Rubber Biosynthesis Focus

A pathway-centered entry for MVA/MEP, IPP/DMAPP, prenyl donors, CPT/CPTL, REF/SRPP, latex/root-associated and terpenoid candidate genes.

This topic is built from precomputed GFF/GO/KEGG/homology candidate sets and linked evidence from expression, proteome, localization, Pfam, Swiss-Prot, PPI, coexpression and TFBS modules. Results are candidate evidence, not experimental validation.

The current database contains 5523 candidate records, 4979 candidate genes, and 8 pathway steps; the main display is centered on the TK1151 reference while OH-1004/LXL04 remains queryable and linked.

Examples TkA01G624900 LXL04_000258

Download current filtered candidate TSV

Cross-species Research Reference

1 reference genes are counted separately from rubber-dandelion candidates. They are literature, omics, or sequence resources from Para rubber tree, guayule, a related dandelion, and Eucommia; external function or homology is not direct validation in rubber dandelion.

1. Choose a speciesClick a species card or use the filter to focus on one reference species and material context.

2. Read the evidence typeRead the evidence and boundary column: direct experiments, omics associations, and sequence resources have different interpretation ranges.

3. Verify the sourceEach DOI, article, or public database entry is clickable; download the current filter for further comparison.

Eucommia records are a trans-polyisoprene comparator only and are excluded from natural cis-rubber candidate and pathway-card counts.

1Hardy rubber treeClick to view · 1 sources · trans-1,4-polyisoprene

Download current cross-species reference TSV

Species and material	Reference gene / sequence ID	Pathway step	Evidence and boundary	Source
Hardy rubber treeEucommia ulmoidestrans-1,4-polyisopreneTransgenic roots	`EuIPI`AB041629.2IDI	Prenyl-donor metabolismTrans-polyisoprene precursor-supply reference	A_direct_genetic_experiment EuIPI overexpression was associated with higher trans-polyisoprene accumulation. Trans-polyisoprene comparator only; excluded from natural cis-rubber candidate conclusions.	10.1186/1472-6750-12-78Overexpression of EuIPI increases trans-polyisoprene accumulation

Hardy rubber tree · EuIPI

Sequence IDAB041629.2

StepPrenyl-donor metabolism · IDI

EvidenceEuIPI overexpression was associated with higher trans-polyisoprene accumulation.

BoundaryTrans-polyisoprene comparator only; excluded from natural cis-rubber candidate conclusions.

Source10.1186/1472-6750-12-78

Pathway Navigation And Candidate Distribution

MVA · Mevalonate pathway

High 40 · Medium 3 · Low 4 MEP · MEP pathway

High 23 · Medium 0 · Low 36 IPP/DMAPP/FPP · Prenyl-donor metabolism

271

High 141 · Medium 83 · Low 47 CPT/CPTL · Cis-prenyltransferase branch

High 0 · Medium 0 · Low 5 REF/SRPP · Rubber-particle proteins

High 0 · Medium 0 · Low 7 Rubber · Rubber biosynthesis candidates

288

High 1 · Medium 287 · Low 0 Terpenoid · Terpenoid metabolism

380

High 72 · Medium 107 · Low 201 Latex/root · Latex/root associated candidates

4466

High 231 · Medium 1284 · Low 2951

377 MVA/MEP and isoprenoid

Click to filter · High 204 · Medium 86 · Low 87 4466 Latex/root related candidates

Click to filter · High 231 · Medium 1284 · Low 2951 300 Rubber biosynthesis

Click to filter · High 1 · Medium 287 · Low 12 380 Terpenoid metabolism

Click to filter · High 72 · Medium 107 · Low 201

Candidate Genes

377 candidates match the current filter; 10 are shown per page (page 4 of 38). TSV exports up to 2000 rows under the current filters. Use pathway nodes or summary cards to filter, then inspect Gene Card and linked modules for evidence details.

Gene ID	Pathway/step	Confidence	Evidence layers	Location	Key evidence	Actions
`LXL04_033947` TK1151: - OH-1004: LXL04_033947	MVA/MEP and isoprenoid MEP pathway	High score 16	GOExpressionLocalizationPfamSwiss-ProtCoexpression	CM104805.1:67678877-67679283 +	GO:0016114	Gene Card Expression Proteome JBrowse
`LXL04_037944` TK1151: - OH-1004: LXL04_037944	MVA/MEP and isoprenoid Prenyl-donor metabolism	High score 16	FunctionGOExpressionLocalizationPfamSwiss-ProtPPICoexpression	CM104807.1:25923792-25925584 +	GO:0008299	Gene Card Expression Proteome JBrowse
`LXL04_038304` TK1151: - OH-1004: LXL04_038304	MVA/MEP and isoprenoid MEP pathway	High score 16	GOExpressionLocalizationPfamSwiss-ProtCoexpression	CM104807.1:36915774-36916379 -	GO:0016114	Gene Card Expression Proteome JBrowse
`TkA04G415850` TK1151: TkA04G415850 OH-1004: LXL04_038305	MVA/MEP and isoprenoid MEP pathway	High score 16	GOExpressionLocalizationPfamSwiss-ProtPPICoexpression	CM104807.1:36941482-36944078 -	GO:0016114	Gene Card Expression Proteome JBrowse
`TkAUNG089850` TK1151: TkAUNG089850;TkA02G042480;TkA02G481170;TkA04G415960;TkA07G148450 OH-1004: LXL04_038308	MVA/MEP and isoprenoid MEP pathway	High score 16	GOExpressionLocalizationPfamSwiss-ProtPPICoexpression	CM104807.1:36967663-36970360 -	GO:0016114	Gene Card Expression Proteome JBrowse
`TkA02G520890` TK1151: TkA02G520890 OH-1004: LXL04_013034	MVA/MEP and isoprenoid MEP pathway	High score 14	GOExpressionLocalizationPfamSwiss-ProtPPICoexpression	CM104801.1:22823670-22831718 +	GO:0016114	Gene Card Expression Proteome JBrowse
`TkA02G402670` TK1151: TkA02G402670 OH-1004: LXL04_014719	MVA/MEP and isoprenoid MEP pathway	High score 14	GOExpressionLocalizationPfamSwiss-ProtCoexpression	CM104801.1:55486680-55489299 -	GO:0016114	Gene Card Expression Proteome JBrowse
`TkA02G535540` TK1151: TkA02G535540;TkA05G451840 OH-1004: LXL04_022221	MVA/MEP and isoprenoid Mevalonate pathway	High score 14	FunctionGOExpressionLocalizationPfamSwiss-ProtCoexpression	CM104802.1:146393099-146395586 -	GO:0008299	Gene Card Expression Proteome JBrowse
`TkA04G317480` TK1151: TkA04G317480;TkA04G319020;TkA04G431020;TkA06G056610 OH-1004: LXL04_025486	MVA/MEP and isoprenoid Prenyl-donor metabolism	High score 14	FunctionGOExpressionLocalizationSwiss-ProtCoexpression	CM104803.1:112454480-112455738 +	GO:0045337	Gene Card Expression Proteome JBrowse
`TkA03G524060` TK1151: TkA03G524060 OH-1004: LXL04_027381	MVA/MEP and isoprenoid Prenyl-donor metabolism	High score 14	FunctionGOExpressionLocalizationPfamSwiss-ProtCoexpression	CM104804.1:14579926-14584822 +	GO:0045337	Gene Card Expression Proteome JBrowse

`LXL04_033947`

MVA/MEP and isoprenoidMEP pathwayHigh · score 16

Source ID-

LocationCM104805.1:67678877-67679283 +

EvidenceGOExpressionLocalizationPfamSwiss-ProtCoexpression

Key evidenceGO:0016114

Gene Card Expression Proteome JBrowse

`LXL04_037944`

MVA/MEP and isoprenoidPrenyl-donor metabolismHigh · score 16

Source ID-

LocationCM104807.1:25923792-25925584 +

EvidenceFunctionGOExpressionLocalizationPfamSwiss-ProtPPICoexpression

Key evidenceGO:0008299

Gene Card Expression Proteome JBrowse

`LXL04_038304`

MVA/MEP and isoprenoidMEP pathwayHigh · score 16

Source ID-

LocationCM104807.1:36915774-36916379 -

EvidenceGOExpressionLocalizationPfamSwiss-ProtCoexpression

Key evidenceGO:0016114

Gene Card Expression Proteome JBrowse

`TkA04G415850`

MVA/MEP and isoprenoidMEP pathwayHigh · score 16

Source IDTkA04G415850

LocationCM104807.1:36941482-36944078 -

EvidenceGOExpressionLocalizationPfamSwiss-ProtPPICoexpression

Key evidenceGO:0016114

Gene Card Expression Proteome JBrowse

`TkAUNG089850`

MVA/MEP and isoprenoidMEP pathwayHigh · score 16

Source IDTkAUNG089850;TkA02G042480;TkA02G481170;TkA04G415960;TkA07G148450

LocationCM104807.1:36967663-36970360 -

EvidenceGOExpressionLocalizationPfamSwiss-ProtPPICoexpression

Key evidenceGO:0016114

Gene Card Expression Proteome JBrowse

`TkA02G520890`

MVA/MEP and isoprenoidMEP pathwayHigh · score 14

Source IDTkA02G520890

LocationCM104801.1:22823670-22831718 +

EvidenceGOExpressionLocalizationPfamSwiss-ProtPPICoexpression

Key evidenceGO:0016114

Gene Card Expression Proteome JBrowse

`TkA02G402670`

MVA/MEP and isoprenoidMEP pathwayHigh · score 14

Source IDTkA02G402670

LocationCM104801.1:55486680-55489299 -

EvidenceGOExpressionLocalizationPfamSwiss-ProtCoexpression

Key evidenceGO:0016114

Gene Card Expression Proteome JBrowse

`TkA02G535540`

MVA/MEP and isoprenoidMevalonate pathwayHigh · score 14

Source IDTkA02G535540;TkA05G451840

LocationCM104802.1:146393099-146395586 -

EvidenceFunctionGOExpressionLocalizationPfamSwiss-ProtCoexpression

Key evidenceGO:0008299

Gene Card Expression Proteome JBrowse

`TkA04G317480`

MVA/MEP and isoprenoidPrenyl-donor metabolismHigh · score 14

Source IDTkA04G317480;TkA04G319020;TkA04G431020;TkA06G056610

LocationCM104803.1:112454480-112455738 +

EvidenceFunctionGOExpressionLocalizationSwiss-ProtCoexpression

Key evidenceGO:0045337

Gene Card Expression Proteome JBrowse

`TkA03G524060`

MVA/MEP and isoprenoidPrenyl-donor metabolismHigh · score 14

Source IDTkA03G524060

LocationCM104804.1:14579926-14584822 +

EvidenceFunctionGOExpressionLocalizationPfamSwiss-ProtCoexpression

Key evidenceGO:0045337

Gene Card Expression Proteome JBrowse

Evidence Boundary

Current results integrate annotation, GO/KEGG, homology, predicted localization, domains, expression/proteome and network evidence. High/Medium/Low indicates evidence density and consistency, not experimental validation.