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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

SmilChr02G002666

Chromosome: Chr02 Coordinates: 46156535-46157296 Strand: + Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr02G002666
NameSmilChr02G002666
Descriptionuncharacterized SmilChr02G002666
Chromosome / SeqIDChr02 / NC_080388.1
Coordinates and Strand46156535 - 46157296 / +

ID Mapping

NCBI Gene IDLOC131009611
GeneID131009611
locus_tag-
NCBI NameLOC131009611
Original querySmilChr02G002666

Open ID mapping

Functional Annotation

SourceGFF basic annotation; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionhit=Os02g0118800; species=rice; confidence=low
Producthit=Os02g0118800; species=rice; confidence=low
ArabidopsisAT3G25270 (AT3G25270)
Ribonuclease H-like superfamily protein [Source:NCBI gene (formerly Entrezgene);Acc:822121]
identity=29.7; qcov=0.613; evalue=2.91e-11; confidence=low
RiceOs02g0118800
-
identity=31; qcov=0.779; evalue=4.66e-15; confidence=low
GO-
KEGG-
PfamPF13966 (zf-RVT)
InterPro-
eggNOG-
NRGeneID:131009611

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Cytoplasm 细胞质 1.00000 XP_057793009.1
2 Nucleus 细胞核 0.20000 XP_057793009.1
3 Chromosome 染色体 0.00000 XP_057793009.1
4 Centromere 着丝粒 0.00000 XP_057793009.1
5 Chromatin 染色质 0.00000 XP_057793009.1

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
Chr2:46156539 G A EMS_canonical_SNV CDS_variant 1 B75
Chr2:46156560 G A EMS_canonical_SNV stop_gained 1 B140
Chr2:46156560 G A EMS_canonical_SNV CDS_variant 1 B140
Chr2:46156578 G A EMS_canonical_SNV stop_gained 28 A18,A21,B112,B119,B12,B123,B124,B128,B135,B136,B27,B3,B41,B44,B46,B61,B63,B95,C14,C22,C24,C29,C33,C47,C5,C55,C69,C73
Chr2:46156596 G A EMS_canonical_SNV CDS_variant 3 B104,B5,D10
Chr2:46156604 C T EMS_canonical_SNV CDS_variant 1 B13
Chr2:46156629 C T EMS_canonical_SNV CDS_variant 1 B100
Chr2:46156646 G A EMS_canonical_SNV CDS_variant 2 A11,B25
Chr2:46156745 G A EMS_canonical_SNV CDS_variant 3 B65,C11,C69
Chr2:46156749 C T EMS_canonical_SNV CDS_variant 1 B7
Chr2:46156759 C T EMS_canonical_SNV CDS_variant 1 D7
Chr2:46156760 G A EMS_canonical_SNV CDS_variant 4 B101,B115,B128,C45

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_057793009.1
253 aa
N
1
126
253
zf-RVT
C
PF13966 zf-RVT 57-150 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057793009.1 Pfam PF13966 zf-RVT Domain 57 150 3.6e-22 79.5 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_057937026.1
ATGGGAGAGTGGTCTGATGGAATCTGGAGTTGGAATTTGAACTGGAAACGCGAGTTGAGGGGGAGAGAACTGGATCAGTTTTCTTCCCTTTCCTCGTTGATCAACAGTTTTGATATTATTGCAGGTAAACCAGGAGGATGGAGGTGGAAAGCTGACCCAAAAGGCATCTTCTCAGTCAAAGAAGCGTACCGTGCCGTTAGCAAATCAACCGAAACCAATTTCAACGATGAGTGTGATCTGAAATTTCTTCAGATTTGGAA...

CDS

1 records

Download CDS FASTA
LOC131009611
ATGGGAGAGTGGTCTGATGGAATCTGGAGTTGGAATTTGAACTGGAAACGCGAGTTGAGGGGGAGAGAACTGGATCAGTTTTCTTCCCTTTCCTCGTTGATCAACAGTTTTGATATTATTGCAGGTAAACCAGGAGGATGGAGGTGGAAAGCTGACCCAAAAGGCATCTTCTCAGTCAAAGAAGCGTACCGTGCCGTTAGCAAATCAACCGAAACCAATTTCAACGATGAGTGTGATCTGAAATTTCTTCAGATTTGGAA...

Protein

1 records

Download Protein FASTA
XP_057793009.1
MGEWSDGIWSWNLNWKRELRGRELDQFSSLSSLINSFDIIAGKPGGWRWKADPKGIFSVKEAYRAVSKSTETNFNDECDLKFLQIWKAKAPFKAKMTAWRLLKGRLATTDNLLRRQVQLPNEELTCILCKDQAESIDHLFFSCQMTTEVWNSILLWIGKHAALHIRAKDHLLAFSNLGSKADNFLLTSVWICVIWSVWNWRNEGKFNKDIWSKDKILAEIKTRVWGWKSAFSLTTSSPDFRSWFVGDQILGCS

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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