Red Sage Omics Salvia miltiorrhiza reference portal
Home Gene Search ID Map Annotation Domains Pfam Tools PPI Subcellular Expression Co-expression Homology GO/KEGG TFBS TF Targets EMS Variants JBrowse BLAST Download About Help
Data
ID Map Annotation Functional Search Specialized Metabolism Literature Evidence Domains Pfam Homology
Tools
Genome Tools Primer Design HR Primer Design Translate BLAST PPI Subcellular Co-expression GO/KEGG Functional Search
Regulation
TFBS TF Targets EMS Variants
Help
About Help Resources and Release
中文 EN

Gene Card

Search by standard ID, NCBI Gene ID, GeneID, locus tag, transcript ID, protein ID, or a manually reviewed literature gene name. The page resolves the query to a Red Sage gene and integrates coordinates, sequences, annotations, subcellular localization, EMS variants, and downloads.
Examples

Resolved gene

SmilChr03G000543

Chromosome: Chr03 Coordinates: 5892401-5893673 Strand: + Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr03G000543
NameSmilChr03G000543
DescriptionF-box protein At3g07870-like
Chromosome / SeqIDChr03 / NC_080389.1
Coordinates and Strand5892401 - 5893673 / +

ID Mapping

NCBI Gene IDLOC131017205
GeneID131017205
locus_tag-
NCBI NameLOC131017205
Original querySmilChr03G000543

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
DescriptionF-box protein At3g07870-like
ProductF-box protein At3g07870-like
ArabidopsisAT3G06240 (AT3G06240)
F-box family protein [Source:NCBI gene (formerly Entrezgene);Acc:819798]
identity=27.9; qcov=0.915; evalue=4.49e-16; confidence=low
Rice-
-
GOGO:0005515 (protein binding)
KEGG-
PfamPF00646 (F-box); PF03478 (Beta-prop_KIB1-4); PF07734 (FBA_1); PF08268 (FBA_3)
InterPro-
eggNOG-
NRGeneID:131017205

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Cytoplasm 细胞质 0.80000 XP_057801924.1
2 Nucleus 细胞核 0.40000 XP_057801924.1
3 Cytosol 细胞质基质 0.20000 XP_057801924.1
4 Chromosome 染色体 0.00000 XP_057801924.1
5 Centromere 着丝粒 0.00000 XP_057801924.1

Open subcellular search

EMS Mutant Variants

The table shows the first 12 candidate EMS variants for this gene. Open the EMS module for full filtering and downloads.

Position REF ALT Type Effect Carriers Samples
Chr3:5892660 G A EMS_canonical_SNV CDS_variant 4 A5,B11,B19,D4
Chr3:5892662 C T EMS_canonical_SNV CDS_variant 1 B66
Chr3:5892797 C T EMS_canonical_SNV CDS_variant 2 B40,C58
Chr3:5892832 G A EMS_canonical_SNV CDS_variant 1 B31
Chr3:5892923 C T EMS_canonical_SNV CDS_variant 2 A5,B19
Chr3:5893082 C T EMS_canonical_SNV CDS_variant 1 B120
Chr3:5893086 G A EMS_canonical_SNV CDS_variant 4 B120,B94,C37,C8
Chr3:5893095 C T EMS_canonical_SNV CDS_variant 1 B140
Chr3:5893301 C T EMS_canonical_SNV CDS_variant 2 B132,C43
Chr3:5893376 C T EMS_canonical_SNV CDS_variant 2 C64,C66
Chr3:5893412 G A EMS_canonical_SNV CDS_variant 3 B31,B44,C86

Open EMS variants

Predicted Protein Domains

Domain results are from the Pfam-A HMM database and HMMER hmmscan; positions are amino-acid coordinates on the corresponding protein sequence.

XP_057801924.1
294 aa
N
1
147
294
F-box
Beta-prop_KIB1-4
FBA_1
FBA_3
C
PF00646 F-box 10-34 aa PF03478 Beta-prop_KIB1-4 27-219 aa PF07734 FBA_1 39-211 aa PF08268 FBA_3 39-216 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057801924.1 Pfam PF00646 F-box Domain 10 34 0.00042 20.8 F-box domain
XP_057801924.1 Pfam PF03478 Beta-prop_KIB1-4 Repeat 27 219 3.4e-08 34.0 KIB1-4 beta-propeller
XP_057801924.1 Pfam PF07734 FBA_1 Repeat 39 211 1.8e-19 70.6 F-box associated beta propeller domain
XP_057801924.1 Pfam PF08268 FBA_3 Repeat 39 216 8.2e-16 58.6 F-box associated beta propeller domain

cDNA / CDS / Protein Sequences

Download genomic DNA (gene region only)

Every public gene has transcript sequence from the reference annotation. Protein-coding genes also have CDS and protein sequences. CDS and protein downloads do not apply to noncoding RNA. Version suffixes of original accessions are retained.

cDNA

1 records

Download cDNA FASTA
XM_057945941.1
CTTAAATACCTCGAACCCTCGAAAGCCACTGCCGCCGCCAGCTATGGAGATCCCAAACACTCGCCGAGATCTCGATCTCCCCCAAGAACTCACCGAAGAAATACTGTCAAGACTTGCGGTGAAATCTCTCCTGAGATTCAGGCTCATTAATATGGAGTCCGTCCGTATAGTGGGGTGCTGTAATGGGCTGGTCTGCTGCTGCATTGATCTCAGGAGAGGGCGTTTCTTATTATGGAATCCTGCCACCAGAATCTCCATGG...

CDS

1 records

Download CDS FASTA
LOC131017205
ATGGAGATCCCAAACACTCGCCGAGATCTCGATCTCCCCCAAGAACTCACCGAAGAAATACTGTCAAGACTTGCGGTGAAATCTCTCCTGAGATTCAGGCTCATTAATATGGAGTCCGTCCGTATAGTGGGGTGCTGTAATGGGCTGGTCTGCTGCTGCATTGATCTCAGGAGAGGGCGTTTCTTATTATGGAATCCTGCCACCAGAATCTCCATGGAATTACCACAATTGGTATTAGAGAATAGAGACTGGCCCTCGTC...

Protein

1 records

Download Protein FASTA
XP_057801924.1
MEIPNTRRDLDLPQELTEEILSRLAVKSLLRFRLINMESVRIVGCCNGLVCCCIDLRRGRFLLWNPATRISMELPQLVLENRDWPSSISGFGWDESSGAYKVFVVLRSSRKFMGRVYSSNTNSWKTVEFFDIGLIHSKAHFVSGKLHWLHIKNTDETDNYEIATFDLKKEELGVMKLPRGAESVRLGVNEGHLTMILEKKRTDFDVWVMKQDCWVKVRDGVVYEPCEVLPSVAPFYAVDEAEIRQVHGSDFKLYDQARDD...

Flanking Sequence Downloads

Upstream/downstream length is capped at 10000 bp. Negative-strand genes are reverse-complemented so the exported FASTA follows transcriptional 5′ to 3′ orientation.

Download upstream Download downstream Download upstream + gene + downstream

JBrowse

Open genome browser