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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

SmilChr01G002110

Chromosome: Chr01 Coordinates: 37152762-37155118 Strand: - Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr01G002110
NameSmilChr01G002110
DescriptionRPM1-interacting protein 4-like
Chromosome / SeqIDChr01 / NC_080387.1
Coordinates and Strand37152762 - 37155118 / -

ID Mapping

NCBI Gene IDLOC131023467
GeneID131023467
locus_tag-
NCBI NameLOC131023467
Original querySmilChr01G002110

Open ID mapping

Functional Annotation

SourceGFF basic annotation; KEGG smil; Pfam-A/HMMER; Arabidopsis/Rice homolog
DescriptionRPM1-interacting protein 4-like
ProductRPM1-interacting protein 4-like
ArabidopsisAT3G25070 (RIN4)
RPM1 interacting protein 4 [Source:NCBI gene (formerly Entrezgene);Acc:822098]
identity=36.7; qcov=1.04; evalue=7.16e-33; confidence=medium
RiceOs03g0848600
-
identity=34.9; qcov=1.08; evalue=1.06e-29; confidence=low
GO-
KEGGsmil04626 (Plant-pathogen interaction - Salvia miltiorrhiza (redroot sage))
PfamPF05627 (AvrRpt-cleavage)
InterPro-
eggNOG-
NRGeneID:131023467

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Cytoskeleton 细胞骨架 1.00000 XP_057808993.1
2 Cell membrane 细胞膜 1.00000 XP_057809002.1
3 Nucleus 细胞核 0.00000 XP_057808993.1
4 Chromosome 染色体 0.00000 XP_057808993.1
5 Centromere 着丝粒 0.00000 XP_057808993.1

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
Chr1:37153200 C T EMS_canonical_SNV CDS_variant 1 A18
Chr1:37153243 G A EMS_canonical_SNV CDS_variant 5 B33,B99,C25,C35,D11
Chr1:37153257 G A EMS_canonical_SNV CDS_variant 2 C10,C40
Chr1:37153624 G A EMS_canonical_SNV CDS_variant 1 B104
Chr1:37153654 G A EMS_canonical_SNV CDS_variant 3 B106,B27,B60
Chr1:37153803 G A EMS_canonical_SNV CDS_variant 2 B22,B41
Chr1:37153807 C CG 1bp_insertion frameshift_variant 1 B52
Chr1:37153807 C CG 1bp_insertion CDS_variant 1 B52
Chr1:37153810 AC A 1bp_deletion frameshift_variant 1 B52
Chr1:37153810 AC A 1bp_deletion CDS_variant 1 B52
Chr1:37153813 GC G 1bp_deletion frameshift_variant 1 B52
Chr1:37153813 GC G 1bp_deletion CDS_variant 1 B52

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_057808993.1
260 aa
N
1
130
260
AvrRpt-cleavage
AvrRpt-cleavage
C
PF05627 AvrRpt-cleavage 4-34 aa PF05627 AvrRpt-cleavage 186-219 aa
XP_057808998.1
258 aa
N
1
129
258
AvrRpt-cleavage
AvrRpt-cleavage
C
PF05627 AvrRpt-cleavage 3-32 aa PF05627 AvrRpt-cleavage 184-217 aa
XP_057809002.1
252 aa
N
1
126
252
AvrRpt-cleavage
AvrRpt-cleavage
C
PF05627 AvrRpt-cleavage 4-34 aa PF05627 AvrRpt-cleavage 186-219 aa
XP_057809006.1
250 aa
N
1
125
250
AvrRpt-cleavage
AvrRpt-cleavage
C
PF05627 AvrRpt-cleavage 3-32 aa PF05627 AvrRpt-cleavage 184-217 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057808993.1 Pfam PF05627 AvrRpt-cleavage Domain 4 34 1.1e-28 98.9 Cleavage site for pathogenic type III effector avirulence factor Avr
XP_057808993.1 Pfam PF05627 AvrRpt-cleavage Domain 186 219 1.1e-28 98.9 Cleavage site for pathogenic type III effector avirulence factor Avr
XP_057808998.1 Pfam PF05627 AvrRpt-cleavage Domain 3 32 7.7e-29 99.5 Cleavage site for pathogenic type III effector avirulence factor Avr
XP_057808998.1 Pfam PF05627 AvrRpt-cleavage Domain 184 217 7.7e-29 99.5 Cleavage site for pathogenic type III effector avirulence factor Avr
XP_057809002.1 Pfam PF05627 AvrRpt-cleavage Domain 4 34 1e-28 99.1 Cleavage site for pathogenic type III effector avirulence factor Avr
XP_057809002.1 Pfam PF05627 AvrRpt-cleavage Domain 186 219 1e-28 99.1 Cleavage site for pathogenic type III effector avirulence factor Avr
XP_057809006.1 Pfam PF05627 AvrRpt-cleavage Domain 3 32 7e-29 99.6 Cleavage site for pathogenic type III effector avirulence factor Avr
XP_057809006.1 Pfam PF05627 AvrRpt-cleavage Domain 184 217 7e-29 99.6 Cleavage site for pathogenic type III effector avirulence factor Avr

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

4 records

Download cDNA FASTA
XM_057953019.1
GTGAAGACTTGGTTAATGCCTTGAGAGGGAGAGAATAGTCAACCATGAGCTGTGGCACTCGGTCAACGGTTGATCAACCTCTCACCTCTTCTTCTTATTTAGACATCAATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCATTGAAGTTGGTGGGAGCTTTCAGCGTTACGTGCTATTTCGTGTTTTGGGTTGATAAGAAAGACACCATTTTCTCCTCTGCTGCTTTCTGGGTTTTGAAGCTGAACAAAAATGGCGA...
XM_057953010.1
GCCTTGAGAGGGAGAGAATAGTCAACCATGAGCTGTGGCACTCGGTCAACGGTTGATCAACCTCTCACCTCTTCTTCTTATTTAGACATCAATCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCATTGAAGTTGGTGGGAGCTTTCAGCGTTACGTGCTATTTCGTGTTTTGGGTTGATAAGAAAGACACCATTTTCTCCTCTGCTGCTTTCTGGGTTTTGAAGCTGAACAAAAATGGCGAAGCAGCGGTCAAATGTG...

CDS

4 records

Download CDS FASTA
LOC131023467
ATGGCGCGGTCAAATGTGCCAAAATTTGGCAACTGGGAAAACGAACAAAATGATGTTCCTTACACGGTTTACTTCAACAATGCAAGGAAAAATAAGGGAGGAAAGATGATAAATCCAAACGATCCTCTAGAGAATCCAGAGATGTTTGCTCATCTAGAACCTTCGCCTCTTGCTGCTGCCGCTCCTCCGACTCCTCCACAAAAACCGAGAGCCAGGCCAGAGGAGCCAATCGGGAGAGGGGCCGTGAGGCCCGCCCCCGA...
LOC131023467
ATGGCGAAGCAGCGGTCAAATGTGCCAAAATTTGGCAACTGGGAAAACGAACAAAATGATGTTCCTTACACGGTTTACTTCAACAATGCAAGGAAAAATAAGGGAGGAAAGATGATAAATCCAAACGATCCTCTAGAGAATCCAGAGATGTTTGCTCATCTAGAACCTTCGCCTCTTGCTGCTGCCGCTCCTCCGACTCCTCCACAAAAACCGAGAGCCAGGCCAGAGGAGCCAATCGGGAGAGGGGCCGTGAGGCCCGC...

Protein

4 records

Download Protein FASTA
XP_057808993.1
MAKQRSNVPKFGNWENEQNDVPYTVYFNNARKNKGGKMINPNDPLENPEMFAHLEPSPLAAAAPPTPPQKPRARPEEPIGRGAVRPAPDQRDGDFRQINSSSTRNEPNYGGRGRGQRSARSARPPSAGSELSFERSPLHPQPRPQANAVARATGSPAWEGPRSHDSSHGTPSRSRLRPVRPDESHEKGAAVPRFGEWDENDPQSAENFTHIFNKVREDRNMSEAGNGSTTPKHPSYAPQRSNEPKVRPTSSIYLSISSNL
XP_057808998.1
MARSNVPKFGNWENEQNDVPYTVYFNNARKNKGGKMINPNDPLENPEMFAHLEPSPLAAAAPPTPPQKPRARPEEPIGRGAVRPAPDQRDGDFRQINSSSTRNEPNYGGRGRGQRSARSARPPSAGSELSFERSPLHPQPRPQANAVARATGSPAWEGPRSHDSSHGTPSRSRLRPVRPDESHEKGAAVPRFGEWDENDPQSAENFTHIFNKVREDRNMSEAGNGSTTPKHPSYAPQRSNEPKVRPTSSIYLSISSNL

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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