2.8 KiB
Executable File
2.8 KiB
Executable File
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：
- 核心启动子元件 (最高优先级)
- 激素响应元件
- 胁迫响应元件
- 转录因子结合位点
- 光响应元件
- 发育调控元件
- 其他 (最低优先级)
参考来源
- PlantCARE Database: https://bioinformatics.psb.ugent.be/webtools/plantcare/
- 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.
- New PLACE Database: https://www.dna.affrc.go.jp/PLACE/