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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

SmilChr04G002533

Chromosome: Chr04 Coordinates: 40429086-40434077 Strand: + Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr04G002533
NameSmilChr04G002533
Descriptionprobable methyltransferase PMT27
Chromosome / SeqIDChr04 / NC_080390.1
Coordinates and Strand40429086 - 40434077 / +

ID Mapping

NCBI Gene IDLOC131021659
GeneID131021659
locus_tag-
NCBI NameLOC131021659
Original querySmilChr04G002533

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionprobable methyltransferase PMT27
Productprobable methyltransferase PMT27
ArabidopsisAT3G51070 (AT3G51070)
S-adenosyl-L-methionine-dependent methyltransferases superfamily protein [Source:NCBI gene (formerly Entrezgene);Acc:824271]
identity=54.6; qcov=1.02; evalue=0; confidence=high
RiceOs06g0712800 (OsSTA181)
-
identity=57; qcov=0.831; evalue=0; confidence=high
GOGO:0005737 (cytoplasm); GO:0005768 (endosome); GO:0005802 (trans-Golgi network); GO:0008168 (methyltransferase activity)
KEGG-
PfamPF03141 (Methyltransf_29); PF08241 (Methyltransf_11); PF13649 (Methyltransf_25)
InterPro-
eggNOG-
NRGeneID:131021659

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Golgi apparatus 高尔基体 1.00000 XP_057806892.1
2 Golgi stack 高尔基堆 0.20000 XP_057806892.1
3 Nucleus 细胞核 0.00000 XP_057806892.1
4 Chromosome 染色体 0.00000 XP_057806892.1
5 Centromere 着丝粒 0.00000 XP_057806892.1

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
Chr4:40430740 C T EMS_canonical_SNV CDS_variant 1 C77
Chr4:40431026 C T EMS_canonical_SNV CDS_variant 4 A18,A22,C4,C49
Chr4:40431120 C T EMS_canonical_SNV CDS_variant 2 C6,D2
Chr4:40431504 C T EMS_canonical_SNV CDS_variant 2 B104,D11
Chr4:40431968 G A EMS_canonical_SNV CDS_variant 1 B30
Chr4:40432283 G A EMS_canonical_SNV CDS_variant 4 B33,B75,B95,D6
Chr4:40432657 C T EMS_canonical_SNV CDS_variant 1 B139
Chr4:40433444 G A EMS_canonical_SNV CDS_variant 1 B93
Chr4:40433487 C T EMS_canonical_SNV CDS_variant 2 B59,C81
Chr4:40433742 C T EMS_canonical_SNV CDS_variant 1 B108
Chr4:40433780 G A EMS_canonical_SNV CDS_variant 5 A1,B139,C18,C22,C27
Chr4:40433788 G A EMS_canonical_SNV CDS_variant 1 B24

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_057806892.1
872 aa
N
1
436
872
Methyltransf_29
Methyltransf_25
Methyltransf_11
C
PF03141 Methyltransf_29 355-860 aa PF13649 Methyltransf_25 473-565 aa PF08241 Methyltransf_11 474-568 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057806892.1 Pfam PF03141 Methyltransf_29 Family 355 860 1.3e-229 763.7 Putative S-adenosyl-L-methionine-dependent methyltransferase
XP_057806892.1 Pfam PF13649 Methyltransf_25 Domain 473 565 5.3e-09 37.4 Methyltransferase domain
XP_057806892.1 Pfam PF08241 Methyltransf_11 Domain 474 568 7.9e-12 46.4 Methyltransferase 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

1 records

Download cDNA FASTA
XM_057950909.1
TGGGAAAAGAATGACAAACCTTAGTGATTCCTATGCATAGTATGCACAAGGAATACCAAAGGAATGGAATTGTGATTCTTTGTTTAATTCAATTCCTATAATTGGTAGCTAGAAATAAAGTTTAGGAATGAAATGAAATTATTTTATTTTATTAATATCAATCCATGTATATGATAGTGTAATATATTGCGTCAATTTCAATCCAGATATTAGACTATTGCTTATATAAAGTTGATAATATTTTATTTTTTCTAAAAATA...

CDS

1 records

Download CDS FASTA
LOC131021659
ATGGCCTCAGGGAAAACTCGCGCCACAAAACGATCCTCGACAACTTCTAGTTATTCATCAGCAACCTCAATCGTAATCCTCGTAGGATTATCTGTATTAGGTTTATGGCTGCTGACCTCCAATTCCTTCACACCATCGCAGCCCCCCGCCACCAAAGCTCCAACCTCCATAGGCCATACTCATCACTCACACGTGCTCCCACAAACTCGCCAAAATGAAAACGACCCCTCTTCTATTTCTGATTCTGATGATGCACTACT...

Protein

1 records

Download Protein FASTA
XP_057806892.1
MASGKTRATKRSSTTSSYSSATSIVILVGLSVLGLWLLTSNSFTPSQPPATKAPTSIGHTHHSHVLPQTRQNENDPSSISDSDDALLIQPETNIENDHTHTDKTFKTEAILTDHVDHQDTKASQDNNHAAEEHDKQAALETQTSEESSMTQKEEIIQETPHSETKMETNDAEDVSAEAGSLTQSSNTTQNQISDEDQQRRIDEHQQREDEQKQQEGQEAQSADPNGAISHDQIQHDEAPIHSHQDGSSSQETDKPHAQAT...

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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