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

SmilChr07G002842

Chromosome: Chr07 Coordinates: 28516198-28519967 Strand: - Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr07G002842
NameSmilChr07G002842
Descriptionuncharacterized SmilChr07G002842
Chromosome / SeqIDChr07 / NC_080393.1
Coordinates and Strand28516198 - 28519967 / -

ID Mapping

NCBI Gene IDLOC130995864
GeneID130995864
locus_tag-
NCBI NameLOC130995864
Original querySmilChr07G002842

Open ID mapping

Functional Annotation

SourceGFF basic annotation; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionbeta-hexosaminidase (DUF1336) [Source:NCBI gene (formerly Entrezgene);Acc:837957]; symbol=AT1G13970; hit=AT1G13970; species=arabidopsis; confidence=high
Productbeta-hexosaminidase (DUF1336) [Source:NCBI gene (formerly Entrezgene);Acc:837957]; symbol=AT1G13970; hit=AT1G13970; species=arabidopsis; confidence=high
ArabidopsisAT1G13970 (AT1G13970)
beta-hexosaminidase (DUF1336) [Source:NCBI gene (formerly Entrezgene);Acc:837957]
identity=48.3; qcov=1.02; evalue=3.63e-152; confidence=high
RiceOs12g0577600
-
identity=62.9; qcov=0.601; evalue=6.22e-142; confidence=high
GO-
KEGG-
PfamPF07059 (EDR2_C)
InterPro-
eggNOG-
NRGeneID:130995864

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Cytosol 细胞质基质 0.80000 XP_057777309.1
2 Cytoplasm 细胞质 0.40000 XP_057777305.1
3 Golgi apparatus 高尔基体 0.20000 XP_057777305.1
4 Nucleus 细胞核 0.00000 XP_057777309.1
5 Chromosome 染色体 0.00000 XP_057777309.1

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
Chr7:28516692 C T EMS_canonical_SNV CDS_variant 3 B140,B26,C2
Chr7:28517079 G A EMS_canonical_SNV CDS_variant 5 B128,C17,C45,C46,C61
Chr7:28517354 C T EMS_canonical_SNV CDS_variant 4 B128,C17,C45,C61
Chr7:28517355 G A EMS_canonical_SNV CDS_variant 1 B68
Chr7:28517678 G A EMS_canonical_SNV CDS_variant 1 C46
Chr7:28517856 G A EMS_canonical_SNV CDS_variant 4 B128,C17,C45,C61
Chr7:28518049 C T EMS_canonical_SNV CDS_variant 1 D10
Chr7:28518126 G A EMS_canonical_SNV CDS_variant 1 B104
Chr7:28518180 C T EMS_canonical_SNV CDS_variant 1 D10
Chr7:28518478 GC G 1bp_deletion frameshift_variant 1 D11
Chr7:28518478 GC G 1bp_deletion CDS_variant 1 D11
Chr7:28518703 C T EMS_canonical_SNV CDS_variant 1 B60

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_057777305.1
517 aa
N
1
258
517
EDR2_C
C
PF07059 EDR2_C 259-500 aa
XP_057777306.1
517 aa
N
1
258
517
EDR2_C
C
PF07059 EDR2_C 259-500 aa
XP_057777307.1
517 aa
N
1
258
517
EDR2_C
C
PF07059 EDR2_C 259-500 aa
XP_057777308.1
517 aa
N
1
258
517
EDR2_C
C
PF07059 EDR2_C 259-500 aa
XP_057777309.1
516 aa
N
1
258
516
EDR2_C
C
PF07059 EDR2_C 258-499 aa
XP_057777310.1
516 aa
N
1
258
516
EDR2_C
C
PF07059 EDR2_C 258-499 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057777305.1 Pfam PF07059 EDR2_C Domain 259 500 4.3e-58 197.4 Protein ENHANCED DISEASE RESISTANCE 2, C-terminal
XP_057777306.1 Pfam PF07059 EDR2_C Domain 259 500 4.3e-58 197.4 Protein ENHANCED DISEASE RESISTANCE 2, C-terminal
XP_057777307.1 Pfam PF07059 EDR2_C Domain 259 500 4.3e-58 197.4 Protein ENHANCED DISEASE RESISTANCE 2, C-terminal
XP_057777308.1 Pfam PF07059 EDR2_C Domain 259 500 4.3e-58 197.4 Protein ENHANCED DISEASE RESISTANCE 2, C-terminal
XP_057777309.1 Pfam PF07059 EDR2_C Domain 258 499 4.3e-58 197.4 Protein ENHANCED DISEASE RESISTANCE 2, C-terminal
XP_057777310.1 Pfam PF07059 EDR2_C Domain 258 499 4.3e-58 197.4 Protein ENHANCED DISEASE RESISTANCE 2, C-terminal

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

6 records

Download cDNA FASTA
XM_057921326.1
TTTGTGTGTGCGTGTGAGTGTCTTTGTTTTTCTGGTAAACATTTGTTTATTTGGATTAAATTCAATACTGATGCATTCAACAGTTGTATTAAAATACCGAATATTTTAACATTGTTAGTTCTTTACAGCACTCTAATCATTTGAAGTCATTTTCATGACTTGAAATTTTTGTAGTTTGTTAGGGAGTTCTTGAAAAAAATTGACAACAACCCTTTTGTTTGTTTAAGTTTATAAATAAACTTTTTATGGAGTTGGGGTTT...
XM_057921322.1
CCGAATATTTTAACATTGTTAGTTCTTTACAGCACTCTAATCATTTGAAGTCATTTTCATGACTTGAAATTTTTGTAGTTTGTTAGGGAGTTCTTGAAAAAAATTGACAACAACCCTTTTGTTTGTTTAAGTTTATAAATAAACTTTTTATGGAGTTGGGGTTTCTCCTACAATCATATTTCTGTTAAGGTGGGAAAGAACCAAAATATTCATACAAAAGTTGAATTTTTTTACTTTTTGGAGAAAAATGATTTTTTTTA...

CDS

6 records

Download CDS FASTA
LOC130995864
ATGGGTAGCTGTGTTTCTAAGCCTAACAGGAAGCTGAAATCAAAGGCGAAACACATCTATAGGTCATGTAAAATCCGCAGAAAGACAGCTCGCTCAAGTGTCATAGCGCCTATAGACCAACCCCCCGATGACGGTGTCGATGCAGATGAATTCTGTTTCCATGAATATGTTATGGTCGACATTACAGATGGTCGGACAGCAGTCTGCAGAAGGTACGAGGTGCAGAGCCCCGAATTCCAGTTTCCTGAGGTGGAACTGAG...
LOC130995864
ATGGGTAGCTGTGTTTCTAAGCCTAACAGGAAGCTGAAATCAAAGGCGAAACACATCTATAGGTCATGTAAAATCCGCAGAAAGACAGCTCGCTCAAGTGTCATAGCGCCTATAGACCAACCCCCCGATGACGGTGTCGATGCAGATGAATTCTGTTTCCATGAATATGTTATGGTCGACATTACAGATGGTCGGACAGCAGTCTGCAGAAGGTACGAGGTGCAGAGCCCCGAATTCCAGTTTCCTGAGGTGGAACTGAG...

Protein

6 records

Download Protein FASTA
XP_057777305.1
MGSCVSKPNRKLKSKAKHIYRSCKIRRKTARSSVIAPIDQPPDDGVDADEFCFHEYVMVDITDGRTAVCRRYEVQSPEFQFPEVELRHNQAVADTGISRDEVWFDTLSILDSDTDEDFVSVVGDSFSSSDSHTESSINGCNEQAVEFGKQNTDFSNSAKADDDAFATSKVGLHHSEETNSAQFVPSMDVADIKQPPYHQGGSITRTRKKSAVAMVAVRRKSDDGDAPAGFCSSEKYLYNPRAGLLIPKSMGEKPSRGSWC...
XP_057777306.1
MGSCVSKPNRKLKSKAKHIYRSCKIRRKTARSSVIAPIDQPPDDGVDADEFCFHEYVMVDITDGRTAVCRRYEVQSPEFQFPEVELRHNQAVADTGISRDEVWFDTLSILDSDTDEDFVSVVGDSFSSSDSHTESSINGCNEQAVEFGKQNTDFSNSAKADDDAFATSKVGLHHSEETNSAQFVPSMDVADIKQPPYHQGGSITRTRKKSAVAMVAVRRKSDDGDAPAGFCSSEKYLYNPRAGLLIPKSMGEKPSRGSWC...

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