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

`SmilChr03G003057`

Chromosome: Chr03 Coordinates: 47466730-47468618 Strand: - Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr03G003057`
Name	SmilChr03G003057
Description	adenylate isopentenyltransferase 3, chloroplastic
Chromosome / SeqID	Chr03 / NC_080389.1
Coordinates and Strand	47466730 - 47468618 / `-`

ID Mapping

NCBI Gene ID	`LOC131016205`
GeneID	`131016205`
locus_tag	`-`
NCBI Name	`LOC131016205`
Original query	`SmilChr03G003057`

Open ID mapping

Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; KEGG smil; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	adenylate isopentenyltransferase 3, chloroplastic
Product	adenylate isopentenyltransferase 3%2C chloroplastic
Arabidopsis	`AT3G63110` (IPT3) isopentenyltransferase 3 [Source:NCBI gene (formerly Entrezgene);Acc:825486] identity=59.4; qcov=0.969; evalue=7.53e-122; confidence=high
Rice	`Os03g0810100` (OsIPT4) - identity=50.8; qcov=0.997; evalue=2.13e-91; confidence=high
GO	GO:0005739 (mitochondrion); GO:0006400 (tRNA modification); GO:0009691 (cytokinin biosynthetic process); GO:0052381 (tRNA dimethylallyltransferase activity)
KEGG	smil00908 (Zeatin biosynthesis - Salvia miltiorrhiza (redroot sage)); smil01100 (Metabolic pathways - Salvia miltiorrhiza (redroot sage)); smil01110 (Biosynthesis of secondary metabolites - Salvia miltiorrhiza (redroot sage))
Pfam	PF01715 (IPPT); PF01745 (IPT)
InterPro	-
eggNOG	-
NR	GeneID:131016205

Open annotation module

Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Chloroplast	叶绿体	1.00000	`XP_057800827.1`
2	Mitochondrion	线粒体	0.20000	`XP_057800827.1`
3	Nucleus	细胞核	0.00000	`XP_057800827.1`
4	Chromosome	染色体	0.00000	`XP_057800827.1`
5	Centromere	着丝粒	0.00000	`XP_057800827.1`

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
`Chr3:47466972`	`C`	`T`	EMS_canonical_SNV	CDS_variant	1	C20
`Chr3:47466997`	`C`	`T`	EMS_canonical_SNV	CDS_variant	4	A15,B11,B63,B89
`Chr3:47467188`	`C`	`T`	EMS_canonical_SNV	CDS_variant	3	B103,B46,C76
`Chr3:47467260`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B49,C45
`Chr3:47467390`	`CA`	`C`	1bp_deletion	frameshift_variant	1	A18
`Chr3:47467390`	`CA`	`C`	1bp_deletion	CDS_variant	1	A18
`Chr3:47467561`	`G`	`A`	EMS_canonical_SNV	CDS_variant	1	B104
`Chr3:47467572`	`C`	`T`	EMS_canonical_SNV	CDS_variant	2	B11,B12
`Chr3:47467868`	`A`	`AT`	1bp_insertion	frameshift_variant	177	A1,A10,A11,A13,A15,A16,A18,A20,A21,A22,A23,A25,A3,A4,A6,A7,A9,B1,B10,B100,B101,B102,B103,B104,B105,B106,B107,B11,B110,B113,B114,B115,B117,B118,B119,B12,B122,B123,B124,B127,B128,B129,B13,B130,B131,B132,B134,B135,B136,B137,B138,B139,B14,B17,B18,B2,B21,B22,B23,B25,B26,B28,B3,B31,B34,B36,B37,B40,B41,B44,B45,B46,B48,B49,B5,B50,B51,B52,B53,B54,B55,B57,B58,B6,B60,B61,B63,B65,B68,B69,B7,B70,B71,B72,B73,B74,B76,B78,B79,B8,B80,B81,B82,B83,B87,B88,B89,B90,B91,B92,B93,B94,B95,B98,C10,C11,C12,C13,C15,C16,C17,C18,C19,C2,C20,C21,C24,C27,C28,C29,C3,C30,C31,C34,C35,C36,C39,C45,C46,C47,C49,C5,C50,C51,C52,C53,C54,C57,C58,C59,C6,C61,C62,C63,C65,C67,C69,C7,C70,C72,C75,C76,C79,C80,C81,C82,C83,C85,C86,C87,D11,D3,D4,D5,D6,D8,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_057800827.1

318 aa

159

318

IPT

IPPT

PF01745 IPT 33-159 aa PF01715 IPPT 67-139 aa PF01715 IPPT 143-242 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057800827.1`	Pfam	`PF01745`	IPT	Domain	33	159	7e-09	36.2	Isopentenyl transferase
`XP_057800827.1`	Pfam	`PF01715`	IPPT	Domain	67	139	8.7e-38	131.1	IPP transferase
`XP_057800827.1`	Pfam	`PF01715`	IPPT	Domain	143	242	8.7e-38	131.1	IPP transferase

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_057944844.1
AAAGAATTCATGTTATTCTACTTCCATTAAAATTATTCTCTCAATCAACATACAAGAACAAGAATCGCATAGTACATTTTCTTCTCAAGATTCAGCACCTCACATTTCTTATGCATATGTTCAAATCTTAGGATAAAAATAGTAGAAATTGTAAACTCAACTGCAAAGTCCTCCTTTAGTAAAAGATGTTGACTTATTAATTAATCTACTTTCTTCTCCCAAGTTGATGCGAATCATTCAGGCTTTTAATTTACAATATC...

CDS

1 records

Download CDS FASTA

LOC131016205
ATGAAAATATCATTCTCTGCATCCAAACAAATACGCCCCTTGCTACACATACCTAGCACCTGCACTCAGCTCCTCCGCCACGGCCCGCCCAAGGAGAAGGTGGTGGTGGTGATGGGCGCCACCGGCGCCGGAAAATCGCGTCTCTCGATCGACCTCGCCACGAGCTTCTCGGCGGAGATCATCAACTCCGACAAAATGCAGGTCTACCAAGGCCTCGAAATCGCCACTAACAAAATCACCGACGAGGAGCTGCGCGGCGT...

Protein

1 records

Download Protein FASTA

XP_057800827.1
MKISFSASKQIRPLLHIPSTCTQLLRHGPPKEKVVVVMGATGAGKSRLSIDLATSFSAEIINSDKMQVYQGLEIATNKITDEELRGVPHHLLGVIDPESDFSAANFRAMASISLQSILSRRQLPIIVGGSNSFVEALVDVNFQSRYDCCFLWVDVAMPVLHSFVSDRVDKMVERGMVDEVRAFFRSDADYSRGIRRAIGVPELDEFFRVESSCDEETRARVLAEAIDAIKMNTSRLACRQLEKIHRLRNIRDWRMHRLDA...

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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