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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

SmilChr03G004200

Chromosome: Chr03 Coordinates: 60630235-60632641 Strand: - Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr03G004200
NameSmilChr03G004200
Descriptionglycosyltransferase family protein 64 C3-like
Chromosome / SeqIDChr03 / NC_080389.1
Coordinates and Strand60630235 - 60632641 / -

ID Mapping

NCBI Gene IDLOC131015076
GeneID131015076
locus_tag-
NCBI NameLOC131015076
Original querySmilChr03G004200

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionglycosyltransferase family protein 64 C3-like
Productglycosyltransferase family protein 64 C3-like
ArabidopsisAT1G80290 (AT1G80290)
Nucleotide-diphospho-sugar transferases superfamily protein [Source:NCBI gene (formerly Entrezgene);Acc:844369]
identity=56.5; qcov=0.78; evalue=8.07e-108; confidence=high
RiceOs06g0705000
-
identity=33.1; qcov=0.666; evalue=1.03e-23; confidence=low
GOGO:0006486 (GO:0006486); GO:0016020 (membrane); GO:0016757 (glycosyltransferase activity)
KEGG-
PfamPF09258 (Glyco_transf_64)
InterPro-
eggNOG-
NRGeneID:131015076

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Golgi apparatus 高尔基体 1.00000 XP_057799275.1
2 Golgi stack 高尔基堆 0.20000 XP_057799277.1
3 Nucleus 细胞核 0.00000 XP_057799275.1
4 Chromosome 染色体 0.00000 XP_057799275.1
5 Centromere 着丝粒 0.00000 XP_057799275.1

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
Chr3:60631410 G A EMS_canonical_SNV CDS_variant 2 C64,C66
Chr3:60631440 C T EMS_canonical_SNV CDS_variant 2 B42,B43
Chr3:60631459 C T EMS_canonical_SNV CDS_variant 2 B42,B43
Chr3:60631549 C T EMS_canonical_SNV CDS_variant 1 B90
Chr3:60631585 C T EMS_canonical_SNV CDS_variant 4 B55,C15,C35,D5
Chr3:60631654 C T EMS_canonical_SNV CDS_variant 2 B54,C25
Chr3:60631755 C T EMS_canonical_SNV CDS_variant 1 B131
Chr3:60631759 C T EMS_canonical_SNV CDS_variant 5 A9,B26,B36,B69,C21
Chr3:60631813 C T EMS_canonical_SNV CDS_variant 5 B62,C25,C33,C41,D10
Chr3:60631861 G A EMS_canonical_SNV CDS_variant 1 B133
Chr3:60631874 G A EMS_canonical_SNV CDS_variant 1 B44
Chr3:60631980 C T EMS_canonical_SNV CDS_variant 2 B104,D11

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_057799275.1
391 aa
N
1
196
391
Glyco_transf_64
C
PF09258 Glyco_transf_64 110-363 aa
XP_057799276.1
389 aa
N
1
194
389
Glyco_transf_64
C
PF09258 Glyco_transf_64 110-363 aa
XP_057799277.1
388 aa
N
1
194
388
Glyco_transf_64
C
PF09258 Glyco_transf_64 110-363 aa
XP_057799278.1
387 aa
N
1
194
387
Glyco_transf_64
C
PF09258 Glyco_transf_64 110-363 aa
XP_057799280.1
393 aa
N
1
196
393
Glyco_transf_64
C
PF09258 Glyco_transf_64 110-363 aa
XP_057799281.1
386 aa
N
1
193
386
Glyco_transf_64
C
PF09258 Glyco_transf_64 110-363 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057799275.1 Pfam PF09258 Glyco_transf_64 Domain 110 363 1.5e-70 238.0 Glycosyl transferase family 64 domain
XP_057799276.1 Pfam PF09258 Glyco_transf_64 Domain 110 363 1.5e-70 238.0 Glycosyl transferase family 64 domain
XP_057799277.1 Pfam PF09258 Glyco_transf_64 Domain 110 363 1.5e-70 238.0 Glycosyl transferase family 64 domain
XP_057799278.1 Pfam PF09258 Glyco_transf_64 Domain 110 363 1.5e-70 238.0 Glycosyl transferase family 64 domain
XP_057799280.1 Pfam PF09258 Glyco_transf_64 Domain 110 363 1.6e-70 238.0 Glycosyl transferase family 64 domain
XP_057799281.1 Pfam PF09258 Glyco_transf_64 Domain 110 363 1.5e-70 238.0 Glycosyl transferase family 64 domain

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

6 records

Download cDNA FASTA
XM_057943295.1
TAAATGTTCGATGAAATGCCGAACGAAATCGGAAAGAAATCCAGAAAATTGACTTTGCTCCGAGTCAATTTGACTCAATTGAAGTCAACTCTGAAAGACATGGTATTACGAAACTGCGATGCCATCATCCTTCTTCACAAATTCAAATCAGCATCAGCTACTAATCAAATCATCAATCAAGATAGTAAAAAACCCAAACATCCAATGAGAATCACAGTCATCTTCTTAATCTCACTTCACCTGCCCCTTTTCGTCATTTC...
XM_057943292.1
TAAATGTTCGATGAAATGCCGAACGAAATCGGAAAGAAATCCAGAAAATTGACTTTGCTCCGAGTCAATTTGACTCAATTGAAGTCAACTCTGAAAGACATGGTATTACGAAACTGCGATGCCATCATCCTTCTTCACAAATTCAAATCAGCATCAGCTACTAATCAAATCATCAATCAAGATAGTAAAAAACCCAAACATCCAATGAGAATCACAGTCATCTTCTTAATCTCACTTCACCTGCCCCTTTTCGTCATTTC...

CDS

6 records

Download CDS FASTA
LOC131015076
ATGTTCGATGAAATGCCGAACGAAATCGGAAAGAAATCCAGAAAATTGACTTTGCTCCGAGTCAATTTGACTCAATTGAAGTCAACTCTGAAAGACATGGTATTACGAAACTGCGATGCCATCATCCTTCTTCACAAATTCAAATCAGCATCAGCTACTAATCAAATCATCAATCAAGATAGTAAAAAACCCAAACATCCAATGAGAATCACAGTCATCTTCTTAATCTCACTTCACCTGCCCCTTTTCGTCATTTCATC...
LOC131015076
ATGTTCGATGAAATGCCGAACGAAATCGGAAAGAAATCCAGAAAATTGACTTTGCTCCGAGTCAATTTGACTCAATTGAAGTCAACTCTGAAAGACATGGTATTACGAAACTGCGATGCCATCATCCTTCTTCACAAATTCAAATCAGCATCAGCTACTAATCAAATCATCAATCAAGATAGTAAAAAACCCAAACATCCAATGAGAATCACAGTCATCTTCTTAATCTCACTTCACCTGCCCCTTTTCGTCATTTCATC...

Protein

6 records

Download Protein FASTA
XP_057799275.1
MFDEMPNEIGKKSRKLTLLRVNLTQLKSTLKDMVLRNCDAIILLHKFKSASATNQIINQDSKKPKHPMRITVIFLISLHLPLFVISSRSIRPPDPQCTRPDPNTLRSDQMTVVINGFSEHRIPLLRSITAAYAASPSVAAVVLLWCNPSTPPRTLSDLTQNLSAAVLRAPSASLNHRFHPWAIIRTRAVLICDDDIEPDPNSVSFAFKVWGSDPDRAVGFFARSHAFDVASRAWIYAMETEKYSIVLTKFMIVSVAYLEI...
XP_057799276.1
MFDEMPNEIGKKSRKLTLLRVNLTQLKSTLKDMVLRNCDAIILLHKFKSASATNQIINQDSKKPKHPMRITVIFLISLHLPLFVISSRSIRPPDPQCTRPDPNTLRSDQMTVVINGFSEHRIPLLRSITAAYAASPSVAAVVLLWCNPSTPPRTLSDLTQNLSAAVLRAPSASLNHRFHPWAIIRTRAVLICDDDIEPDPNSVSFAFKVWGSDPDRAVGFFARSHAFDVASRAWIYAMETEKYSIVLTKFMIVSVAYLEI...

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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