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

`SmilChr03G002635`

Chromosome: Chr03 Coordinates: 41916624-41920663 Strand: + Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr03G002635`
Name	SmilChr03G002635
Description	probable E3 ubiquitin-protein ligase RHG1A
Chromosome / SeqID	Chr03 / NC_080389.1
Coordinates and Strand	41916624 - 41920663 / `+`

ID Mapping

NCBI Gene ID	`LOC131015826`
GeneID	`131015826`
locus_tag	`-`
NCBI Name	`LOC131015826`
Original query	`SmilChr03G002635`

Open ID mapping

Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	probable E3 ubiquitin-protein ligase RHG1A
Product	probable E3 ubiquitin-protein ligase RHG1A
Arabidopsis	`AT5G45290` (AT5G45290) RING/U-box superfamily protein [Source:NCBI gene (formerly Entrezgene);Acc:834565] identity=50.6; qcov=0.196; evalue=6.04e-14; confidence=weak
Rice	`Os02g0798600` - identity=44.5; qcov=0.495; evalue=1.03e-40; confidence=medium
GO	GO:0008270 (zinc ion binding)
KEGG	-
Pfam	PF00097 (zf-C3HC4); PF12678 (zf-rbx1); PF13639 (zf-RING_2); PF13923 (zf-C3HC4_2); PF17123 (zf-RING_11)
InterPro	-
eggNOG	-
NR	GeneID:131015826

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Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Cytoplasm	细胞质	1.00000	`XP_057800246.1`
2	Nucleus	细胞核	0.60000	`XP_057800245.1`
3	Chromosome	染色体	0.00000	`XP_057800245.1`
4	Centromere	着丝粒	0.00000	`XP_057800245.1`
5	Chromatin	染色质	0.00000	`XP_057800245.1`

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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
`Chr3:41916825`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	A21,B66
`Chr3:41917537`	`G`	`A`	EMS_canonical_SNV	CDS_variant	4	B29,C14,C20,C72
`Chr3:41917814`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B22,B48
`Chr3:41918198`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	C10
`Chr3:41919668`	`G`	`A`	EMS_canonical_SNV	CDS_variant	4	B29,C14,C20,C72
`Chr3:41920246`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B94
`Chr3:41920450`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B97
`Chr3:41920488`	`C`	`T`	EMS_canonical_SNV	CDS_variant	4	A5,B126,B62,C80

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_057800245.1

505 aa

252

505

zf-rbx1

zf-RING_11

zf-C3HC4_2

zf-RING_2

zf-C3HC4

PF12678 zf-rbx1 439-485 aa PF17123 zf-RING_11 442-470 aa PF13923 zf-C3HC4_2 442-484 aa PF13639 zf-RING_2 442-485 aa PF00097 zf-C3HC4 443-484 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057800245.1`	Pfam	`PF12678`	zf-rbx1	Domain	439	485	5.2e-09	36.9	RING-H2 zinc finger domain
`XP_057800245.1`	Pfam	`PF17123`	zf-RING_11	Domain	442	470	1.8e-10	41.0	RING-like zinc finger
`XP_057800245.1`	Pfam	`PF13923`	zf-C3HC4_2	Domain	442	484	1.7e-08	34.9	Zinc finger, C3HC4 type (RING finger)
`XP_057800245.1`	Pfam	`PF13639`	zf-RING_2	Domain	442	485	1.2e-14	55.0	Ring finger domain
`XP_057800245.1`	Pfam	`PF00097`	zf-C3HC4	Domain	443	484	6.2e-10	39.5	Zinc finger, C3HC4 type (RING finger)

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_057944262.1
AGTTGTTAAGTTGTGATTTGTTGGTTGTATGGGGCCCACCCAACACGTTAACCTGCCAACCTCTGACCGCTCACTACATTGCTTTCCTGCATCATCATCTTCTCCCAAACCACAAATTCTCTCGTTTCCGAGCAACAAGCTTCATGGGTTGGAGCAGCAATCATCATCTTCATCCTAAATCCTCAAACTCTCGTGACTCCAGGCTCCGCCGCACAAAGCGCAAACTCTCGCATATCTTTTGTGGCGCTTTCCGTTCCAAG...

XM_057944263.1
ACACGTTAACCTGCCAACCTCTGACCGCTCACTACATTGCTTTCCTGCATCATCATCTTCTCCCAAACCACAAATTCTCTCGTTTCCGAGCAACAAGCTTCATGGGTTGGAGCAGCAATCATCATCTTCATCCTAAATCCTCAAACTCTCGTGACTCCAGGCTCCGCCGCACAAAGCGCAAACTCTCGCATATCTTTTGTGGCGCTTTCCGTTCCAAGTCAACCCTTCCGGAGCTGGGAGATGGCCCAGAGATAACTTCA...

CDS

2 records

Download CDS FASTA

LOC131015826
ATGGGTTGGAGCAGCAATCATCATCTTCATCCTAAATCCTCAAACTCTCGTGACTCCAGGCTCCGCCGCACAAAGCGCAAACTCTCGCATATCTTTTGTGGCGCTTTCCGTTCCAAGTCAACCCTTCCGGAGCTGGGAGATGGCCCAGAGATAACTTCAATTAGCTATGCTGAAAGCTTAGCTCCTGTTGATGCTCAAAACTCGACCTTAGAATCCTCTTCTGTTTTCAAGTCAGAAGCAGGGGACACAGTATCCGTATG...

Protein

2 records

Download Protein FASTA

XP_057800245.1
MGWSSNHHLHPKSSNSRDSRLRRTKRKLSHIFCGAFRSKSTLPELGDGPEITSISYAESLAPVDAQNSTLESSSVFKSEAGDTVSVCENGDSSERSSNTDPESGPFNVQSSRDLKTLPQQPAQESVSGNATNCIAAVIHDPDTITEDTASICPVHDQSQGLTVPHAHSNDIVEYSRNAAVGYNSSDSRSLSIVSDSLPRFEYPGDDRAHVSTTSSSGFLVSDSDQNLINGDLLRLDLVSISSNSLSGSIAEISSHETRRN...

XP_057800246.1
MGWSSNHHLHPKSSNSRDSRLRRTKRKLSHIFCGAFRSKSTLPELGDGPEITSISYAESLAPVDAQNSTLESSSVFKSEAGDTVSVCENGDSSERSSNTDPESGPFNVQSSRDLKTLPQQPAQESVSGNATNCIAAVIHDPDTITEDTASICPVHDQSQGLTVPHAHSNDIVEYSRNAAVGYNSSDSRSLSIVSDSLPRFEYPGDDRAHVSTTSSSGFLVSDSDQNLINGDLLRLDLVSISSNSLSGSIAEISSHETRRN...

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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