All Gene Models with closed Issues

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Issue Gene model Version Description Resolution Status
ASMBLY-1080 add1 RefGen_B73 v2 Gene add1 is missing exons, and is split into two B73_V2 gene models: GRMZM2G120178|GRMZM2G050800; based on Genbank sequence accession FJ469779 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Fixed in v4 (Zm00001d010862). Resolved
ASMBLY-1092 cesa9 RefGen_B73 v2 There may be an assembly error near gene cesa, which has a partial identical duplicate:GRMZM2G150404 with B73_V2 gene model GRMZM2G018241; based on Genbank sequence accession AF200533 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Assembly error is fixed in v4. Resolved
ASMBLY-1101 cko1 RefGen_B73 v2 Gene cko1 is missing exons in the sequence; has wrong exons in middle of transcript shown for B73_V2 gene model GRMZM2G146644; based on Genbank sequence accession Y18377 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Fixed in v4 (Zm00001d039520). Resolved
ASMBLY-1077 cpn1 RefGen_B73 v2 Gene cpn1 is split into two B73_V2 gene models: GRMZM2G458208|GRMZM2G111477; based on Genbank sequence accession L21007 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Fixed in v4 (Zm00001d014090). Resolved
ASMBLY-1073 fer2 RefGen_B73 v2 The CDS is wrongly annotated for fer2; instead it is misannotated as the 3' UTR in B73_V2 gene model GRMZM2G147266; based on Genbank sequence accession X61392 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Fixed in v4 (Zm00001d023225) Resolved
ASMBLY-1087 GRMZM2G017087 RefGen_B73 v2 Gene kn1 is missing 5' UTR in B73_V2 gene model GRMZM2G017087; based on Genbank sequence accession X61308 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand -1 Fixed in v4 (Zm00001d033859). Resolved
ASMBLY-1092 GRMZM2G018241 RefGen_B73 v2 There may be an assembly error near gene cesa, which has a partial identical duplicate:GRMZM2G150404 with B73_V2 gene model GRMZM2G018241; based on Genbank sequence accession AF200533 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Assembly error is fixed in v4. Resolved
ASMBLY-1068 GRMZM2G025222 RefGen_B73 v2 5' end of CDS for gene spi1 is lost in gap near B73_V2 gene model GRMZM2G025222; based on Genbank sequence accession EU910940 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand -1 Fixed in v4 (Zm00001d044069). Resolved
ASMBLY-222 GRMZM2G048092 RefGen_B73 v3 GRMZM2G061821 and GRMZM2G048092 are most likely the N and C-terminal sections of Moco Sulfurase. These genes come from the same BAC but are on different contigs within the BAC. The conserved domains defined by these gene models are a single gene in all plants except maize. Fixed in v4 (Zm00001d036635). Resolved
ASMBLY-1080 GRMZM2G050800 RefGen_B73 v2 Gene add1 is missing exons, and is split into two B73_V2 gene models: GRMZM2G120178|GRMZM2G050800; based on Genbank sequence accession FJ469779 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Fixed in v4 (Zm00001d010862). Resolved
ASMBLY-1071 GRMZM2G051338 RefGen_B73 v2 5' UTR of gene zcn15 is unannotated for B73_V2 gene model GRMZM2G051338; based on Genbank sequence accession EU241930 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand 1 Fixed in v4 (Zm00001d036242). Resolved
ASMBLY-222 GRMZM2G061821 RefGen_B73 v3 GRMZM2G061821 and GRMZM2G048092 are most likely the N and C-terminal sections of Moco Sulfurase. These genes come from the same BAC but are on different contigs within the BAC. The conserved domains defined by these gene models are a single gene in all plants except maize. Fixed in v4 (Zm00001d036635). Resolved
ASMBLY-1108 GRMZM2G069028 RefGen_B73 v4 maize has four wox3 paralogs - these are named ns1 (chromosome 2L) , ns2 (chromosome 4L), wox3A, and wox3B. The ns1 and ns2 genes are described in Nardmann et al. 2004. wox3A and wox3B are described in Nardmann et al 2007. The loci ns1, ns2 are paralogous to wox3a, wox3b, and wox3a and wox3b are duplicate factors. Renamed hb loci from Grassius (Yilman et al., 2009) to wox3a, wox3b (Nardmann et al., 2007). The 'classical' names assigned by wet-lab researchers are generally preferred over those provided by database analyses. In this case, the wet-lab paper also has an earlier publication date. Change is effective September 5th, 2017. Closed
ASMBLY-1064 GRMZM2G084799 RefGen_B73 v2 3' UTR of gene p1 is missing from B73_V2 gene model GRMZM2G084799; based on Genbank sequence accession U57002 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand -1 Fixed in v4 (Zm00001d028854). Resolved
ASMBLY-1077 GRMZM2G111477 RefGen_B73 v2 Gene cpn1 is split into two B73_V2 gene models: GRMZM2G458208|GRMZM2G111477; based on Genbank sequence accession L21007 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Fixed in v4 (Zm00001d014090). Resolved
ASMBLY-1080 GRMZM2G120178 RefGen_B73 v2 Gene add1 is missing exons, and is split into two B73_V2 gene models: GRMZM2G120178|GRMZM2G050800; based on Genbank sequence accession FJ469779 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Fixed in v4 (Zm00001d010862). Resolved
ASMBLY-221 GRMZM2G121570 RefGen_B73 v3 GRMZM2G121570 is a myb transcription factor that is missing 830 bp from 5' end of gene. Fixed in v4 (Zm00001d033265). Resolved
ASMBLY-1108 GRMZM2G122537 RefGen_B73 v4 maize has four wox3 paralogs - these are named ns1 (chromosome 2L) , ns2 (chromosome 4L), wox3A, and wox3B. The ns1 and ns2 genes are described in Nardmann et al. 2004. wox3A and wox3B are described in Nardmann et al 2007. The loci ns1, ns2 are paralogous to wox3a, wox3b, and wox3a and wox3b are duplicate factors. Renamed hb loci from Grassius (Yilman et al., 2009) to wox3a, wox3b (Nardmann et al., 2007). The 'classical' names assigned by wet-lab researchers are generally preferred over those provided by database analyses. In this case, the wet-lab paper also has an earlier publication date. Change is effective September 5th, 2017. Closed
ASMBLY-220 GRMZM2G128228 RefGen_B73 v3 Fixed in v4 (Zm00001d016836). Resolved
ASMBLY-1108 GRMZM2G140083 RefGen_B73 v4 maize has four wox3 paralogs - these are named ns1 (chromosome 2L) , ns2 (chromosome 4L), wox3A, and wox3B. The ns1 and ns2 genes are described in Nardmann et al. 2004. wox3A and wox3B are described in Nardmann et al 2007. The loci ns1, ns2 are paralogous to wox3a, wox3b, and wox3a and wox3b are duplicate factors. Renamed hb loci from Grassius (Yilman et al., 2009) to wox3a, wox3b (Nardmann et al., 2007). The 'classical' names assigned by wet-lab researchers are generally preferred over those provided by database analyses. In this case, the wet-lab paper also has an earlier publication date. Change is effective September 5th, 2017. Closed
ASMBLY-1101 GRMZM2G146644 RefGen_B73 v2 Gene cko1 is missing exons in the sequence; has wrong exons in middle of transcript shown for B73_V2 gene model GRMZM2G146644; based on Genbank sequence accession Y18377 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Fixed in v4 (Zm00001d039520). Resolved
ASMBLY-1073 GRMZM2G147266 RefGen_B73 v2 The CDS is wrongly annotated for fer2; instead it is misannotated as the 3' UTR in B73_V2 gene model GRMZM2G147266; based on Genbank sequence accession X61392 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Fixed in v4 (Zm00001d023225) Resolved
ASMBLY-1094 GRMZM2G156861 RefGen_B73 v2 Gene lox1 is one of 2 tandem duplicates merged into B73_V2 gene model GRMZM2G156861; based on Genbank sequence accession DQ335760 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand 1 Fixed in v4 (Zm00001d042541). Resolved
ASMBLY-219 GRMZM2G173923 RefGen_B73 v3 5'-end is missing. AC205396.3-Contig82 is not inserted in the correct location in the genome. Closed
ASMBLY-1072 GRMZM2G307906 RefGen_B73 v2 CDS is wrongly annotated for gene ms45 in B73_V2 gene model GRMZM2G307906; based on Genbank sequence accession AF360356 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Fixed in v4 (Zm00001d047858). Resolved
ASMBLY-1069 GRMZM2G338454 RefGen_B73 v2 5' end of gene zcn3 is lost in a gap near B73_V2 gene model GRMZM2G338454; based on Genbank sequence accession EU241919 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand -1 Fixed in v4 (Zm00001d023420). Resolved
ASMBLY-1077 GRMZM2G458208 RefGen_B73 v2 Gene cpn1 is split into two B73_V2 gene models: GRMZM2G458208|GRMZM2G111477; based on Genbank sequence accession L21007 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Fixed in v4 (Zm00001d014090). Resolved
ASMBLY-1099 GRMZM2G531231 RefGen_B73 v2 Gene zag4 has a weird gene model B73_V2 gene model GRMZM2G531231; based on Genbank sequence accession L46399 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand -1 Fixed in v4 (Zm00001d045227). Resolved
ASMBLY-1100 GRMZM5G803935 RefGen_B73 v2 Gene ts4 encodes a miroRNA and it is questionable that it should be assigned a CDS for B73_V2 gene model GRMZM5G803935; based on Genbank sequence accession GQ905588 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand 1 Fixed in v4. Resolved
ASMBLY-1102 GRMZM6G986387 RefGen_B73 v3 Hydroperoxide lyase (HPL1) does not have a gene model assigned to it. It appears that gene model GRMZM6G986387 sits instead in reverse-strand orientation on part of HPL1. Fixed in v4 (Zm00001d054067). Resolved
ASMBLY-1102 hpl1 RefGen_B73 v3 Hydroperoxide lyase (HPL1) does not have a gene model assigned to it. It appears that gene model GRMZM6G986387 sits instead in reverse-strand orientation on part of HPL1. Fixed in v4 (Zm00001d054067). Resolved
ASMBLY-1087 kn1 RefGen_B73 v2 Gene kn1 is missing 5' UTR in B73_V2 gene model GRMZM2G017087; based on Genbank sequence accession X61308 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand -1 Fixed in v4 (Zm00001d033859). Resolved
ASMBLY-1094 lox1 RefGen_B73 v2 Gene lox1 is one of 2 tandem duplicates merged into B73_V2 gene model GRMZM2G156861; based on Genbank sequence accession DQ335760 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand 1 Fixed in v4 (Zm00001d042541). Resolved
ASMBLY-1072 ms45 RefGen_B73 v2 CDS is wrongly annotated for gene ms45 in B73_V2 gene model GRMZM2G307906; based on Genbank sequence accession AF360356 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Fixed in v4 (Zm00001d047858). Resolved
ASMBLY-1108 ns1 RefGen_B73 v4 maize has four wox3 paralogs - these are named ns1 (chromosome 2L) , ns2 (chromosome 4L), wox3A, and wox3B. The ns1 and ns2 genes are described in Nardmann et al. 2004. wox3A and wox3B are described in Nardmann et al 2007. The loci ns1, ns2 are paralogous to wox3a, wox3b, and wox3a and wox3b are duplicate factors. Renamed hb loci from Grassius (Yilman et al., 2009) to wox3a, wox3b (Nardmann et al., 2007). The 'classical' names assigned by wet-lab researchers are generally preferred over those provided by database analyses. In this case, the wet-lab paper also has an earlier publication date. Change is effective September 5th, 2017. Closed
ASMBLY-1108 ns2 RefGen_B73 v4 maize has four wox3 paralogs - these are named ns1 (chromosome 2L) , ns2 (chromosome 4L), wox3A, and wox3B. The ns1 and ns2 genes are described in Nardmann et al. 2004. wox3A and wox3B are described in Nardmann et al 2007. The loci ns1, ns2 are paralogous to wox3a, wox3b, and wox3a and wox3b are duplicate factors. Renamed hb loci from Grassius (Yilman et al., 2009) to wox3a, wox3b (Nardmann et al., 2007). The 'classical' names assigned by wet-lab researchers are generally preferred over those provided by database analyses. In this case, the wet-lab paper also has an earlier publication date. Change is effective September 5th, 2017. Closed
ASMBLY-1064 p1 RefGen_B73 v2 3' UTR of gene p1 is missing from B73_V2 gene model GRMZM2G084799; based on Genbank sequence accession U57002 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand -1 Fixed in v4 (Zm00001d028854). Resolved
ASMBLY-14 ppr4 RefGen_B73 v3 Sequence NP_001105869 is not in B73_V3 per Barkan review (Table 1 summary). Belcher et al 2015 BBA . doi:10.1016/j.bbabio.2015.02.014 Looking at the NCBI annotation, it is placed at NC_024463.1 (4773716..4774253) on Chromosome 5. This region on the MaizeGDB B73_V3 browser shows an NCBI gene, but there are no gene models in the 5b+ gene model set. Fixed in v4 (Zm00001d026654). Resolved
ASMBLY-1068 spi1 RefGen_B73 v2 5' end of CDS for gene spi1 is lost in gap near B73_V2 gene model GRMZM2G025222; based on Genbank sequence accession EU910940 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand -1 Fixed in v4 (Zm00001d044069). Resolved
ASMBLY-1100 ts4 RefGen_B73 v2 Gene ts4 encodes a miroRNA and it is questionable that it should be assigned a CDS for B73_V2 gene model GRMZM5G803935; based on Genbank sequence accession GQ905588 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand 1 Fixed in v4. Resolved
ASMBLY-1108 wox3a RefGen_B73 v4 maize has four wox3 paralogs - these are named ns1 (chromosome 2L) , ns2 (chromosome 4L), wox3A, and wox3B. The ns1 and ns2 genes are described in Nardmann et al. 2004. wox3A and wox3B are described in Nardmann et al 2007. The loci ns1, ns2 are paralogous to wox3a, wox3b, and wox3a and wox3b are duplicate factors. Renamed hb loci from Grassius (Yilman et al., 2009) to wox3a, wox3b (Nardmann et al., 2007). The 'classical' names assigned by wet-lab researchers are generally preferred over those provided by database analyses. In this case, the wet-lab paper also has an earlier publication date. Change is effective September 5th, 2017. Closed
ASMBLY-1108 wox3b RefGen_B73 v4 maize has four wox3 paralogs - these are named ns1 (chromosome 2L) , ns2 (chromosome 4L), wox3A, and wox3B. The ns1 and ns2 genes are described in Nardmann et al. 2004. wox3A and wox3B are described in Nardmann et al 2007. The loci ns1, ns2 are paralogous to wox3a, wox3b, and wox3a and wox3b are duplicate factors. Renamed hb loci from Grassius (Yilman et al., 2009) to wox3a, wox3b (Nardmann et al., 2007). The 'classical' names assigned by wet-lab researchers are generally preferred over those provided by database analyses. In this case, the wet-lab paper also has an earlier publication date. Change is effective September 5th, 2017. Closed
ASMBLY-1099 zag4 RefGen_B73 v2 Gene zag4 has a weird gene model B73_V2 gene model GRMZM2G531231; based on Genbank sequence accession L46399 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand -1 Fixed in v4 (Zm00001d045227). Resolved
ASMBLY-1071 zcn15 RefGen_B73 v2 5' UTR of gene zcn15 is unannotated for B73_V2 gene model GRMZM2G051338; based on Genbank sequence accession EU241930 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand 1 Fixed in v4 (Zm00001d036242). Resolved
ASMBLY-1069 zcn3 RefGen_B73 v2 5' end of gene zcn3 is lost in a gap near B73_V2 gene model GRMZM2G338454; based on Genbank sequence accession EU241919 (Classical genes list, Schnable J & Freeeling M 2011 PLoS One 108:4069-74 ). Strand -1 Fixed in v4 (Zm00001d023420). Resolved
ASMBLY-1108 Zm00001d004889 RefGen_B73 v4 maize has four wox3 paralogs - these are named ns1 (chromosome 2L) , ns2 (chromosome 4L), wox3A, and wox3B. The ns1 and ns2 genes are described in Nardmann et al. 2004. wox3A and wox3B are described in Nardmann et al 2007. The loci ns1, ns2 are paralogous to wox3a, wox3b, and wox3a and wox3b are duplicate factors. Renamed hb loci from Grassius (Yilman et al., 2009) to wox3a, wox3b (Nardmann et al., 2007). The 'classical' names assigned by wet-lab researchers are generally preferred over those provided by database analyses. In this case, the wet-lab paper also has an earlier publication date. Change is effective September 5th, 2017. Closed
ASMBLY-1108 Zm00001d010998 RefGen_B73 v4 maize has four wox3 paralogs - these are named ns1 (chromosome 2L) , ns2 (chromosome 4L), wox3A, and wox3B. The ns1 and ns2 genes are described in Nardmann et al. 2004. wox3A and wox3B are described in Nardmann et al 2007. The loci ns1, ns2 are paralogous to wox3a, wox3b, and wox3a and wox3b are duplicate factors. Renamed hb loci from Grassius (Yilman et al., 2009) to wox3a, wox3b (Nardmann et al., 2007). The 'classical' names assigned by wet-lab researchers are generally preferred over those provided by database analyses. In this case, the wet-lab paper also has an earlier publication date. Change is effective September 5th, 2017. Closed
ASMBLY-1108 Zm00001d035535 RefGen_B73 v4 maize has four wox3 paralogs - these are named ns1 (chromosome 2L) , ns2 (chromosome 4L), wox3A, and wox3B. The ns1 and ns2 genes are described in Nardmann et al. 2004. wox3A and wox3B are described in Nardmann et al 2007. The loci ns1, ns2 are paralogous to wox3a, wox3b, and wox3a and wox3b are duplicate factors. Renamed hb loci from Grassius (Yilman et al., 2009) to wox3a, wox3b (Nardmann et al., 2007). The 'classical' names assigned by wet-lab researchers are generally preferred over those provided by database analyses. In this case, the wet-lab paper also has an earlier publication date. Change is effective September 5th, 2017. Closed
ASMBLY-1108 Zm00001d052598 RefGen_B73 v4 maize has four wox3 paralogs - these are named ns1 (chromosome 2L) , ns2 (chromosome 4L), wox3A, and wox3B. The ns1 and ns2 genes are described in Nardmann et al. 2004. wox3A and wox3B are described in Nardmann et al 2007. The loci ns1, ns2 are paralogous to wox3a, wox3b, and wox3a and wox3b are duplicate factors. Renamed hb loci from Grassius (Yilman et al., 2009) to wox3a, wox3b (Nardmann et al., 2007). The 'classical' names assigned by wet-lab researchers are generally preferred over those provided by database analyses. In this case, the wet-lab paper also has an earlier publication date. Change is effective September 5th, 2017. Closed