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

`SmilChr01G000013`

Chromosome: Chr01 Coordinates: 286077-286661 Strand: - Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr01G000013`
Name	SmilChr01G000013
Description	uncharacterized SmilChr01G000013
Chromosome / SeqID	Chr01 / NC_080387.1
Coordinates and Strand	286077 - 286661 / `-`

ID Mapping

NCBI Gene ID	`LOC131006430`
GeneID	`131006430`
locus_tag	`-`
NCBI Name	`LOC131006430`
Original query	`LOC131006430`

Open ID mapping

Functional Annotation

Source	GFF basic annotation; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	hit=Os12g0142900; species=rice; confidence=weak
Product	hit=Os12g0142900; species=rice; confidence=weak
Arabidopsis	`-` -
Rice	`Os12g0142900` - identity=24.2; qcov=1; evalue=6.44e-08; confidence=weak
GO	-
KEGG	-
Pfam	PF08284 (RVP_2); PF13650 (Asp_protease_2); PF13975 (gag-asp_proteas); PF30863 (PRO_PEG10-RTL1)
InterPro	-
eggNOG	-
NR	GeneID:131006430

Open annotation module

Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Cytoplasm	细胞质	0.80000	`XP_057789582.1`
2	Cytosol	细胞质基质	0.60000	`XP_057789582.1`
3	Nucleus	细胞核	0.00000	`XP_057789582.1`
4	Chromosome	染色体	0.00000	`XP_057789582.1`
5	Centromere	着丝粒	0.00000	`XP_057789582.1`

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
`Chr1:286236`	`G`	`A`	EMS_canonical_SNV	CDS_variant	5	B138,C4,C49,C6,C9
`Chr1:286310`	`GA`	`G`	1bp_deletion	frameshift_variant	1	B71
`Chr1:286310`	`GA`	`G`	1bp_deletion	CDS_variant	1	B71
`Chr1:286321`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	A24
`Chr1:286323`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	B64,C21
`Chr1:286341`	`G`	`A`	EMS_canonical_SNV	CDS_variant	3	B113,B127,C32
`Chr1:286355`	`G`	`A`	EMS_canonical_SNV	stop_gained	2	B97,C14
`Chr1:286355`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	B97,C14
`Chr1:286385`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	A1,B105
`Chr1:286413`	`G`	`A`	EMS_canonical_SNV	CDS_variant	3	B118,B97,C14
`Chr1:286419`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B46
`Chr1:286434`	`AAC`	`A`	2bp_deletion	frameshift_variant	3	B110,C31,C60

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_057789582.1

194 aa

194

RVP_2

Asp_protease_2

gag-asp_proteas

PRO_PEG10-RTL1

PF08284 RVP_2 5-108 aa PF13650 Asp_protease_2 7-90 aa PF13975 gag-asp_proteas 8-92 aa PF30863 PRO_PEG10-RTL1 12-108 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057789582.1`	Pfam	`PF08284`	RVP_2	Domain	5	108	8.9e-26	91.0	Retroviral aspartyl protease
`XP_057789582.1`	Pfam	`PF13650`	Asp_protease_2	Domain	7	90	2.4e-06	28.9	Aspartyl protease
`XP_057789582.1`	Pfam	`PF13975`	gag-asp_proteas	Domain	8	92	6.9e-07	30.5	gag-polyprotein putative aspartyl protease
`XP_057789582.1`	Pfam	`PF30863`	PRO_PEG10-RTL1	Domain	12	108	1.9e-08	35.4	PEG10/RTL1 protease 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_057933599.1
ATGGATACGCTACTCAGCACGCCTGTTATACTTTTGTTCGACACGAGTACTTCACATTCTTTCATTTCAAGTGCATGCGTCGACACTCTAGAACTCAAACAGGAAAGTGCTAATCAGGATATGAGAATTTCTTCACCAATAGGAGGGGTGACGACAGTTACACACGTTTGCTCGAACTTAGATTTGAACATAAGATCACTTAAGGTTGTAGTGAACAACTTGCATGTTATACCAATATGGGACGTGGACGTAATCCTAGG...

CDS

1 records

Download CDS FASTA

LOC131006430
ATGGATACGCTACTCAGCACGCCTGTTATACTTTTGTTCGACACGAGTACTTCACATTCTTTCATTTCAAGTGCATGCGTCGACACTCTAGAACTCAAACAGGAAAGTGCTAATCAGGATATGAGAATTTCTTCACCAATAGGAGGGGTGACGACAGTTACACACGTTTGCTCGAACTTAGATTTGAACATAAGATCACTTAAGGTTGTAGTGAACAACTTGCATGTTATACCAATATGGGACGTGGACGTAATCCTAGG...

Protein

1 records

Download Protein FASTA

XP_057789582.1
MDTLLSTPVILLFDTSTSHSFISSACVDTLELKQESANQDMRISSPIGGVTTVTHVCSNLDLNIRSLKVVVNNLHVIPIWDVDVILGMDWLAENYATILCKEREISFKYPGKDALSFHGISMDRNIPIISALQARKKMNKKDCRAFLVYLDGEAGTERAIEDVKVVREYNDVFPDNLPGLPPNRQVEFTIELEP

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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