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

`SmilChr03G001777`

Chromosome: Chr03 Coordinates: 24220761-24228199 Strand: - Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr03G001777`
Name	SmilChr03G001777
Description	uncharacterized SmilChr03G001777
Chromosome / SeqID	Chr03 / NC_080389.1
Coordinates and Strand	24220761 - 24228199 / `-`

ID Mapping

NCBI Gene ID	`LOC131018559`
GeneID	`131018559`
locus_tag	`-`
NCBI Name	`LOC131018559`
Original query	`SmilChr03G001777`

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=30.2; qcov=0.258; evalue=3.57e-31; confidence=weak
Rice	`Os06g0484800` - identity=27; qcov=0.665; evalue=4.29e-61; confidence=low
GO	GO:0003676 (nucleic acid binding); GO:0004523 (RNA-DNA hybrid ribonuclease activity)
KEGG	-
Pfam	PF00078 (RVT_1); PF13456 (RVT_3)
InterPro	-
eggNOG	-
NR	GeneID:131018559

Open annotation module

Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Cytoplasm	细胞质	1.00000	`XP_057803256.1`
2	Cytosol	细胞质基质	0.80000	`XP_057803256.1`
3	Nucleus	细胞核	0.60000	`XP_057803256.1`
4	Chromosome	染色体	0.00000	`XP_057803256.1`
5	Centromere	着丝粒	0.00000	`XP_057803256.1`

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
`Chr3:24220835`	`CT`	`C`	1bp_deletion	frameshift_variant	38	A15,A19,A7,B100,B105,B11,B12,B133,B134,B20,B28,B29,B30,B38,B44,B45,B59,B69,B71,B85,B98,C14,C17,C35,C38,C39,C44,C46,C51,C58,C62,C63,C67,C68,C82,C86,D4,D8
`Chr3:24220842`	`A`	`AT`	1bp_insertion	frameshift_variant	18	A15,B11,B12,B20,B29,B30,B38,B44,B59,B85,C35,C39,C46,C51,C58,C62,C67,C82
`Chr3:24220855`	`GAA`	`G`	2bp_deletion	frameshift_variant	17	A7,B100,B105,B133,B28,B71,C14,C17,C27,C32,C38,C63,C68,C82,C86,D3,D9
`Chr3:24220859`	`G`	`GTA`	2bp_insertion	frameshift_variant	15	A7,B100,B105,B133,B28,B71,C14,C17,C32,C38,C63,C68,C82,C86,D9
`Chr3:24220870`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B40,B69
`Chr3:24220873`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B58
`Chr3:24220881`	`C`	`T`	EMS_canonical_SNV	CDS_variant	4	A21,B111,B128,B42
`Chr3:24220883`	`G`	`A`	EMS_canonical_SNV	CDS_variant	5	A21,B111,B128,B42,B53
`Chr3:24220892`	`C`	`T`	EMS_canonical_SNV	CDS_variant	5	A21,B111,B128,B42,C17
`Chr3:24220914`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B79
`Chr3:24220916`	`TAG`	`T`	2bp_deletion	frameshift_variant	170	A1,A11,A15,A19,A20,A21,A23,A24,A25,A3,A4,A5,A7,A8,A9,B1,B100,B101,B103,B104,B105,B106,B109,B11,B110,B111,B112,B113,B114,B115,B117,B12,B120,B121,B124,B126,B127,B128,B13,B130,B131,B132,B133,B135,B136,B137,B14,B140,B15,B2,B20,B21,B23,B24,B27,B28,B3,B30,B31,B34,B35,B36,B38,B39,B40,B41,B42,B43,B44,B45,B46,B47,B49,B5,B50,B51,B53,B54,B55,B56,B57,B58,B59,B60,B63,B64,B65,B66,B67,B68,B69,B7,B70,B71,B72,B73,B77,B78,B81,B83,B85,B9,B93,B94,B95,B96,B97,B98,C1,C10,C12,C14,C16,C17,C19,C2,C21,C22,C23,C24,C25,C27,C28,C29,C3,C31,C32,C35,C36,C38,C39,C41,C43,C44,C45,C46,C47,C48,C49,C5,C51,C53,C55,C56,C57,C58,C59,C62,C63,C64,C65,C66,C67,C68,C7,C72,C74,C75,C77,C78,C79,C8,C81,C82,C83,C86,C9,D10,D4,D9
`Chr3:24220922`	`A`	`AGT`	2bp_insertion	frameshift_variant	154	A1,A11,A15,A19,A20,A21,A23,A25,A3,A4,A5,A7,A8,A9,B1,B100,B103,B104,B105,B106,B109,B110,B111,B112,B113,B114,B115,B117,B120,B121,B122,B123,B124,B126,B127,B128,B13,B130,B131,B132,B133,B135,B137,B14,B140,B15,B2,B20,B21,B23,B24,B27,B28,B3,B30,B31,B35,B36,B38,B39,B40,B41,B42,B43,B44,B45,B46,B47,B49,B50,B53,B54,B55,B56,B57,B58,B59,B60,B63,B64,B65,B66,B67,B68,B69,B7,B71,B72,B73,B77,B78,B83,B85,B9,B93,B94,B95,B96,B97,B98,C1,C12,C14,C16,C17,C2,C22,C23,C24,C27,C28,C29,C31,C32,C36,C38,C39,C41,C43,C45,C46,C47,C48,C49,C5,C51,C53,C55,C56,C57,C58,C59,C62,C63,C64,C65,C66,C67,C68,C7,C72,C74,C75,C77,C78,C79,C8,C81,C82,C83,C86,C9,D4,D9

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_057803256.1

1037 aa

518

1037

RVT_1

RVT_3

PF00078 RVT_1 214-454 aa PF13456 RVT_3 811-931 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057803256.1`	Pfam	`PF00078`	RVT_1	Domain	214	454	2.6e-28	100.0	Reverse transcriptase (RNA-dependent DNA polymerase)
`XP_057803256.1`	Pfam	`PF13456`	RVT_3	Domain	811	931	4.1e-19	69.4	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_057947273.1
ATGGTGGAGAACTCTTGGAACAGCCAGATTGACGTCAACTGCCCCATTTATAAAGTCATGGCTAAGCTCAAGTGGCTGCGTAAAGAGCTACGCATTTGGAACAGAACGGTTTTCGGCAATGTGGATCAGTTTATTTCTGATTCACAGCAGGATCTTCTTGAGATTCAGAATTTAGTCTCTCAACAGGGGTACACCGATAGCCTTTTTAATGCGGAGATTTTCGCTCAAGCTAAAATTAATGTGGTTCTGAGTCGTAAAAA...

CDS

1 records

Download CDS FASTA

LOC131018559
ATGGTGGAGAACTCTTGGAACAGCCAGATTGACGTCAACTGCCCCATTTATAAAGTCATGGCTAAGCTCAAGTGGCTGCGTAAAGAGCTACGCATTTGGAACAGAACGGTTTTCGGCAATGTGGATCAGTTTATTTCTGATTCACAGCAGGATCTTCTTGAGATTCAGAATTTAGTCTCTCAACAGGGGTACACCGATAGCCTTTTTAATGCGGAGATTTTCGCTCAAGCTAAAATTAATGTGGTTCTGAGTCGTAAAAA...

Protein

1 records

Download Protein FASTA

XP_057803256.1
MVENSWNSQIDVNCPIYKVMAKLKWLRKELRIWNRTVFGNVDQFISDSQQDLLEIQNLVSQQGYTDSLFNAEIFAQAKINVVLSRKNSLLKQKSRVSWLNDGDRNTAFFHAMLKYKKRHHIIPHLDIQGSMVYDQDEIGNHIVEFFSTLFTEDNMEEIDIVALEATIDHVVSPSQNDMLTRIPENDEITAAVFDMDPHSAAGLDGFSDVVNSLTDLRLIVLSNFLFKIISKVLAKRLSIVAMSCVSANQFGFISGRSIHE...

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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