Red Sage Omics Salvia miltiorrhiza reference portal
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Public data scope: Chr01–Chr08. Module and data release manifest

Help

All major pages support Chinese and English. The language switch preserves query parameters, so you can search first and then switch language on the same result page.

Identifier Search Rules

The portal uses the standard Gene ID first, for example SmilChr01G000001.

Most search boxes also accept NCBI Gene ID, GeneID, locus tag, transcript ID, and Protein ID. The system resolves the input to a standard gene before returning module-specific results.

Standard ID: SmilChr01G000001 LOC ID: LOC131007145 NCBI GeneID: 131007145 Protein ID: XP_057790285.1

Curation and Evidence Standards

Standard IDs and Literature Names

Standard IDs are the primary display and download identifiers. Literature names enter the mapping table only after manual review; Gene Cards retain mapping method, confidence, and source papers. Low-confidence mappings are candidate clues only.

GO / KEGG

Annotations are limited to imported database records and homology support. Missing GO or KEGG terms do not demonstrate absence of function; KEGG coverage of specialized metabolism remains incomplete.

TFBS / Targets

Results use 4 kb upstream sequences and precomputed PWM motif scans. Normalized-score thresholds rank and filter hits; they are not significance cutoffs calibrated by Red Sage ChIP, DAP-seq, EMSA, or reporter assays. Every hit is a candidate cis element or candidate target.

PPI

The PPI page separates a local heuristic candidate score from Salvia splendens STRING homolog-transfer evidence. Their overlap can prioritize candidates, but is not Red Sage experimental evidence and must not be described as a direct physical interaction.

Common Examples

Gene Card

View basic information, sequences, annotations, localization, expression, variants, and JBrowse links for one gene.

SmilChr01G000001 LOC131007145 131007145 XP_057790285.1

Pfam Search

Search by Pfam ID or keyword to find Red Sage genes in the same family.

PF00069

Protein Domains

View Pfam domain positions and schematics for a gene or protein.

SmilChr01G000001 LOC131007145 131007145 XP_057790285.1

Subcellular Localization

Return the five most likely subcellular locations.

SmilChr01G000001 LOC131007145 131007145 XP_057790285.1

Expression Atlas

View expression values by study and condition.

SmilChr05G000084 LOC131026563 131026563 XP_057812434.1

Co-expression

Find genes with the most similar expression patterns from expression matrices.

SmilChr01G000001 LOC131007145 131007145 XP_057790285.1

Protein Interaction

Enter one gene for Top10/Top20 candidate partners, or score two submitted sequences.

SmilChr05G001096 LOC130985803 130985803 XP_057764913.1

GO / KEGG

Show one GO/KEGG annotation row per gene and generate enrichment plots for gene sets.

GO/KEGG

Genome Tools

Extract sequences, overlapping genes, and PCR primer candidates by standard chromosome interval.

Chr01:47739-50415

TFBS

Scan possible binding sites in a 4000 bp promoter or submitted DNA sequence.

SmilChr01G000001 LOC131007145 131007145 XP_057790285.1

EMS Variants

Filter EMS candidate variants by gene, material, or genomic interval.

SmilChr01G000001 LOC131007145 131007145 XP_057790285.1

JBrowse

Browse the eight standard chromosomes and gene structure annotations.

JBrowse

BLAST

Search against Genome, cDNA, CDS, or Protein databases.

BLAST

JBrowse Guide

  1. Open JBrowse and search a standard Gene ID or a coordinate such as Chr01:100000-120000.
  2. Enable the reference-sequence and gene-annotation tracks from the track list; zoom in to inspect exons, CDS features, and strand direction.
  3. Coordinates and IDs follow the portal reference genome version. Return to the Gene Card with the same standard ID for sequences, annotations, variants, or expression.

Open JBrowse

Suggested Workflows

From Candidate Gene to Function

Gene Card -> annotation -> Pfam/domains -> subcellular localization -> expression -> co-expression -> PPI.

From Region to Candidate Genes

Genome Tools -> JBrowse -> genes in interval -> EMS variants -> Gene Card.

From Family to Gene Members

Pfam Search -> Gene Card -> expression/co-expression -> sequence download.