Species | Oryza sativa (Rice) [ GR_tax:013681 ] | ||||||||||||||||||||
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Accession | GR:0061010 | ||||||||||||||||||||
Gene Symbol | WX1 | ||||||||||||||||||||
Gene Name | GLUTINOUS ENDOSPERM | ||||||||||||||||||||
Synonyms (18) |
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E.C. Numbers (2) |
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Pathway Reactions (3) |
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Chromosome No. | 6 | ||||||||||||||||||||
Gene Type | CDS (Protein coding) | ||||||||||||||||||||
Has Phenotype | yes | ||||||||||||||||||||
Description | The Waxy (Wx) gene encodes a granule-bound starch synthase (GBSS) that plays a key role in the amylose synthesis of rice. It is expressed in the seed endosperm and pollen grains, that carry starch grains. At sub-cellular level the protein is localized in the amyloplasts. This gene undergoes alternative splicing of its transcripts suggesting that the amylose content of rice endosperm is regulated at the level of Wx transcript processing, and more specifically, at the stage of intron I excision from the Wx pre-mRNA. The alternative splicing is affected by the change in temperature. It is a single copy gene in rice. The phenotype shows white and non-translucent endosperm which turns brown to the iodine staining. |
# | Gene-1 | Gene-1 object | Mode of action | Gene-2 | Gene-2 object | Evidence | Evidence code | Comment |
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1 | DU1 | protein | down-regulates | WX1 | RNA | Zeng-D et al., 2007 | IGI | regulates the pre-mRNA splicing of Waxy (Wx) transcript |
Map Type | Map Set | Name | Map | Position | Ext. Links | |||
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Sequence | Gramene Annotated Nipponbare Sequence 2009 | BNL6.32 | Chr. 6 | 1,764,623-1,769,657bp | View Comparative Map | |||
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Map Type | Map Set | Name | Map | Position | Ext. Links | |||
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Genetic | IGCN sativa/eichingeri RFLP | BNL6.32 | 6 | 0-0cM | View Comparative Map | |||
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Map Type | Map Set | Name | Map | Position | Ext. Links | |||
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Genetic | Cornell RFLP 1994 | BNL6.32 | 6 | -1.5--1.5cM | View Comparative Map | |||
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Cornell RFLP 2001 | BNL6.32 | 6 | 6.7-6.7cM | View Comparative Map | ||||
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Map Position [ View in Marker DB ] | |||||
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# | Map Set Name | Linkage Group | Start Position | Stop Position | CMap Feature Acc |
1 | Cornell RFLP 2001 | 6 | 6.7 cM | 6.7 cM | cu-sl-2001-6-4 |
2 | JRGP RFLP 2000 | 6 | 8.2 cM | 8.2 cM | jrgp-2000-6-40 |
3 | IGCN 1998 | 6 | 5.7 cM | 5.7 cM | igcn-1998-6-3 |
4 | Cornell RFLP 1994 | 6 | -1.5 cM | -1.5 cM | cu-sl-1994-6-2 |
5 | Hokkaido Morphological 2000 | 6 | 22 cM | 22 cM | morph-2000-6-4 |
6 | IGCN sativa/eichingeri RFLP | 6 | 0 cM | 0 cM | yah2001a-73 |
7 | IGCAS ZYQ8/JX17 DH QTL 2000 | 6 | 0 cM | 0 cM | bajs2000a-68 |
8 | IGCN ZYQ8/JX17 RI QTL 2001 | 6 | 0 cM | 0 cM | hep2001a-68 |
9 | AGEBC KDM105/CT999 RI QTL 2000 | 6 | 22.1 cM | 22.1 cM | lajc2000a-92 |
10 | CNRRI Wai/CB QTL 1996 | 6 | 0 cM | 0 cM | linhx1996b-57 |
11 | JRGP Nip/Kas F2 QTL 2000 | 6 | 8.2 cM | 8.2 cM | rgp2000a-2151 |
12 | IGCN ZYQ18/JX17 DH QTL 1998 | 6 | 5.7 cM | 5.7 cM | shl1998a-257 |
13 | Zh97/Ming63 CNHZAU F2 QTL 1999 | 6 | 8 cM | 8 cM | tay1999a-71 |
14 | IRRI Mor/CO39 QTL 1994 | 6 | 0 cM | 0 cM | wag1994a-61 |
15 | IRRI Pal/IR42 F2 QTL 1995 | 6a | 0 cM | 0 cM | wup1995a-1 |
16 | Cornell 9024/LH422 RI QTL 1996 | 6 | 4.4 cM | 4.4 cM | xiaoj1996a-69 |
17 | CNHZAU Zh97/Ming63 RI QTL 2002 | 6 | 12.9 cM | 12.9 cM | xiy2002a-136 |
18 | IGCAS ZYQ8/JX17 F2 QTL 1995 | 6 | 0 cM | 0 cM | yunxu1995a-23 |
19 | CNRRI Tes/CB QTL 1997 | 6 | 0 cM | 0 cM | zhj1997a-75 |
20 | Rice japonica MSU6 | Chr. 6 | 1764623 bp | 1769657 bp | grjp2009a-6-GR:0061010 |
Trait | glutinous endosperm (TO:0000098) |
Plant Structure | endosperm (PO:0009089) |
Cellular Component | amyloplast (GO:0009501), plastid (GO:0009536), amyloplast starch grain (GO:0009568) |
Molecular Function | glycogen (starch) synthase activity (GO:0004373) |
Biological Process | starch metabolic process (GO:0005982) |
Environment | watering regimen (EO:0007383), unknown environment (EO:0007403) |
Species | Accession | Trait Symbol | Trait Name | Evidence |
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Oryza sativa | AQBP002 | AMYCN | amylose content | He-P et al., 1999 (IAGP) |
Chr | Start | Stop | Exp | Num. SNP Positions | |
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chr6 | 1,764,623 | 1,769,657 | ~160K SNPs x 20 accessions (McNally 2... | 8 | Search for SNPs |
chr6 | 1,764,623 | 1,769,657 | '1536 chip' - 1311 SNPs x 395 rice ac... | 2 | Search for SNPs |
chr6 | 1,764,623 | 1,769,657 | Huang X, et al, Nat Genetics 2010 Nov... | 13 | Search for SNPs |
chr6 | 1,764,623 | 1,769,657 | RiceDiversity 44K SNP assay, 34 trait... | 13 | Search for SNPs |
chr6 | 1,764,623 | 1,769,657 | RiceDiversity 44K SNP assay, 34 trait... | 3 | Search for SNPs |