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

SmilChr03G001528

Chromosome: Chr03 Coordinates: 19040345-19042956 Strand: - Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr03G001528
NameSmilChr03G001528
Descriptionputative wall-associated receptor kinase-like 16
Chromosome / SeqIDChr03 / NC_080389.1
Coordinates and Strand19040345 - 19042956 / -

ID Mapping

NCBI Gene IDLOC131017992
GeneID131017992
locus_tag-
NCBI NameLOC131017992
Original querySmilChr03G001528

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionputative wall-associated receptor kinase-like 16
Productputative wall-associated receptor kinase-like 16
ArabidopsisAT1G21240 (WAK3)
wall associated kinase 3 [Source:NCBI gene (formerly Entrezgene);Acc:838719]
identity=44.2; qcov=1.01; evalue=0; confidence=medium
RiceOs02g0111600 (OsWAK11)
-
identity=42.2; qcov=0.978; evalue=0; confidence=medium
GOGO:0004674 (protein serine/threonine kinase activity); GO:0005509 (calcium ion binding); GO:0005524 (ATP binding); GO:0005886 (plasma membrane); GO:0006468 (protein phosphorylation); GO:0007166 (cell surface receptor signaling pathway); GO:0030247 (polysaccharide binding)
KEGG-
PfamPF00069 (Pkinase); PF07645 (EGF_CA); PF07714 (PK_Tyr_Ser-Thr); PF13947 (GUB_WAK_bind)
InterPro-
eggNOG-
NRGeneID:131017992

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Cell membrane 细胞膜 1.00000 XP_057802734.1
2 Nucleus 细胞核 0.00000 XP_057802734.1
3 Chromosome 染色体 0.00000 XP_057802734.1
4 Centromere 着丝粒 0.00000 XP_057802734.1
5 Chromatin 染色质 0.00000 XP_057802734.1

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
Chr3:19040468 C T EMS_canonical_SNV CDS_variant 1 B85
Chr3:19040525 ATT A 2bp_deletion frameshift_variant 1 C71
Chr3:19040525 ATT A 2bp_deletion CDS_variant 1 C71
Chr3:19040548 C T EMS_canonical_SNV CDS_variant 4 B117,C60,D11,D7
Chr3:19040573 C T EMS_canonical_SNV CDS_variant 4 B41,B74,B85,C74
Chr3:19040728 C T EMS_canonical_SNV CDS_variant 3 B118,B13,C58
Chr3:19040743 C T EMS_canonical_SNV CDS_variant 3 A11,A8,C78
Chr3:19040767 C T EMS_canonical_SNV CDS_variant 1 B104
Chr3:19040777 G A EMS_canonical_SNV CDS_variant 3 A11,A8,B29
Chr3:19040800 A AAT 2bp_insertion frameshift_variant 4 B6,B9,C71,C78
Chr3:19040800 A AAT 2bp_insertion CDS_variant 4 B6,B9,C71,C78
Chr3:19040805 T TAC 2bp_insertion frameshift_variant 3 B108,B85,C23

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_057802734.1
757 aa
N
1
378
757
GUB_WAK_bind
EGF_CA
Pkinase
PK_Tyr_Ser-Thr
C
PF13947 GUB_WAK_bind 40-96 aa PF07645 EGF_CA 299-336 aa PF00069 Pkinase 425-691 aa PF07714 PK_Tyr_Ser-Thr 430-695 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057802734.1 Pfam PF13947 GUB_WAK_bind Domain 40 96 4.3e-08 34.1 Wall-associated receptor kinase galacturonan-binding
XP_057802734.1 Pfam PF07645 EGF_CA Domain 299 336 6.8e-08 33.3 Calcium-binding EGF domain
XP_057802734.1 Pfam PF00069 Pkinase Domain 425 691 2.3e-45 155.8 Protein kinase domain
XP_057802734.1 Pfam PF07714 PK_Tyr_Ser-Thr Domain 430 695 2.8e-45 155.4 Protein tyrosine and serine/threonine kinase

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_057946751.1
TGGTAACAAGTGTGCTTTATCGATCAGAATCATGGTGTTTGAGAAACTCAACAACATGCAGGCTTCAATTCTGCTCATCATGTTCATTTTGGCCTCCTCTCCAACACTACTACTCTCATCACAGAATCCCCCCTTAGCTAAGCTCAAGTGCGAAGATCGTTGCGGCGATATACGCATCCCATTCCCTTTCGGCACCACAGAAGAATGCTACATCGACCAGAGTTTTTGGGTCACTTGCAACGACACCGGTTTCAATCCTC...

CDS

1 records

Download CDS FASTA
LOC131017992
ATGGTGTTTGAGAAACTCAACAACATGCAGGCTTCAATTCTGCTCATCATGTTCATTTTGGCCTCCTCTCCAACACTACTACTCTCATCACAGAATCCCCCCTTAGCTAAGCTCAAGTGCGAAGATCGTTGCGGCGATATACGCATCCCATTCCCTTTCGGCACCACAGAAGAATGCTACATCGACCAGAGTTTTTGGGTCACTTGCAACGACACCGGTTTCAATCCTCCGAAGCTCTTCTGGTGGGACACGTCAGTCGA...

Protein

1 records

Download Protein FASTA
XP_057802734.1
MVFEKLNNMQASILLIMFILASSPTLLLSSQNPPLAKLKCEDRCGDIRIPFPFGTTEECYIDQSFWVTCNDTGFNPPKLFWWDTSVEITDISLDGQIKLQWFIAKNCYYNGKSNISNNPFSWLPKYFTVNNTANKFTIVGCDAYGFVSGRRIERNFTTGCTAMCSSEADLTEGECDGVGCCQTTIPKDVWTVELEVRSYSNYTNVSDFNTCSYAFVVEDASFKFSKANLTNLSRVTKLPLVVDWAIGNGTCEEAKSDATT...

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