PlantAI-dev/scripts/promoter_element_categories.md

植物顺式作用元件分类规则 (PlantCARE-based)

分类体系

1. 核心启动子元件 (Core Promoter Elements)

• TATA-box: TATA-box, AT~TATA-box, TATA
• CAAT-box: CAAT-box, CCAAT-box
• Inr (Initiator): Inr, Y-patch

2. 光响应元件 (Light Responsive Elements)

• G-box/G-Box: G-box, G-Box, G-box-like
• GT1-motif: GT1-motif, GT-1
• I-box: I-box, I-box core
• Sp1: Sp1 (light responsive)
• Box 4: Box 4
• GATA-motif: GATA-motif

3. 激素响应元件 (Hormone Responsive Elements)

3.1 ABA响应

• ABRE: ABRE, ABA-responsive element

3.2 赤霉素响应

• P-box: P-box, GARE (gibberellin-responsive element)
• Py-box: Py-box

3.3 茉莉酸响应

• CGTCA-motif: CGTCA-motif
• TGACG-motif: TGACG-motif

3.4 水杨酸响应

• TCA-element: TCA-element
• as-1: as-1

3.5 生长素响应

• TGA-element: TGA-element
• AuxRE: AuxRE

3.6 乙烯响应

• ERE: ERE (ethylene-responsive element)

4. 胁迫响应元件 (Stress Responsive Elements)

4.1 干旱/脱水

• DRE/CRT: DRE, CRT (C-repeat)
• MBS: MBS (MYB binding site, drought)

4.2 低温

• LTR: LTR (low temperature responsive)

4.3 厌氧

• ARE: ARE (anaerobic responsive element)

4.4 氧化胁迫

• STRE: STRE (stress responsive element)

4.5 伤口/病原体

• W box: W box, W-box
• WRE: WRE3, WRE

5. 转录因子结合位点 (TF Binding Sites)

5.1 MYB家族

• MYB: MYB, Myb, MYB-like sequence, MYB recognition site
• MBS: MBS (MYB binding site)
• MRE: MRE (MYB recognition element)

5.2 MYC/bHLH家族

• MYC: MYC, MYC recognition site
• E-box: E-box, CANNTG

5.3 WRKY家族

• W box: W box (也是WRKY结合位点)

5.4 bZIP家族

• ABRE: ABRE (也是bZIP结合位点)
• G-box: G-box (也是bZIP结合位点)

6. 发育调控元件 (Developmental Elements)

6.1 种子特异性

• RY-element: RY-element, CATGCATG
• AAGAA-motif: AAGAA-motif

6.2 分生组织

• CAT-box: CAT-box

6.3 胚乳

• GCN4-motif: GCN4-motif
• Skn-1 motif: Skn-1 motif

7. 其他功能元件

• TCT-motif: TCT-motif
• Unnamed: Unnamed__1, Unnamed__4, Unnamed__6 等

分类优先级规则

当一个元件可能属于多个类别时，按以下优先级：

1. 核心启动子元件 (最高优先级)
2. 激素响应元件
3. 胁迫响应元件
4. 转录因子结合位点
5. 光响应元件
6. 发育调控元件
7. 其他 (最低优先级)

参考来源

1. PlantCARE Database: https://bioinformatics.psb.ugent.be/webtools/plantcare/
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.
3. New PLACE Database: https://www.dna.affrc.go.jp/PLACE/