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.

Resolved gene

`SmilChr01G000188`

Chromosome: Chr01 Coordinates: 3223441-3230307 Strand: - Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr01G000188`
Name	SmilChr01G000188
Description	sucrose synthase 3-like
Chromosome / SeqID	Chr01 / NC_080387.1
Coordinates and Strand	3223441 - 3230307 / `-`

ID Mapping

NCBI Gene ID	`LOC131007293`
GeneID	`131007293`
locus_tag	`-`
NCBI Name	`LOC131007293`
Original query	`SmilChr01G000188`

Open ID mapping

Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; KEGG smil; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	sucrose synthase 3-like
Product	sucrose synthase 3-like
Arabidopsis	`AT4G02280` (SUS3) sucrose synthase 3 [Source:NCBI gene (formerly Entrezgene);Acc:828081] identity=78.6; qcov=0.991; evalue=0; confidence=high
Rice	`Os03g0340500` (SUS4) - identity=78.8; qcov=0.995; evalue=0; confidence=high
GO	GO:0005985 (sucrose metabolic process); GO:0016157 (sucrose synthase activity)
KEGG	smil00500 (Starch and sucrose metabolism - Salvia miltiorrhiza (redroot sage)); smil01100 (Metabolic pathways - Salvia miltiorrhiza (redroot sage)); smil01110 (Biosynthesis of secondary metabolites - Salvia miltiorrhiza (redroot sage))
Pfam	PF00534 (Glycos_transf_1); PF00862 (GT-B_Sucrose_synth); PF13692 (Glyco_trans_1_4); PF24861 (SUS_N); PF24862 (SUS_EPBD)
InterPro	-
eggNOG	-
NR	GeneID:131007293

Open annotation module

Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Cytosol	细胞质基质	1.00000	`XP_057790418.1`
2	Cytoplasm	细胞质	0.80000	`XP_057790418.1`
3	Nucleus	细胞核	0.00000	`XP_057790418.1`
4	Chromosome	染色体	0.00000	`XP_057790418.1`
5	Centromere	着丝粒	0.00000	`XP_057790418.1`

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
`Chr1:3224045`	`G`	`GAA`	2bp_insertion	frameshift_variant	50	A13,A14,A16,A22,A7,A8,B100,B108,B111,B112,B115,B119,B122,B126,B128,B13,B134,B136,B15,B16,B18,B27,B48,B5,B52,B60,B63,B7,B73,B76,B8,B81,B84,B97,B98,C1,C19,C36,C40,C41,C43,C47,C49,C59,C69,C9,D1,D2,D6,D9
`Chr1:3224409`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	D11
`Chr1:3224777`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B49
`Chr1:3225218`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B138
`Chr1:3226128`	`G`	`A`	EMS_canonical_SNV	CDS_variant	4	B129,B17,B2,C4
`Chr1:3226741`	`C`	`T`	EMS_canonical_SNV	CDS_variant	4	B56,B96,C8,D6
`Chr1:3226793`	`C`	`T`	EMS_canonical_SNV	CDS_variant	3	B125,B90,B92
`Chr1:3226801`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B75
`Chr1:3227909`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B118
`Chr1:3228221`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B35,C48
`Chr1:3228227`	`C`	`T`	EMS_canonical_SNV	CDS_variant	3	A21,B124,D5
`Chr1:3228551`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B65

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_057790418.1

814 aa

407

814

SUS_N

SUS_EPBD

GT-B_Sucrose_synth

Glycos_transf_1

Glyco_trans_1_4

PF24861 SUS_N 10-122 aa PF24862 SUS_EPBD 157-244 aa PF00862 GT-B_Sucrose_synth 267-554 aa PF00534 Glycos_transf_1 566-728 aa PF13692 Glyco_trans_1_4 573-719 aa

XP_057790419.1

811 aa

406

811

SUS_N

SUS_EPBD

GT-B_Sucrose_synth

Glycos_transf_1

Glyco_trans_1_4

PF24861 SUS_N 10-122 aa PF24862 SUS_EPBD 157-244 aa PF00862 GT-B_Sucrose_synth 267-554 aa PF00534 Glycos_transf_1 566-728 aa PF13692 Glyco_trans_1_4 573-719 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057790418.1`	Pfam	`PF24861`	SUS_N	Domain	10	122	6.2e-48	162.4	Sucrose synthase N-terminal
`XP_057790418.1`	Pfam	`PF24862`	SUS_EPBD	Domain	157	244	3.5e-33	114.6	Sucrose synthase EPBD domain
`XP_057790418.1`	Pfam	`PF00862`	GT-B_Sucrose_synth	Domain	267	554	1.6e-167	556.3	Sucrose synthase first GT-B domain
`XP_057790418.1`	Pfam	`PF00534`	Glycos_transf_1	Domain	566	728	1.8e-24	86.9	Glycosyl transferases group 1
`XP_057790418.1`	Pfam	`PF13692`	Glyco_trans_1_4	Domain	573	719	1.6e-10	42.1	Glycosyl transferases group 1
`XP_057790419.1`	Pfam	`PF24861`	SUS_N	Domain	10	122	6.1e-48	162.5	Sucrose synthase N-terminal
`XP_057790419.1`	Pfam	`PF24862`	SUS_EPBD	Domain	157	244	3.4e-33	114.6	Sucrose synthase EPBD domain
`XP_057790419.1`	Pfam	`PF00862`	GT-B_Sucrose_synth	Domain	267	554	1.6e-167	556.4	Sucrose synthase first GT-B domain
`XP_057790419.1`	Pfam	`PF00534`	Glycos_transf_1	Domain	566	728	1.8e-24	86.9	Glycosyl transferases group 1
`XP_057790419.1`	Pfam	`PF13692`	Glyco_trans_1_4	Domain	573	719	1.6e-10	42.1	Glycosyl transferases group 1

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

2 records

Download cDNA FASTA

XM_057934436.1
AATATAACTCGAAATATTCCAAAAATTCTGTTTTAGAAACTACGTGGTTGTATTTAATTAACCCACACGGCTTCAGTGTAATCCATCAACTGCCACCTTTTCTCTCTCCCTCTCTCCTCCCTCTCTCAGCTCTCTGTCCAGTCCTGTGCTGTGCTGTACATATTGAATCAGCATCACTCCGATTCTCTCGCGTTTGATTTTCAAGTTCCAATCCCCAGAAATAGGAGAAATTTAGGTCAGAAATTTGTAATTATTCGGTA...

XM_057934435.1
AGAAACTACGTGGTTGTATTTAATTAACCCACACGGCTTCAGTGTAATCCATCAACTGCCACCTTTTCTCTCTCCCTCTCTCCTCCCTCTCTCAGCTCTCTGTCCAGTCCTGTGCTGTGCTGTACATATTGAATCAGCATCACTCCGATTCTCTCGCGTTTGATTTTCAAGTTCCAATCCCCAGAAATAGGAGAAATTTAGGTCAGAAATTTGTAATTATTCGGTATACACTTGAGATCTCAATGGGGAAGCCGAGATTA...

CDS

2 records

Download CDS FASTA

LOC131007293
ATGGGGAAGCCGAGATTACAGAAATTGCCCAGCATGAGAGAAAGGGTTGAAGACACTCTTTCCGCTCACAGAAACGAACTCGTCGCTCTCCTTTCCCGATATGTGGCTCAGGGGAAGAGTATACTTCAGCCCCATCACCTAATTGACGAGCTCGAAAACATCATCTGCGTTGATTCTGCCAAGAATACTCTATGTGATGGCCCTTTCAGTGAAGTTTTGAAGTCTGCTCAAGAAGCTATCGTATTACCACCTTTTGTTGC...

Protein

2 records

Download Protein FASTA

XP_057790418.1
MGKPRLQKLPSMRERVEDTLSAHRNELVALLSRYVAQGKSILQPHHLIDELENIICVDSAKNTLCDGPFSEVLKSAQEAIVLPPFVAIAIRPRPGVWEFVRVNVYELSVEELKVSEYLRFKEDLVDGQKDDPYLLELDFEPFNSSFPRPSRSSSIGNGVQFLNRHLSSIMFRNKDSLEPLLDFLRVHRHKGHVLMLNDRIERISQLESALAKAEDYVCKLPPETPYSELEFALQGMGFERGWGDTAERVVQMMHLLSDIL...

XP_057790419.1
MGKPRLQKLPSMRERVEDTLSAHRNELVALLSRYVAQGKSILQPHHLIDELENIICVDSAKNTLCDGPFSEVLKSAQEAIVLPPFVAIAIRPRPGVWEFVRVNVYELSVEELKVSEYLRFKEDLVDGQKDDPYLLELDFEPFNSSFPRPSRSSSIGNGVQFLNRHLSSIMFRNKDSLEPLLDFLRVHRHKGHVLMLNDRIERISQLESALAKAEDYVCKLPPETPYSELEFALQGMGFERGWGDTAERVVQMMHLLSDIL...

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