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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.
Examples

Resolved gene

SmilChr03G000707

Chromosome: Chr03 Coordinates: 7864881-7869100 Strand: - Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr03G000707
NameSmilChr03G000707
Descriptionphosphoribulokinase, chloroplastic
Chromosome / SeqIDChr03 / NC_080389.1
Coordinates and Strand7864881 - 7869100 / -

ID Mapping

NCBI Gene IDLOC131017332
GeneID131017332
locus_tag-
NCBI NameLOC131017332
Original querySmilChr03G000707

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; KEGG smil; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionphosphoribulokinase, chloroplastic
Productphosphoribulokinase%2C chloroplastic
ArabidopsisAT1G32060 (PRK)
phosphoribulokinase [Source:NCBI gene (formerly Entrezgene);Acc:840098]
identity=82.9; qcov=0.995; evalue=0; confidence=high
RiceOs02g0698000 (OsPrk)
-
identity=82.3; qcov=1.01; evalue=0; confidence=high
GOGO:0005524 (ATP binding); GO:0005737 (cytoplasm); GO:0005975 (carbohydrate metabolic process); GO:0008974 (phosphoribulokinase activity); GO:0009507 (chloroplast)
KEGGsmil00710 (Carbon fixation by Calvin cycle - Salvia miltiorrhiza (redroot sage)); smil01100 (Metabolic pathways - Salvia miltiorrhiza (redroot sage)); smil01200 (Carbon metabolism - Salvia miltiorrhiza (redroot sage))
PfamPF00485 (PRK)
InterPro-
eggNOG-
NRGeneID:131017332

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Chloroplast 叶绿体 1.00000 XP_057802038.1
2 Chloroplast stroma 叶绿体基质 1.00000 XP_057802038.1
3 Nucleus 细胞核 0.00000 XP_057802038.1
4 Chromosome 染色体 0.00000 XP_057802038.1
5 Centromere 着丝粒 0.00000 XP_057802038.1

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
Chr3:7865142 C T EMS_canonical_SNV CDS_variant 1 B123
Chr3:7865143 G A EMS_canonical_SNV CDS_variant 2 B130,B53
Chr3:7865182 G A EMS_canonical_SNV CDS_variant 2 B130,B53
Chr3:7865203 C T EMS_canonical_SNV CDS_variant 4 B24,B40,B93,C53
Chr3:7865212 C T EMS_canonical_SNV CDS_variant 2 B133,B2
Chr3:7865432 G A EMS_canonical_SNV CDS_variant 1 C12
Chr3:7865437 AGG A 2bp_deletion frameshift_variant 24 B105,B132,B19,B22,B3,B47,B55,B56,B57,B62,B69,B75,B80,B96,C13,C30,C41,C47,C56,C62,C70,C81,C86,D7
Chr3:7865450 G A EMS_canonical_SNV CDS_variant 1 C71
Chr3:7865468 G A EMS_canonical_SNV CDS_variant 5 B105,B52,C72,C78,C8
Chr3:7865471 G A EMS_canonical_SNV CDS_variant 3 A10,B48,D5
Chr3:7865498 G A EMS_canonical_SNV CDS_variant 4 B105,B52,C78,C8
Chr3:7865600 G A EMS_canonical_SNV CDS_variant 1 B100

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_057802038.1
399 aa
N
1
200
399
PRK
C
PF00485 PRK 55-253 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057802038.1 Pfam PF00485 PRK Domain 55 253 6.1e-80 268.4 Phosphoribulokinase / Uridine kinase family

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_057946055.1
AAATTAATTGTATAAAACACAAAATCCATTTCATATATAAATAAAAAAAAATATACTATACTACTCAAGGGAGTAACTAAAAATTTATATATATAAAAAAAATCAACAATTGCCAATCAAAATACCTTAAACAGTGACACACGACACCCAAAAACAGCCTCCTATCCTCAAAAACTCGCATCATTTTTACTCTAAACCACACACCCTCCCCTCCCTATATCTCTCATTTTTTCTGTCCTCACAATTTTATCATTCATCTC...

CDS

1 records

Download CDS FASTA
LOC131017332
ATGGCAGCAGTCTCCACAGTCTACACACTCAACTCCACCTGCTCAATCTCCACACCATCAAAGCCCCTCACACACAAACACCTAGTCTTCTTCACCACCACCACCGCCACGAAGAGATCATCGCGGCGGGCGATATCATGCTCCGGCGAGGACAAGACGGTGGTGATCGGGCTGGCGGCGGACTCGGGGTGCGGGAAGTCGACGTTCATGCGGCGGCTGACCTCCGTGTTCGGGGGCGCGGCGGAGCCCCCGAAGGGAGG...

Protein

1 records

Download Protein FASTA
XP_057802038.1
MAAVSTVYTLNSTCSISTPSKPLTHKHLVFFTTTTATKRSSRRAISCSGEDKTVVIGLAADSGCGKSTFMRRLTSVFGGAAEPPKGGNPDSNTLISDTTTVICLDDYHSLDRTGRKEKGVTALDPRANDFDLMYQQVKALKDGTPVDKPIYNHVSGLLDPPELIKPPKILVIEGLHPMYDQRVRDLLDFSIYLDISNEVKFAWKIQRDMAERGHSLESIKASIEARKPDFDAYIDPQKQYADAVIEVLPTQLIPDDNEGK...

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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JBrowse

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