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

`SmilChr04G000786`

Chromosome: Chr04 Coordinates: 9676495-9678700 Strand: - Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr04G000786`
Name	SmilChr04G000786
Description	cis-prenyltransferase 4, chloroplastic-like
Chromosome / SeqID	Chr04 / NC_080390.1
Coordinates and Strand	9676495 - 9678700 / `-`

ID Mapping

NCBI Gene ID	`LOC131022635`
GeneID	`131022635`
locus_tag	`-`
NCBI Name	`LOC131022635`
Original query	`SmilChr04G000786`

Open ID mapping

Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; KEGG smil; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	cis-prenyltransferase 4, chloroplastic-like
Product	cis-prenyltransferase 4%2C chloroplastic-like
Arabidopsis	`AT5G58770` (cPT4) Undecaprenyl pyrophosphate synthetase family protein [Source:NCBI gene (formerly Entrezgene);Acc:835991] identity=62.9; qcov=0.674; evalue=2.72e-104; confidence=high
Rice	`Os01g0857200` - identity=57.3; qcov=0.701; evalue=4.25e-96; confidence=high
GO	GO:0002094 (GO:0002094); GO:0009409 (response to cold); GO:0009570 (chloroplast stroma); GO:0009668 (plastid membrane organization); GO:0016094 (polyprenol biosynthetic process)
KEGG	smil00900 (Terpenoid backbone biosynthesis - Salvia miltiorrhiza (redroot sage)); smil01110 (Biosynthesis of secondary metabolites - Salvia miltiorrhiza (redroot sage))
Pfam	PF01255 (Prenyltransf)
InterPro	-
eggNOG	-
NR	GeneID:131022635

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Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Chloroplast	叶绿体	1.00000	`XP_057808128.1`
2	Chloroplast stroma	叶绿体基质	1.00000	`XP_057808128.1`
3	Nucleus	细胞核	0.00000	`XP_057808128.1`
4	Chromosome	染色体	0.00000	`XP_057808128.1`
5	Centromere	着丝粒	0.00000	`XP_057808128.1`

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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
`Chr4:9677208`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	C39,C75
`Chr4:9677310`	`G`	`A`	EMS_canonical_SNV	CDS_variant	4	A1,B103,B73,C77
`Chr4:9677442`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	C23
`Chr4:9678012`	`CTG`	`C`	2bp_deletion	frameshift_variant	1	B2
`Chr4:9678012`	`CTG`	`C`	2bp_deletion	CDS_variant	1	B2
`Chr4:9678189`	`G`	`A`	EMS_canonical_SNV	CDS_variant	2	C39,C75
`Chr4:9678225`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	C10,D6
`Chr4:9678230`	`G`	`A`	EMS_canonical_SNV	CDS_variant	4	B38,B39,B72,C13
`Chr4:9678403`	`C`	`CCG`	2bp_insertion	frameshift_variant	1	C75
`Chr4:9678403`	`C`	`CCG`	2bp_insertion	CDS_variant	1	C75
`Chr4:9678417`	`G`	`A`	EMS_canonical_SNV	stop_gained	158	A1,A10,A11,A13,A14,A15,A16,A18,A19,A2,A20,A22,A23,A25,A4,A5,A6,A7,A8,B1,B10,B100,B101,B103,B104,B105,B106,B108,B109,B112,B117,B118,B119,B121,B123,B124,B125,B126,B128,B129,B13,B131,B132,B134,B135,B136,B138,B139,B14,B16,B19,B2,B20,B21,B22,B25,B27,B28,B3,B31,B34,B35,B36,B38,B39,B40,B42,B43,B44,B45,B48,B49,B5,B53,B54,B55,B57,B58,B6,B60,B62,B65,B66,B67,B7,B70,B71,B72,B73,B74,B76,B79,B8,B80,B82,B83,B85,B86,B87,B89,B9,B93,B94,B97,B98,B99,C16,C17,C18,C19,C20,C22,C23,C26,C27,C28,C3,C30,C31,C32,C39,C4,C41,C43,C44,C46,C47,C48,C49,C50,C51,C52,C54,C55,C58,C6,C60,C61,C62,C63,C68,C72,C75,C76,C78,C8,C80,C81,C82,C84,C85,C9,D11,D2,D3,D4,D5,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_057808128.1

344 aa

172

344

Prenyltransf

PF01255 Prenyltransf 121-343 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057808128.1`	Pfam	`PF01255`	Prenyltransf	Family	121	343	3.5e-78	262.8	Putative undecaprenyl diphosphate synthase

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_057952145.1
TACCTACCTTTTGTCATTATATTTACAAGGTCTATGGAAATTTTAATGCCTCAAAAAATGGATAATTTATTACTAGGCCAAAGGTTATTGTAAAGTAAAAAATAGTTAAACTACAAATATTTTAACTTATTTAAAATATGAAAAAGAAAAAGAAAAAAAGAAGACATAGTTGCCATCTTCATCGGCTGGCCACTCATTAATGGATCAGTTAAAACTCATAAAACTTCAAAAATCAGTGCCGCCTTCCAATTTTAGAAACC...

CDS

1 records

Download CDS FASTA

LOC131022635
ATGGATCAGTTAAAACTCATAAAACTTCAAAAATCAGTGCCGCCTTCCAATTTTAGAAACCCTAAACTCCCGCCTTTCCAAAACCAACCGCGGCGGCAGCGAATGGCGTCTCTCCAACTCCGCCTCTCTTTCACCCCCTCGCCACTCAAGCTCCGGCAGCAGGTGCCGCGCCGCTCACTCGACCTCAAGCTGCCGCCGCGCGCGTTGTCTTCAGCCATCAAAGCCGCCACTGTAAACGGGCATCCCGGCGAGGACGCCTT...

Protein

1 records

Download Protein FASTA

XP_057808128.1
MDQLKLIKLQKSVPPSNFRNPKLPPFQNQPRRQRMASLQLRLSFTPSPLKLRQQVPRRSLDLKLPPRALSSAIKAATVNGHPGEDALLKGTTAPAQFSGEDSVALPAGLRRESIPRHVAVIMDGNRRWARMRGFPVGSGYEAGVRALRRMVELCCKLGIKVLTVFAFSSDNWFRPKVEVDVLMALFDRGLREELQYLVSADVRISIMGDSSKLFNSLQALLANAMETTQNNSRLHLIVAVNYSGRSDVVQACQKLAVEVK...

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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