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

`SmilChr03G000928`

Chromosome: Chr03 Coordinates: 10612371-10613598 Strand: + Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr03G000928`
Name	SmilChr03G000928
Description	uncharacterized SmilChr03G000928
Chromosome / SeqID	Chr03 / NC_080389.1
Coordinates and Strand	10612371 - 10613598 / `+`

ID Mapping

NCBI Gene ID	`LOC131017589`
GeneID	`131017589`
locus_tag	`-`
NCBI Name	`LOC131017589`
Original query	`SmilChr03G000928`

Open ID mapping

Functional Annotation

Source	GFF basic annotation; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	hit=Os08g0315200; species=rice; confidence=medium
Product	hit=Os08g0315200; species=rice; confidence=medium
Arabidopsis	`-` -
Rice	`Os08g0315200` - identity=35.8; qcov=0.548; evalue=1.36e-26; confidence=medium
GO	-
KEGG	-
Pfam	PF03732 (PEG10_N-capsid); PF19259 (Ty3_capsid)
InterPro	-
eggNOG	-
NR	GeneID:131017589

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Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Nucleus	细胞核	0.60000	`XP_057802378.1`
2	Cytoplasm	细胞质	0.60000	`XP_057802378.1`
3	Nucleoplasm	核质	0.20000	`XP_057802378.1`
4	Cytoplasmic granule	细胞质颗粒	0.20000	`XP_057802378.1`
5	Cytoplasmic ribonucleoprotein granule	Cytoplasmic ribonucleoprotein granule	0.20000	`XP_057802378.1`

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
`Chr3:10612607`	`G`	`A`	EMS_canonical_SNV	CDS_variant	5	B1,B129,B134,C70,C87
`Chr3:10612627`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B56,C74
`Chr3:10612638`	`AAT`	`A`	2bp_deletion	frameshift_variant	1	C43
`Chr3:10612638`	`AAT`	`A`	2bp_deletion	CDS_variant	1	C43
`Chr3:10612649`	`C`	`T`	EMS_canonical_SNV	CDS_variant	3	B104,B132,C58
`Chr3:10612663`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	C58
`Chr3:10612674`	`C`	`T`	EMS_canonical_SNV	CDS_variant	5	B112,B28,B56,C27,C67
`Chr3:10612675`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	A3
`Chr3:10612761`	`C`	`T`	EMS_canonical_SNV	stop_gained	3	B29,B35,C49
`Chr3:10612761`	`C`	`T`	EMS_canonical_SNV	CDS_variant	3	B29,B35,C49
`Chr3:10612762`	`G`	`A`	EMS_canonical_SNV	CDS_variant	3	A16,B111,C46
`Chr3:10612767`	`C`	`T`	EMS_canonical_SNV	CDS_variant	3	B2,B64,C86

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_057802378.1

321 aa

160

321

PEG10_N-capsid

Ty3_capsid

PF03732 PEG10_N-capsid 76-155 aa PF19259 Ty3_capsid 76-234 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057802378.1`	Pfam	`PF03732`	PEG10_N-capsid	Domain	76	155	1.2e-14	55.1	Retrotransposon-derived protein PEG10, N-terminal capsid-like domain
`XP_057802378.1`	Pfam	`PF19259`	Ty3_capsid	Domain	76	234	4.5e-09	36.7	Ty3 transposon capsid-like protein

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_057946395.1
ATGCAAGTTATTATGAGAAAGTTCAGTATACAAGTTATTATGTTGAAGATTATTGCAGCTATGAATTTTATTTCGGAATTTTACAGTTCATGACATTGAGATTTGATGAGTTCAAACTTTTCATGTTGAATATAGTCCTCGAATTAGGAATAACCTAGCATTTTCCTAGAAAAGTCTTGTTTTATAATCCCTTATTTATGTGATAGTGCCTCTGAATATAGAACCATGAGGAATACGCGTGCACATTCCCACCACGCCGA...

CDS

1 records

Download CDS FASTA

LOC131017589
ATGAGGAATACGCGTGCACATTCCCACCACGCCGAGAACTCAAATACAAATTCCGAAGCAGAAGCTGGACAACCTCATCCAACTAATGGAGGAGACTTCATGAGTCAATTTCTGAGCGCCTTACAAGGTTTTGTCCAACAGCAAACCCAAACTCAGGCTACGCAGCGAGACCTAAACCAGACCTCTAACACAATGGATCAAGCGGTAGAGCGATTTCGGAATTATAATCCGCCACGATTCAATGGACGTGATGGACCGCT...

Protein

1 records

Download Protein FASTA

XP_057802378.1
MRNTRAHSHHAENSNTNSEAEAGQPHPTNGGDFMSQFLSALQGFVQQQTQTQATQRDLNQTSNTMDQAVERFRNYNPPRFNGRDGPLAAEEWLEELERIFTHINCTEEQKVSCAVFQLKEDARQWWKHFYRLLGEEDRNVLNWKIFKGVVMDKYFPLSFREKKETEFFELKQGNMTIEEYERKFNELARFAPHLVDTEDKMIARFRKGLRTDIKGIMAAHVIEDFSDLVKRAEEVATALGSNIPAQKPANQPMKRKWENY...

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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