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

SmilChr03G002503

Chromosome: Chr03 Coordinates: 39865434-39871291 Strand: - Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr03G002503
NameSmilChr03G002503
Descriptiontranscription factor MYB3R-3-like
Chromosome / SeqIDChr03 / NC_080389.1
Coordinates and Strand39865434 - 39871291 / -

ID Mapping

NCBI Gene IDLOC131016668
GeneID131016668
locus_tag-
NCBI NameLOC131016668
Original querySmilChr03G002503

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptiontranscription factor MYB3R-3-like
Producttranscription factor MYB3R-3-like
ArabidopsisAT5G02320 (MYB3R-5)
myb domain protein 3r-5 [Source:NCBI gene (formerly Entrezgene);Acc:831802]
identity=48.9; qcov=0.979; evalue=1.79e-146; confidence=high
RiceOs01g0841500 (OsMYB3R-2)
-
identity=71; qcov=0.422; evalue=5.29e-102; confidence=low
GOGO:0000978 (RNA polymerase II cis-regulatory region sequence-specific DNA binding); GO:0000981 (DNA-binding transcription factor activity, RNA polymerase II-specific); GO:0005634 (nucleus); GO:0006355 (regulation of DNA-templated transcription)
KEGG-
PfamPF00249 (Myb_DNA-binding); PF13921 (Myb_DNA-bind_6)
InterPro-
eggNOG-
NRGeneID:131016668

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Nucleus 细胞核 1.00000 XP_057801356.1
2 Chromosome 染色体 0.00000 XP_057801356.1
3 Centromere 着丝粒 0.00000 XP_057801356.1
4 Chromatin 染色质 0.00000 XP_057801356.1
5 Telomere 端粒 0.00000 XP_057801356.1

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
Chr3:39866691 C T EMS_canonical_SNV CDS_variant 3 B127,B23,C27
Chr3:39867201 C T EMS_canonical_SNV CDS_variant 1 B132
Chr3:39867226 G A EMS_canonical_SNV CDS_variant 5 A13,B140,B77,C13,D7
Chr3:39867267 C T EMS_canonical_SNV CDS_variant 2 B122,B24
Chr3:39867505 GC G 1bp_deletion frameshift_variant 1 C54
Chr3:39867505 GC G 1bp_deletion CDS_variant 1 C54
Chr3:39867581 G A EMS_canonical_SNV CDS_variant 1 B24
Chr3:39867660 G A EMS_canonical_SNV CDS_variant 5 B100,B127,B23,B59,C27
Chr3:39870667 C T EMS_canonical_SNV CDS_variant 5 B125,B26,B51,B59,C15

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_057801356.1
524 aa
N
1
262
524
Myb_DNA-binding
Myb_DNA-bind_6
Myb_DNA-binding
Myb_DNA-bind_6
Myb_DNA-binding
Myb_DNA-bind_6
C
PF00249 Myb_DNA-binding 59-105 aa PF13921 Myb_DNA-bind_6 62-118 aa PF00249 Myb_DNA-binding 111-157 aa PF13921 Myb_DNA-bind_6 114-174 aa PF00249 Myb_DNA-binding 163-206 aa PF13921 Myb_DNA-bind_6 166-211 aa
XP_057801357.1
524 aa
N
1
262
524
Myb_DNA-binding
Myb_DNA-bind_6
Myb_DNA-binding
Myb_DNA-bind_6
Myb_DNA-binding
Myb_DNA-bind_6
C
PF00249 Myb_DNA-binding 59-105 aa PF13921 Myb_DNA-bind_6 62-118 aa PF00249 Myb_DNA-binding 111-157 aa PF13921 Myb_DNA-bind_6 114-174 aa PF00249 Myb_DNA-binding 163-206 aa PF13921 Myb_DNA-bind_6 166-211 aa
XP_057801358.1
524 aa
N
1
262
524
Myb_DNA-binding
Myb_DNA-bind_6
Myb_DNA-binding
Myb_DNA-bind_6
Myb_DNA-binding
Myb_DNA-bind_6
C
PF00249 Myb_DNA-binding 59-105 aa PF13921 Myb_DNA-bind_6 62-118 aa PF00249 Myb_DNA-binding 111-157 aa PF13921 Myb_DNA-bind_6 114-174 aa PF00249 Myb_DNA-binding 163-206 aa PF13921 Myb_DNA-bind_6 166-211 aa
XP_057801359.1
524 aa
N
1
262
524
Myb_DNA-binding
Myb_DNA-bind_6
Myb_DNA-binding
Myb_DNA-bind_6
Myb_DNA-binding
Myb_DNA-bind_6
C
PF00249 Myb_DNA-binding 59-105 aa PF13921 Myb_DNA-bind_6 62-118 aa PF00249 Myb_DNA-binding 111-157 aa PF13921 Myb_DNA-bind_6 114-174 aa PF00249 Myb_DNA-binding 163-206 aa PF13921 Myb_DNA-bind_6 166-211 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057801356.1 Pfam PF00249 Myb_DNA-binding Domain 59 105 1.5e-52 176.2 Myb-like DNA-binding domain
XP_057801356.1 Pfam PF13921 Myb_DNA-bind_6 Domain 62 118 9.6e-41 138.5 Myb-like DNA-binding domain
XP_057801356.1 Pfam PF00249 Myb_DNA-binding Domain 111 157 1.5e-52 176.2 Myb-like DNA-binding domain
XP_057801356.1 Pfam PF13921 Myb_DNA-bind_6 Domain 114 174 9.6e-41 138.5 Myb-like DNA-binding domain
XP_057801356.1 Pfam PF00249 Myb_DNA-binding Domain 163 206 1.5e-52 176.2 Myb-like DNA-binding domain
XP_057801356.1 Pfam PF13921 Myb_DNA-bind_6 Domain 166 211 9.6e-41 138.5 Myb-like DNA-binding domain
XP_057801357.1 Pfam PF00249 Myb_DNA-binding Domain 59 105 1.5e-52 176.2 Myb-like DNA-binding domain
XP_057801357.1 Pfam PF13921 Myb_DNA-bind_6 Domain 62 118 9.6e-41 138.5 Myb-like DNA-binding domain
XP_057801357.1 Pfam PF00249 Myb_DNA-binding Domain 111 157 1.5e-52 176.2 Myb-like DNA-binding domain
XP_057801357.1 Pfam PF13921 Myb_DNA-bind_6 Domain 114 174 9.6e-41 138.5 Myb-like DNA-binding domain
XP_057801357.1 Pfam PF00249 Myb_DNA-binding Domain 163 206 1.5e-52 176.2 Myb-like DNA-binding domain
XP_057801357.1 Pfam PF13921 Myb_DNA-bind_6 Domain 166 211 9.6e-41 138.5 Myb-like DNA-binding domain
XP_057801358.1 Pfam PF00249 Myb_DNA-binding Domain 59 105 1.5e-52 176.2 Myb-like DNA-binding domain
XP_057801358.1 Pfam PF13921 Myb_DNA-bind_6 Domain 62 118 9.6e-41 138.5 Myb-like DNA-binding domain
XP_057801358.1 Pfam PF00249 Myb_DNA-binding Domain 111 157 1.5e-52 176.2 Myb-like DNA-binding domain
XP_057801358.1 Pfam PF13921 Myb_DNA-bind_6 Domain 114 174 9.6e-41 138.5 Myb-like DNA-binding domain
XP_057801358.1 Pfam PF00249 Myb_DNA-binding Domain 163 206 1.5e-52 176.2 Myb-like DNA-binding domain
XP_057801358.1 Pfam PF13921 Myb_DNA-bind_6 Domain 166 211 9.6e-41 138.5 Myb-like DNA-binding domain
XP_057801359.1 Pfam PF00249 Myb_DNA-binding Domain 59 105 1.5e-52 176.2 Myb-like DNA-binding domain
XP_057801359.1 Pfam PF13921 Myb_DNA-bind_6 Domain 62 118 9.6e-41 138.5 Myb-like DNA-binding domain
XP_057801359.1 Pfam PF00249 Myb_DNA-binding Domain 111 157 1.5e-52 176.2 Myb-like DNA-binding domain
XP_057801359.1 Pfam PF13921 Myb_DNA-bind_6 Domain 114 174 9.6e-41 138.5 Myb-like DNA-binding domain
XP_057801359.1 Pfam PF00249 Myb_DNA-binding Domain 163 206 1.5e-52 176.2 Myb-like DNA-binding domain
XP_057801359.1 Pfam PF13921 Myb_DNA-bind_6 Domain 166 211 9.6e-41 138.5 Myb-like DNA-binding 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

4 records

Download cDNA FASTA
XM_057945376.1
TTATATAAAATATTTACTCGTTTTCTCTCTCTACTTTCAACGGGCAAGGTTTTTCGCAGCTCGGGTATTTTCTCTCTCTAAATTCAGAGATTTTTAGTTTTCTTAGGGCTTGGGAATCCGAGGAGCTAGTTTCTCAATTGGTGAGCTGTGATCAATCGAAGATTTATGCGAGGTTTTGATTTGTCTTCGTACGATGTTCTTGGCTACGGAGTTTTGTGCTGTGATTGGGGCTTTTAATTGTCGATTATCATTTGTTTATG...
XM_057945373.1
TATATAAAATATTTACTCGTTTTCTCTCTCTACTTTCAACGGGCAAGGTTTTTCGCAGCTCGGGTATTTTCTCTCTCTAAATTCAGAGATTTTTAGTTTTCTTAGGGCTTGGGAATCCGAGGAGCTAGTTTCTCAATTGGTGAGGAAGTTTAGGATTATGGAATTGTGATGAAGTATAGGGATTAATGGCAGAGGTAAAATTGGATGAATTTTGCCTTGAGAACAAGGAATCTGCTGTTGCTTCAAGCTCCTCTGTTTCG...

CDS

4 records

Download CDS FASTA
LOC131016668
ATGGCAGAGGTAAAATTGGATGAATTTTGCCTTGAGAACAAGGAATCTGCTGTTGCTTCAAGCTCCTCTGTTTCGGAGAATAGTAGTAGCACCGCACTAAAGTCGCCTGGGGTAACTAGTCCAAGAAGTGTTTCTCCAGCCCATAGACGAACTACCGGCCCAATTAGAAGAGCAAAAGGAGGTTGGACTCCAGAGGAGGACGATACATTAAGAAAAGCTGTTGCAGCTTTTAGAGGGAAGTCTTGGAAGAAAATAGCTGA...
LOC131016668
ATGGCAGAGGTAAAATTGGATGAATTTTGCCTTGAGAACAAGGAATCTGCTGTTGCTTCAAGCTCCTCTGTTTCGGAGAATAGTAGTAGCACCGCACTAAAGTCGCCTGGGGTAACTAGTCCAAGAAGTGTTTCTCCAGCCCATAGACGAACTACCGGCCCAATTAGAAGAGCAAAAGGAGGTTGGACTCCAGAGGAGGACGATACATTAAGAAAAGCTGTTGCAGCTTTTAGAGGGAAGTCTTGGAAGAAAATAGCTGA...

Protein

4 records

Download Protein FASTA
XP_057801356.1
MAEVKLDEFCLENKESAVASSSSVSENSSSTALKSPGVTSPRSVSPAHRRTTGPIRRAKGGWTPEEDDTLRKAVAAFRGKSWKKIAEFFPHRSEVQCLHRWQKVLNPELVKGPWTPEEDEKITKLVAKYGPTKWSVIAKSLPGRIGKQCRERWHNHLNPDIKKDAWTLEEELTLLNAHRINGNKWAELAKLLPGRTDNAIKNHWNSSLKKKLDFYLATGSLPPVAKNVLLNGARDIGRSTLVGSPFLALCDTTDLCKVED...
XP_057801357.1
MAEVKLDEFCLENKESAVASSSSVSENSSSTALKSPGVTSPRSVSPAHRRTTGPIRRAKGGWTPEEDDTLRKAVAAFRGKSWKKIAEFFPHRSEVQCLHRWQKVLNPELVKGPWTPEEDEKITKLVAKYGPTKWSVIAKSLPGRIGKQCRERWHNHLNPDIKKDAWTLEEELTLLNAHRINGNKWAELAKLLPGRTDNAIKNHWNSSLKKKLDFYLATGSLPPVAKNVLLNGARDIGRSTLVGSPFLALCDTTDLCKVED...

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