112 lines
2.8 KiB
Markdown
112 lines
2.8 KiB
Markdown
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# 植物顺式作用元件分类规则 (PlantCARE-based)
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## 分类体系
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### 1. 核心启动子元件 (Core Promoter Elements)
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- **TATA-box**: TATA-box, AT~TATA-box, TATA
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- **CAAT-box**: CAAT-box, CCAAT-box
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- **Inr (Initiator)**: Inr, Y-patch
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### 2. 光响应元件 (Light Responsive Elements)
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- **G-box/G-Box**: G-box, G-Box, G-box-like
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- **GT1-motif**: GT1-motif, GT-1
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- **I-box**: I-box, I-box core
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- **Sp1**: Sp1 (light responsive)
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- **Box 4**: Box 4
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- **GATA-motif**: GATA-motif
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### 3. 激素响应元件 (Hormone Responsive Elements)
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#### 3.1 ABA响应
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- **ABRE**: ABRE, ABA-responsive element
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#### 3.2 赤霉素响应
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- **P-box**: P-box, GARE (gibberellin-responsive element)
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- **Py-box**: Py-box
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#### 3.3 茉莉酸响应
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- **CGTCA-motif**: CGTCA-motif
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- **TGACG-motif**: TGACG-motif
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#### 3.4 水杨酸响应
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- **TCA-element**: TCA-element
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- **as-1**: as-1
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#### 3.5 生长素响应
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- **TGA-element**: TGA-element
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- **AuxRE**: AuxRE
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#### 3.6 乙烯响应
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- **ERE**: ERE (ethylene-responsive element)
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### 4. 胁迫响应元件 (Stress Responsive Elements)
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#### 4.1 干旱/脱水
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- **DRE/CRT**: DRE, CRT (C-repeat)
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- **MBS**: MBS (MYB binding site, drought)
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#### 4.2 低温
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- **LTR**: LTR (low temperature responsive)
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#### 4.3 厌氧
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- **ARE**: ARE (anaerobic responsive element)
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#### 4.4 氧化胁迫
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- **STRE**: STRE (stress responsive element)
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#### 4.5 伤口/病原体
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- **W box**: W box, W-box
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- **WRE**: WRE3, WRE
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### 5. 转录因子结合位点 (TF Binding Sites)
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#### 5.1 MYB家族
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- **MYB**: MYB, Myb, MYB-like sequence, MYB recognition site
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- **MBS**: MBS (MYB binding site)
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- **MRE**: MRE (MYB recognition element)
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#### 5.2 MYC/bHLH家族
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- **MYC**: MYC, MYC recognition site
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- **E-box**: E-box, CANNTG
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#### 5.3 WRKY家族
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- **W box**: W box (也是WRKY结合位点)
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#### 5.4 bZIP家族
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- **ABRE**: ABRE (也是bZIP结合位点)
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- **G-box**: G-box (也是bZIP结合位点)
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### 6. 发育调控元件 (Developmental Elements)
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#### 6.1 种子特异性
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- **RY-element**: RY-element, CATGCATG
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- **AAGAA-motif**: AAGAA-motif
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#### 6.2 分生组织
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- **CAT-box**: CAT-box
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#### 6.3 胚乳
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- **GCN4-motif**: GCN4-motif
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- **Skn-1 motif**: Skn-1 motif
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### 7. 其他功能元件
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- **TCT-motif**: TCT-motif
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- **Unnamed**: Unnamed__1, Unnamed__4, Unnamed__6 等
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## 分类优先级规则
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当一个元件可能属于多个类别时，按以下优先级：
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1. 核心启动子元件 (最高优先级)
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2. 激素响应元件
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3. 胁迫响应元件
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4. 转录因子结合位点
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5. 光响应元件
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6. 发育调控元件
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7. 其他 (最低优先级)
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## 参考来源
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1. PlantCARE Database: https://bioinformatics.psb.ugent.be/webtools/plantcare/
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2. Lescot et al. (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res.
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3. New PLACE Database: https://www.dna.affrc.go.jp/PLACE/
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