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

`SmilChr03G001153`

Chromosome: Chr03 Coordinates: 13308143-13312276 Strand: - Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr03G001153`
Name	SmilChr03G001153
Description	uncharacterized SmilChr03G001153
Chromosome / SeqID	Chr03 / NC_080389.1
Coordinates and Strand	13308143 - 13312276 / `-`

ID Mapping

NCBI Gene ID	`LOC131018376`
GeneID	`131018376`
locus_tag	`-`
NCBI Name	`LOC131018376`
Original query	`SmilChr03G001153`

Open ID mapping

Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	hit=Os06g0484800; species=rice; confidence=low
Product	hit=Os06g0484800; species=rice; confidence=low
Arabidopsis	`AT3G24255` (AT3G24255) RNA-directed DNA polymerase (reverse transcriptase)-related family protein [Source:NCBI gene (formerly Entrezgene);Acc:822013] identity=28.2; qcov=0.32; evalue=7.37e-41; confidence=low
Rice	`Os06g0484800` - identity=27.3; qcov=0.617; evalue=3.59e-98; confidence=low
GO	GO:0003676 (nucleic acid binding); GO:0004523 (RNA-DNA hybrid ribonuclease activity)
KEGG	-
Pfam	PF00078 (RVT_1); PF13456 (RVT_3); PF13966 (zf-RVT)
InterPro	-
eggNOG	-
NR	GeneID:131018376

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Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Cytoplasm	细胞质	1.00000	`XP_057803087.1`
2	Nucleus	细胞核	0.60000	`XP_057803087.1`
3	Cytosol	细胞质基质	0.40000	`XP_057803087.1`
4	Chromosome	染色体	0.00000	`XP_057803087.1`
5	Centromere	着丝粒	0.00000	`XP_057803087.1`

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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
`Chr3:13308293`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	C40
`Chr3:13308324`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B127
`Chr3:13308348`	`C`	`T`	EMS_canonical_SNV	CDS_variant	4	A6,B18,C59,C7
`Chr3:13308354`	`G`	`A`	EMS_canonical_SNV	CDS_variant	3	B106,B73,C75
`Chr3:13308407`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	B104
`Chr3:13308430`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B24,B38
`Chr3:13308442`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	C8
`Chr3:13308456`	`G`	`A`	EMS_canonical_SNV	CDS_variant	3	A5,A9,C45
`Chr3:13308461`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B24,C33
`Chr3:13308487`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	C11,C69
`Chr3:13308488`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	B137,C53
`Chr3:13308536`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	D6

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_057803087.1

1377 aa

688

1377

RVT_1

zf-RVT

RVT_3

PF00078 RVT_1 499-758 aa PF13966 zf-RVT 1015-1096 aa PF13456 RVT_3 1226-1345 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057803087.1`	Pfam	`PF00078`	RVT_1	Domain	499	758	7.6e-30	105.0	Reverse transcriptase (RNA-dependent DNA polymerase)
`XP_057803087.1`	Pfam	`PF13966`	zf-RVT	Domain	1015	1096	9.5e-15	55.7	zinc-binding in reverse transcriptase
`XP_057803087.1`	Pfam	`PF13456`	RVT_3	Domain	1226	1345	1.2e-17	64.7	Reverse transcriptase-like

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_057947104.1
ATGAATCTTCTCGTTTGGAATGTCCGAGGACTTACGGACGAGTCTAAACGACTTCTCAAGGAGCATTGTCGTTCCTTTTCTCCATTGATTTTGGGCATCATTGAGCCCAAATCAAAGTTTCGCAAAATTCAGATGAGTTTCTGGCAATCTCTGAATCTCACGCCTCGCCACCAGAATTGTAGATTGCCGCGGCGATCTAACATTTGGTTTTTGGCCCAGCCTGCTGTTGCCACTACCATTCTATTCTCTTCAGATCAGGT...

CDS

1 records

Download CDS FASTA

LOC131018376
ATGAATCTTCTCGTTTGGAATGTCCGAGGACTTACGGACGAGTCTAAACGACTTCTCAAGGAGCATTGTCGTTCCTTTTCTCCATTGATTTTGGGCATCATTGAGCCCAAATCAAAGTTTCGCAAAATTCAGATGAGTTTCTGGCAATCTCTGAATCTCACGCCTCGCCACCAGAATTGTAGATTGCCGCGGCGATCTAACATTTGGTTTTTGGCCCAGCCTGCTGTTGCCACTACCATTCTATTCTCTTCAGATCAGGT...

Protein

1 records

Download Protein FASTA

XP_057803087.1
MNLLVWNVRGLTDESKRLLKEHCRSFSPLILGIIEPKSKFRKIQMSFWQSLNLTPRHQNCRLPRRSNIWFLAQPAVATTILFSSDQVVVSNCTWQNLCFRVAVIHGANDAVLRRNLWADLLNYIDGNTVFIGDFNAVKGAHERLSTVLPSRSSCADFCRFIDDTGFLEPSSSGLQFSWSGRRFLPNHVETLLDRALISSSFDNIWDFVNSHVLPRLTSDHSAIVLQCKSRFAPGKRPFRFQHLWMDHAGFLDLVRDSWDA...

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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