Species | Oryza sativa (Rice) [ GR_tax:013681 ] | ||||||||||
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Accession | GR:0060724 | ||||||||||
Gene Symbol | RC | ||||||||||
Gene Name | BROWN PERICARP AND SEED COAT | ||||||||||
Synonyms (10) |
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E.C. Numbers (0) | |||||||||||
Pathway Reactions (0) | |||||||||||
Chromosome No. | 7 | ||||||||||
Gene Type | Not sequenced | ||||||||||
Has Phenotype | yes | ||||||||||
Description | The gene is responsible for the production of pigment in the so-called brown pericarp rice, which has dark-brown irregular speckles on a reddish brown background. When Rc co-exists with Rd (red pericarp and seed coat; GR:0060733), the color of Rc develops over the entire surface, giving a dark red color to the pericarp and seed coat. Rc is regarded to have an effect of accumulating the pigment in the pigment layers. It encodes for a Basic Helix-Loop-Helix protein that is a positive regulator of proanthocyanidin. Rc is an ortholog of maize INTENSIFIER1 (GR:0200268), a negative regulator of anthocyanin production. |
Nucleotide (DNA) |
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Map Type | Map Set | Name | Map | Position | Ext. Links | |||
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Sequence | Gramene Annotated Nipponbare Sequence 2009 | BNL6.32 | Chr. 7 | 6,061,890-6,068,318bp | View Comparative Map | |||
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Map Type | Map Set | Name | Map | Position | Ext. Links | |||
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Genetic | Hokkaido Morphological 2000 | BNL6.32 | 7 | 52-52cM | View Comparative Map | |||
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JRGP RFLP 2000 | BNL6.32 | 7 | 43.8-44.4cM | View Comparative Map | ||||
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QTL | JNIG W1944/Peik QTL 2002 | BNL6.32 | 7 | 114-114cM | View Comparative Map | |||
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JRGP Nip/Kas F2 QTL 2000 | BNL6.32 | 7 | 44.1-44.1cM | View Comparative Map | ||||
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NDSU EM93/SS18 BC QTL 2004 | BNL6.32 | 7 | 59.7-59.7cM | 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 | JRGP RFLP 2000 | 7 | 43.8 cM | 44.4 cM | jrgp-2000-7-232 |
2 | Hokkaido Morphological 2000 | 7 | 52 cM | 52 cM | morph-2000-7-7 |
3 | JNIG W1944/Peik QTL 2002 | 7 | 114 cM | 114 cM | cah2002a-122 |
4 | NDSU EM93/SS18 BC QTL 2004 | 7 | 59.7 cM | 59.7 cM | gux2004a-85 |
5 | JRGP Nip/Kas F2 QTL 2000 | 7 | 44.1 cM | 44.1 cM | rgp2000a-2684 |
6 | Rice japonica MSU6 | Chr. 7 | 6061890 bp | 6068318 bp | grjp2009a-7-GR:0060724 |
Trait | seed coat color (TO:0000190), endosperm color (TO:0000487), pericarp color (TO:0000707) |
Plant Structure | seed coat (PO:0009088), endosperm (PO:0009089) |
Plant Growth and Development Stage | whole plant fruit ripening stage (PO:0007010), whole plant fruit ripening complete stage (PO:0007038), inflorescence emergence stage (PO:0007041), whole plant fruit formation stage (PO:0007042) |
Cereal Plant Growth Stage | 08-dough stage (GRO:0007042), 06-heading stage (GRO:0007044), 09-mature grain stage (GRO:0007045), 07-milk stage (GRO:0007046) |
Biological Process | flavonoid metabolic process (GO:0009812), anthocyanin-containing compound metabolic process (GO:0046283) |
Chr | Start | Stop | Exp | Num. SNP Positions | |
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chr7 | 6,061,890 | 6,068,318 | ~160K SNPs x 20 accessions (McNally 2... | 4 | Search for SNPs |
chr7 | 6,061,890 | 6,068,318 | '1536 chip' - 1311 SNPs x 395 rice ac... | 0 | |
chr7 | 6,061,890 | 6,068,318 | Huang X, et al, Nat Genetics 2010 Nov... | 35 | Search for SNPs |
chr7 | 6,061,890 | 6,068,318 | RiceDiversity 44K SNP assay, 34 trait... | 35 | Search for SNPs |
chr7 | 6,061,890 | 6,068,318 | RiceDiversity 44K SNP assay, 34 trait... | 2 | Search for SNPs |