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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

SmilChr03G000116

Chromosome: Chr03 Coordinates: 1280394-1281020 Strand: - Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr03G000116
NameSmilChr03G000116
Descriptionuncharacterized SmilChr03G000116
Chromosome / SeqIDChr03 / NC_080389.1
Coordinates and Strand1280394 - 1281020 / -

ID Mapping

NCBI Gene IDLOC131015749
GeneID131015749
locus_tag-
NCBI NameLOC131015749
Original queryLOC131015749

Open ID mapping

Functional Annotation

SourceGFF basic annotation; Pfam-A/HMMER; Arabidopsis/Rice homolog
DescriptionRibonuclease H-like superfamily protein [Source:NCBI gene (formerly Entrezgene);Acc:822121]; symbol=AT3G25270; hit=AT3G25270; species=arabidopsis; confidence=low
ProductRibonuclease H-like superfamily protein [Source:NCBI gene (formerly Entrezgene);Acc:822121]; symbol=AT3G25270; hit=AT3G25270; species=arabidopsis; confidence=low
ArabidopsisAT3G25270 (AT3G25270)
Ribonuclease H-like superfamily protein [Source:NCBI gene (formerly Entrezgene);Acc:822121]
identity=31.4; qcov=0.659; evalue=2.29e-13; confidence=low
RiceOs02g0118800
-
identity=27.9; qcov=0.947; evalue=3.7e-12; confidence=low
GO-
KEGG-
PfamPF13966 (zf-RVT)
InterPro-
eggNOG-
NRGeneID:131015749

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Cytoplasm 细胞质 0.80000 XP_057800154.1
2 Cytosol 细胞质基质 0.20000 XP_057800154.1
3 Cell membrane 细胞膜 0.20000 XP_057800154.1
4 Endoplasmic reticulum membrane 内质网膜 0.20000 XP_057800154.1
5 Nucleus 细胞核 0.00000 XP_057800154.1

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
Chr3:1280475 C T EMS_canonical_SNV stop_gained 2 B90,B92
Chr3:1280475 C T EMS_canonical_SNV CDS_variant 2 B90,B92
Chr3:1280490 G A EMS_canonical_SNV CDS_variant 1 C26
Chr3:1280572 G A EMS_canonical_SNV CDS_variant 4 A6,B114,B29,C30
Chr3:1280577 C T EMS_canonical_SNV CDS_variant 3 B63,B83,D9
Chr3:1280583 G A EMS_canonical_SNV CDS_variant 2 A8,B41
Chr3:1280632 G A EMS_canonical_SNV CDS_variant 2 A24,C42
Chr3:1280666 C T EMS_canonical_SNV CDS_variant 1 B104
Chr3:1280670 C T EMS_canonical_SNV CDS_variant 3 B46,C32,C68
Chr3:1280687 GC G 1bp_deletion frameshift_variant 1 C25
Chr3:1280687 GC G 1bp_deletion CDS_variant 1 C25
Chr3:1280713 G A EMS_canonical_SNV CDS_variant 1 A3

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_057800154.1
208 aa
N
1
104
208
zf-RVT
C
PF13966 zf-RVT 14-107 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057800154.1 Pfam PF13966 zf-RVT Domain 14 107 3.2e-19 70.1 zinc-binding in reverse transcriptase

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_057944171.1
ATGGATGGGTGGAGATGGAAATCCACCCCTTACGGATGTTTCACAGTAAATTCAGCCTATAAAGAACTGAGCTCACAGTCTGGCCCTCCGGCGGACCTCGACGACAAACTGATCTGGCAAATGATCTGGAAAGCTCCAACTCCTCCCAAAGTCATAACCACAGTTTGGAAAGCACTTCGAGGAAGATTGGCGACCTGCGAAAATCTGATGAAAAGACGTGTGATCGCGCAAAATTCTGAGGCTAAGTGTGCTTTCTGCAA...

CDS

1 records

Download CDS FASTA
LOC131015749
ATGGATGGGTGGAGATGGAAATCCACCCCTTACGGATGTTTCACAGTAAATTCAGCCTATAAAGAACTGAGCTCACAGTCTGGCCCTCCGGCGGACCTCGACGACAAACTGATCTGGCAAATGATCTGGAAAGCTCCAACTCCTCCCAAAGTCATAACCACAGTTTGGAAAGCACTTCGAGGAAGATTGGCGACCTGCGAAAATCTGATGAAAAGACGTGTGATCGCGCAAAATTCTGAGGCTAAGTGTGCTTTCTGCAA...

Protein

1 records

Download Protein FASTA
XP_057800154.1
MDGWRWKSTPYGCFTVNSAYKELSSQSGPPADLDDKLIWQMIWKAPTPPKVITTVWKALRGRLATCENLMKRRVIAQNSEAKCAFCKTEIETSEHIFFSCSKTEEIWKFLLLWIGKQTALSIKMKDHFLAFINLGSKEDLRFLLGSWMCTIWCIWKGRNECKFNNGIWNKDKMTGEIKTRVWGWLQVFGTPTVLPDFRRWLHSALLHG

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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