIN-formed protein11 R. S. Khangura, S. Sapkota, C. F. Marco
Zm00001d006116 2:199001851-199007982 phosphatidylethanolamine-binding protein18 P. Qiao, C. F. Marco, M. K. Tello-Ruiz, M. Stitzer, R. S. Khangura
Zm00001d007395 2:230685598-230692435   R. S. Khangura, H. Wu
Zm00001d039260 3:750258-754984 golden plant2 H. Wu
Zm00001d039371 3:2709285-2712754 TCP-transcription factor 33 C. F. Marco
Zm00001d040331 3:38375080-38380515 SUN domain protein2 F-M. Hsu, R. Wasikowski
Zm00001d041781 3:137903169-137908918 Zea AGAMOUS homolog2 C. F. Marco, M. K. Tello-Ruiz
Zm00001d041882 3:142230896-142233815 ATPase1 J. Zhan
Zm00001d041947 3:144956319-144967571   C. F. Marco, K. Wimalanathan
Zm00001d041991 3:146847940-146851037   M. K. Tello-Ruiz
Zm00001d042287 3:159074669-159084170 myb transcription factor2 C. F. Marco, J. Zhan
Zm00001d042445 3:167821561-167825000 terminal ear1 H. Wu
Zm00001d042879 3:182649721-182654210 transcription associated factor1 S. Sapkota, M. K. Tello-Ruiz, R. Wasikowski, S. Sapkota
Zm00001d043146 3:190108063-190112698 ribonuclease III domain protein1 M. Stitzer, R. S. Khangura
Zm00001d043175 3:190628817-190634540 cystatin1 C. F. Marco
Zm00001d043179 3:190701685-190704770 PIN-formed protein9 C. F. Marco, R. S. Khangura, S. Sapkota
Zm00001d043423 3:199284014-199285462   R. Wasikowski
Zm00001d044705 3:235432714-235437168 phosphatidylethanolamine-binding protein1 H. Wu, C. F. Marco
Zm00001d048702 4:3574390-3576530 benzoxazinone synthesis3 R. S. Khangura
Zm00001d049239 4:22371774-22374938 adenosyl homocysteine hydrolase1 S. Sapkota
Zm00001d049610 4:37573636-37577238 orange pericarp1 R. S. Khangura, M. Okoro
Zm00001d049995 4:58642687-58647338 nitrate reductase(NADH)1 P. Qiao, R. Wasikowski
Zm00001d050032 4:61315575-61321350 brittle endosperm2 R. S. Khangura
Zm00001d050259 4:77087087-77098401   K. Wimalanathan, J. Williams, C. F. Marco, J. Zhan
Zm00001d050265 4:77232457-77236007 hypersensitive induced reaction1 R. S. Khangura, C. F. Marco
Zm00001d050350 4:82930195-82941888 kanadi3 M. K. Tello-Ruiz
Zm00001d051465 4:159603384-159610425 zea agamous5 P. Qiao
Zm00001d051514 4:161089336-161097086   D. Micklos, K. Wimalanathan, C. F. Marco
Zm00001d051898 4:173925846-173928349 ser/thr protein phosphatase1 R. S. Khangura
Zm00001d052537 4:192553796-192554988 phosphatidylethanolamine-binding protein6 F-M. Hsu, C. F. Marco
Zm00001d053899 4:243343911-243347704 Rho-related protein from plants2 R. Wasikowski, C. F. Marco
Zm00001d054075 4:245956890-245959339   M. K. Tello-Ruiz
Zm00001d013258 5:7193149-7199073 Zea mays MADS31 J. Zhan, S. Sapkota, M. K. Tello-Ruiz, C. F. Marco
Zm00001d013631 5:15866934-15871877 TATA-binding protein2 C. F. Marco
Zm00001d013777 5:19923773-19930072 MYB-related-transcription factor 40 C. F. Marco, J. Zhan
Zm00001d014842 5:65145138-65146204 chitinase3 C. F. Marco
Zm00001d014858 5:65680729-65683012 high mobility group protein1 R. S. Khangura
Zm00001d014947 5:69452584-69455758 invertase2 R. S. Khangura, M. K. Tello-Ruiz, C. F. Marco
Zm00001d015366 5:86475220-86478975 camouflage1 C. F. Marco
Zm00001d015450 5:90962311-90968591 SUN domain protein1 P. Qiao, M. Okoro
Zm00001d015618 5:101493553-101498009 brown midrib1 S. Sapkota
Zm00001d016708 5:173403817-173408283 cell wall invertase1 M. K. Tello-Ruiz
Zm00001d017111 5:185769105-185772037 glossy8 C. F. Marco
Zm00001d017288 5:191817119-191819914 plasma membrane intrinsic protein2 C. F. Marco
Zm00001d017614 5:201741196-201748623 bearded-ear1 M. Stitzer
Zm00001d018415 5:220297125-220299214 proliferating cell nuclear antigen1 C. F. Marco
Zm00001d018535 5:222621124-222631121 brick1 F-M. Hsu, C. F. Marco
Zm00001d035760 6:46129120-46129656 zein protein, 15kDa15 C. F. Marco
Zm00001d036242 6:79177907-79179890 phosphatidylethanolamine-binding protein15 C. F. Marco
Zm00001d036370 6:85905987-85906962 chitinase2 C. F. Marco, R. Wasikowski, F-M. Hsu
Zm00001d037386 6:124045008-124049689 transmembrane protein20 S. Sapkota, M. K. Tello-Ruiz
Zm00001d037439 6:125464175-125465714 phosphatidylethanolamine-binding protein11 C. F. Marco
Zm00001d037737 6:135893605-135901920 Zea AGAMOUS homolog1 M. K. Tello-Ruiz, S. Sapkota
Zm00001d038725 6:163368049-163369489 phosphatidylethanolamine-binding protein7 R. Wasikowski, C. F. Marco, F-M. Hsu
Zm00001d039132 6:170742212-170753847   P. Qiao, C. F. Marco, M. K. Tello-Ruiz
Zm00001d019030 7:13540226-13541566 maternally expressed gene6 J. Zhan, C. F. Marco
Zm00001d019148 7:19180261-19184573 shugoshin centromeric cohesion1 R. S. Khangura, F-M. Hsu
Zm00001d019565 7:43071903-43073370 plasma membrane intrinsic protein2 C. F. Marco
Zm00001d019648 7:47990040-47993872 nucleic acid binding protein1 H. Wu, C. F. Marco
Zm00001d020383 7:110507409-110508756 plasma membrane intrinsic protein1 S. Sapkota, C. F. Marco
Zm00001d020636 7:125837492-125842596 cysteine protease2 C. F. Marco
Zm00001d020971 7:138210336-138221164 iojap striping1 C. F. Marco, P. Qiao, H. Wu
Zm00001d021526 7:155153847-155156140 nucleotide diphosphate kinase1 H. Wu
Zm00001d008882 8:23705985-23714926 Zea mays MADS2 M. K. Tello-Ruiz, R. S. Khangura
Zm00001d009431 8:64107616-64111865 farnesyl pyrophosphate synthase1 M. Okoro, R. S. Khangura
Zm00001d011277 8:145550689-145553038 SUN domain protein5 C. F. Marco
Zm00001d011377 8:148947109-148951347   H. Wu, R. S. Khangura, C. F. Marco
Zm00001d012561 8:176655420-176657307 cystatin2 R. S. Khangura
Zm00001d045054 9:11188093-11192433 sesquiterpene cyclase1 R. Wasikowski, C. F. Marco
Zm00001d045055 9:11218973-11220493 bronze1 F-M. Hsu, C. F. Marco
Zm00001d045563 9:26822040-26825680 dwarf plant3 C. F. Marco, M. K. Tello-Ruiz
Zm00001d045735 9:36009335-36013889 constans1 J. Zhan
Zm00001d047522 9:133460977-133469214 vacuolar sorting receptor homolog1 C. F. Marco
Zm00001d048082 9:149613002-149621302 Zea mays MADS8 R. Wasikowski, F-M. Hsu
Zm00001d023904 10:27313349-27316275 auxin binding protein homolog4 J. Zhan
Zm00001d024009 10:36528738-36535462 cytokinin inducible protease1 H. Wu
Zm00001d024698 10:83962005-83966353 fertilization independent endosperm2 C. F. Marco
Zm00001d025267 10:111824838-111828519 high chlorophyll fluorescence106c H. Wu
Zm00001d025354 10:115243957-115246970 invertase cell wall5 M. K. Tello-Ruiz
Zm00001d025355 10:115297049-115299501 invertase cell wall3 M. K. Tello-Ruiz, S. Sapkota, R. S. Khangura
Zm00001d025943 10:134290813-134294851   M. K. Tello-Ruiz
Zm00001d026088 10:138129427-138138311 outer cell layer2 C. F. Marco
Zm00001d026148 10:139803834-139806665 inhibitor of striate1 F-M. Hsu, C. F. Marco