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

SmilChr07G002131

Chromosome: Chr07 Coordinates: 19479097-19485668 Strand: + Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr07G002131
NameSmilChr07G002131
Descriptionuncharacterized SmilChr07G002131
Chromosome / SeqIDChr07 / NC_080393.1
Coordinates and Strand19479097 - 19485668 / +

ID Mapping

NCBI Gene IDLOC130993213
GeneID130993213
locus_tag-
NCBI NameLOC130993213
Original querySmilChr07G002131

Open ID mapping

Functional Annotation

SourceGFF basic annotation; Pfam-A/HMMER; Arabidopsis/Rice homolog
DescriptionRPA1A; symbol=RPA1A; hit=Os02g0776800; species=rice; confidence=low
ProductRPA1A; symbol=RPA1A; hit=Os02g0776800; species=rice; confidence=low
ArabidopsisAT5G45400 (RPA70C)
Replication factor-A protein 1-like protein [Source:NCBI gene (formerly Entrezgene);Acc:834576]
identity=25.8; qcov=1; evalue=5.67e-06; confidence=low
RiceOs02g0776800 (RPA1A)
-
identity=25.8; qcov=1; evalue=1.25e-06; confidence=low
GO-
KEGG-
PfamPF16900 (REPA_OB_2)
InterPro-
eggNOG-
NRGeneID:130993213

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Nucleus 细胞核 1.00000 XP_057774004.1
2 Chromosome 染色体 0.20000 XP_057774004.1
3 Centromere 着丝粒 0.00000 XP_057774004.1
4 Chromatin 染色质 0.00000 XP_057774004.1
5 Telomere 端粒 0.00000 XP_057774004.1

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
Chr7:19479201 C T EMS_canonical_SNV CDS_variant 5 B11,B138,B31,C42,D8
Chr7:19479429 G A EMS_canonical_SNV CDS_variant 1 B11
Chr7:19480308 C T EMS_canonical_SNV CDS_variant 4 B118,B49,C64,C71
Chr7:19480314 G A EMS_canonical_SNV CDS_variant 2 A19,B18
Chr7:19480318 G A EMS_canonical_SNV CDS_variant 3 A19,B18,B48
Chr7:19480329 C T EMS_canonical_SNV CDS_variant 2 B140,B76
Chr7:19480348 G A EMS_canonical_SNV CDS_variant 1 B104
Chr7:19480361 C T EMS_canonical_SNV CDS_variant 5 A22,B11,B61,B69,C75
Chr7:19480399 G A EMS_canonical_SNV CDS_variant 2 B13,B82
Chr7:19480414 C T EMS_canonical_SNV stop_gained 63 A11,A13,A21,A23,A5,A6,B100,B105,B109,B113,B114,B115,B118,B12,B122,B124,B125,B131,B133,B2,B20,B23,B25,B26,B40,B47,B48,B52,B53,B57,B62,B71,B78,B84,B94,B99,C14,C22,C23,C26,C28,C34,C4,C47,C5,C51,C54,C56,C57,C60,C61,C64,C65,C66,C7,C79,C80,C81,C83,C85,D2,D3,D4
Chr7:19480439 G A EMS_canonical_SNV CDS_variant 2 B139,B32
Chr7:19480568 G A EMS_canonical_SNV CDS_variant 5 A25,B140,B44,B95,C77

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_057774004.1
228 aa
N
1
114
228
REPA_OB_2
C
PF16900 REPA_OB_2 34-126 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057774004.1 Pfam PF16900 REPA_OB_2 Domain 34 126 2.1e-08 34.7 Replication protein A OB 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_057918021.1
GGTCGACCACTTGTATATGCTTGGCTTCGGCCTTGCCACCCAAATTGAGCAACTGGATGAAGGCTTCGAAATTCTGGAAAATGGATTTAATTTTATTCCCTTTACAGATATTCCTACACACGATCCCACTTTCTTTTTGGATGTTCTTGGGGAGGTTATGACCCACACTATTAACATAGTTAAAGTCGAAATCAGAACTGGCAAGGCATCCAAGTGTGACATAACATTAGCCGATGCAGACGGCACGCAAGTAACCTGTG...

CDS

1 records

Download CDS FASTA
LOC130993213
ATGCTTGGCTTCGGCCTTGCCACCCAAATTGAGCAACTGGATGAAGGCTTCGAAATTCTGGAAAATGGATTTAATTTTATTCCCTTTACAGATATTCCTACACACGATCCCACTTTCTTTTTGGATGTTCTTGGGGAGGTTATGACCCACACTATTAACATAGTTAAAGTCGAAATCAGAACTGGCAAGGCATCCAAGTGTGACATAACATTAGCCGATGCAGACGGCACGCAAGTAACCTGTGTCTTATGGGGATCACT...

Protein

1 records

Download Protein FASTA
XP_057774004.1
MLGFGLATQIEQLDEGFEILENGFNFIPFTDIPTHDPTFFLDVLGEVMTHTINIVKVEIRTGKASKCDITLADADGTQVTCVLWGSLAEELKTFMENKSAEDKEPVMVALQFAKISTFRGQIKVSSMKNPSNFFICPDIKEVKDFILRRGVSRSSSCNDTITDISIGQQALNRNEWLDAAHARRLCDLIKSEECGTFNCKGTILNFHPQESWYYEACGNDRCLKGIAR

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