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

`SmilChr03G000405`

Chromosome: Chr03 Coordinates: 4411547-4413026 Strand: - Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr03G000405`
Name	SmilChr03G000405
Description	clavaminate synthase-like protein At3g21360
Chromosome / SeqID	Chr03 / NC_080389.1
Coordinates and Strand	4411547 - 4413026 / `-`

ID Mapping

NCBI Gene ID	`LOC131016923`
GeneID	`131016923`
locus_tag	`-`
NCBI Name	`LOC131016923`
Original query	`SmilChr03G000405`

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Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	clavaminate synthase-like protein At3g21360
Product	clavaminate synthase-like protein At3g21360
Arabidopsis	`AT3G21360` (AT3G21360) 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily protein [Source:NCBI gene (formerly Entrezgene);Acc:821690] identity=40.6; qcov=0.985; evalue=4e-82; confidence=medium
Rice	`Os08g0383800` (B1090H08.29) - identity=73.6; qcov=0.985; evalue=3.92e-173; confidence=high
GO	GO:0016491 (oxidoreductase activity)
KEGG	-
Pfam	PF02668 (TauD)
InterPro	-
eggNOG	-
NR	GeneID:131016923

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Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Cytosol	细胞质基质	1.00000	`XP_057801709.1`
2	Cytoplasm	细胞质	0.80000	`XP_057801709.1`
3	Nucleus	细胞核	0.00000	`XP_057801709.1`
4	Chromosome	染色体	0.00000	`XP_057801709.1`
5	Centromere	着丝粒	0.00000	`XP_057801709.1`

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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
`Chr3:4411637`	`G`	`A`	EMS_canonical_SNV	CDS_variant	3	B107,B122,C39
`Chr3:4411642`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B112
`Chr3:4411649`	`C`	`CCA`	2bp_insertion	frameshift_variant	1	B19
`Chr3:4411649`	`C`	`CCA`	2bp_insertion	CDS_variant	1	B19
`Chr3:4411712`	`C`	`T`	EMS_canonical_SNV	CDS_variant	3	A11,B19,B35
`Chr3:4411723`	`G`	`A`	EMS_canonical_SNV	CDS_variant	5	C10,C23,C55,C60,D1
`Chr3:4411729`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B115
`Chr3:4411748`	`G`	`A`	EMS_canonical_SNV	CDS_variant	3	B114,C15,C9
`Chr3:4411752`	`C`	`T`	EMS_canonical_SNV	CDS_variant	4	A7,B136,B95,C23
`Chr3:4411755`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B103,C65
`Chr3:4411767`	`T`	`TAG`	2bp_insertion	frameshift_variant	15	A20,A9,B113,B135,B22,B76,B78,B82,C1,C20,C27,C62,C70,C83,C9
`Chr3:4411769`	`GCA`	`G`	2bp_deletion	frameshift_variant	16	A20,A9,B113,B135,B22,B76,B78,B82,C1,C20,C24,C27,C62,C70,C83,C9

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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_057801709.1

323 aa

162

323

TauD

PF02668 TauD 47-318 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057801709.1`	Pfam	`PF02668`	TauD	Domain	47	318	1.2e-30	108.0	Taurine catabolism dioxygenase TauD, TfdA family

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_057945726.1
ATCTTCCCAAATTCATATAAATATTGCTGCAAGTAAAATCAAATTGTGCATCCATAATTTTAAGCATATTTTTGTACAATCTACGTTTACTACATGCTGATGGAGATGAGCTGCAAATACTTCAAGGTAGGAAGGTGCGAAGGGCAGAAGGTGGTGGACGGCGAAGCTGTGCCGCTAGTGCTGCAGCCCCCGGAGGGCGGCGGAGGCAAGGTGGAGGGGCTGCTGTGGGCCATAAGGGAGAACAAGGAGTGGTTCGAGAA...

CDS

1 records

Download CDS FASTA

LOC131016923
ATGCTGATGGAGATGAGCTGCAAATACTTCAAGGTAGGAAGGTGCGAAGGGCAGAAGGTGGTGGACGGCGAAGCTGTGCCGCTAGTGCTGCAGCCCCCGGAGGGCGGCGGAGGCAAGGTGGAGGGGCTGCTGTGGGCCATAAGGGAGAACAAGGAGTGGTTCGAGAAGACGATAGTGAAAAACAGTGTCGTCCTCCTCCAAGGCTTCCACATCAAGAATGCCCACGAGTTCAACGACATAGTCGAGGCCTTCGGGTGGGA...

Protein

1 records

Download Protein FASTA

XP_057801709.1
MLMEMSCKYFKVGRCEGQKVVDGEAVPLVLQPPEGGGGKVEGLLWAIRENKEWFEKTIVKNSVVLLQGFHIKNAHEFNDIVEAFGWEDIRYVGPAPRTHVYKRVWTANEGPLSEFIYYHHEMVLIKEFPEKVILFCEVPPPEGGETPIVPSFRVTERMLEEYPEMVEEMERKGLRYTFTAISKNDTSSMRGRGWEDAFGTSDRVEAEKRGKALGMEMEWLAEGGVKTILGPRPLTRVFEGRKGRRMWFNTVVGMHGNELS...

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.

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