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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

SmilChr06G001569

Chromosome: Chr06 Coordinates: 17136675-17138134 Strand: - Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr06G001569
NameSmilChr06G001569
Descriptionuncharacterized SmilChr06G001569
Chromosome / SeqIDChr06 / NC_080392.1
Coordinates and Strand17136675 - 17138134 / -

ID Mapping

NCBI Gene IDLOC130990584
GeneID130990584
locus_tag-
NCBI NameLOC130990584
Original querySmilChr06G001569

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionhit=Os06g0523701; species=rice; confidence=medium
Producthit=Os06g0523701; species=rice; confidence=medium
Arabidopsis-
-
RiceOs06g0523701
-
identity=35.6; qcov=0.474; evalue=6.34e-44; confidence=medium
GOGO:0003676 (nucleic acid binding)
KEGG-
PfamPF24964 (DUF7769)
InterPro-
eggNOG-
NRGeneID:130990584

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Nucleus 细胞核 1.00000 XP_057770789.1
2 Chromosome 染色体 0.20000 XP_057770789.1
3 Centromere 着丝粒 0.00000 XP_057770789.1
4 Chromatin 染色质 0.00000 XP_057770789.1
5 Telomere 端粒 0.00000 XP_057770789.1

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
Chr6:17136811 G A EMS_canonical_SNV CDS_variant 2 C23,C85
Chr6:17136924 G A EMS_canonical_SNV CDS_variant 1 C23
Chr6:17137038 C T EMS_canonical_SNV CDS_variant 5 A4,B15,C10,C78,C87
Chr6:17137613 C T EMS_canonical_SNV stop_gained 1 C24
Chr6:17137613 C T EMS_canonical_SNV CDS_variant 1 C24
Chr6:17137635 G A EMS_canonical_SNV CDS_variant 1 C24
Chr6:17137727 C T EMS_canonical_SNV CDS_variant 3 B31,C24,C64
Chr6:17137764 C T EMS_canonical_SNV CDS_variant 3 B31,C24,C64
Chr6:17137777 C T EMS_canonical_SNV CDS_variant 3 B31,C24,C64
Chr6:17137795 C T EMS_canonical_SNV CDS_variant 3 B31,C24,C64
Chr6:17137825 C T EMS_canonical_SNV CDS_variant 2 B31,C64
Chr6:17137856 G A EMS_canonical_SNV CDS_variant 3 C12,C49,C72

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_057770789.1
456 aa
N
1
228
456
DUF7769
C
PF24964 DUF7769 10-61 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057770789.1 Pfam PF24964 DUF7769 Domain 10 61 6.5e-11 42.5 Domain of unknown function (DUF7769)

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_057914806.1
ATGGCAGACAAGCGAAAAAAGGCAAACTTGACAGAAATTGAAAGAAACAACATTGCACAATGGCTTCTCCAAAACAGCAAGGACTTCAAGCTTCGGTACGGCGCGAAGAAAGAGGCAGCAGCTATGTTCAACATCGATGTGAGGACGGTTTGGCGACTGTGGACAGCAGCACGCGCACAAAAAATGATGGGAAGACCTGTACAACTCGTTTCAATGAAGAAAGGATCAACACATAGCGATAAAAAGGTAATCGACGTGGA...

CDS

1 records

Download CDS FASTA
LOC130990584
ATGGCAGACAAGCGAAAAAAGGCAAACTTGACAGAAATTGAAAGAAACAACATTGCACAATGGCTTCTCCAAAACAGCAAGGACTTCAAGCTTCGGTACGGCGCGAAGAAAGAGGCAGCAGCTATGTTCAACATCGATGTGAGGACGGTTTGGCGACTGTGGACAGCAGCACGCGCACAAAAAATGATGGGAAGACCTGTACAACTCGTTTCAATGAAGAAAGGATCAACACATAGCGATAAAAAGGTAATCGACGTGGA...

Protein

1 records

Download Protein FASTA
XP_057770789.1
MADKRKKANLTEIERNNIAQWLLQNSKDFKLRYGAKKEAAAMFNIDVRTVWRLWTAARAQKMMGRPVQLVSMKKGSTHSDKKVIDVEKVKQLSVLERSTIRKMANKLEVSKSLVGVWIKEKKIRAHTNAIKPLLTQQNRLSRLTWSLSQLSAISANGRIKFQPMYNTIHIDEKWFYLTKTSDRYYLLPDEIEPYRACKSKRFIEKIMFIAVVSRPQYDNEGKMIFDGKFGIFPFTTVVPAVRNSKNRMRGTLETKAIQAI...

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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