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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

SmilChr01G000068

Chromosome: Chr01 Coordinates: 1118456-1123317 Strand: + Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr01G000068
NameSmilChr01G000068
Descriptionuncharacterized SmilChr01G000068
Chromosome / SeqIDChr01 / NC_080387.1
Coordinates and Strand1118456 - 1123317 / +

ID Mapping

NCBI Gene IDLOC131006455
GeneID131006455
locus_tag-
NCBI NameLOC131006455
Original queryLOC131006455

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionhit=Os06g0484800; species=rice; confidence=low
Producthit=Os06g0484800; species=rice; confidence=low
ArabidopsisAT3G24255 (AT3G24255)
RNA-directed DNA polymerase (reverse transcriptase)-related family protein [Source:NCBI gene (formerly Entrezgene);Acc:822013]
identity=27.9; qcov=0.317; evalue=7.56e-45; confidence=low
RiceOs06g0484800
-
identity=29.5; qcov=0.529; evalue=7.4e-100; confidence=low
GOGO:0003676 (nucleic acid binding); GO:0004523 (RNA-DNA hybrid ribonuclease activity)
KEGG-
PfamPF00078 (RVT_1); PF13456 (RVT_3); PF13966 (zf-RVT)
InterPro-
eggNOG-
NRGeneID:131006455

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Cytoplasm 细胞质 1.00000 XP_057789598.1
2 Cytosol 细胞质基质 0.80000 XP_057789598.1
3 Nucleus 细胞核 0.20000 XP_057789598.1
4 Chromosome 染色体 0.00000 XP_057789598.1
5 Centromere 着丝粒 0.00000 XP_057789598.1

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
Chr1:1118477 TG T 1bp_deletion frameshift_variant 2 A20,C54
Chr1:1118477 TG T 1bp_deletion CDS_variant 2 A20,C54
Chr1:1118488 C T EMS_canonical_SNV CDS_variant 1 B13
Chr1:1118490 G A EMS_canonical_SNV CDS_variant 1 D8
Chr1:1118502 C T EMS_canonical_SNV CDS_variant 4 B66,C39,C73,D11
Chr1:1118537 C T EMS_canonical_SNV CDS_variant 1 A20
Chr1:1118538 G A EMS_canonical_SNV CDS_variant 3 B66,C39,C73
Chr1:1118552 G A EMS_canonical_SNV CDS_variant 3 B66,C39,C73
Chr1:1118589 C T EMS_canonical_SNV CDS_variant 2 B26,B30
Chr1:1118644 G A EMS_canonical_SNV CDS_variant 4 A1,A7,B19,C81
Chr1:1118648 G A EMS_canonical_SNV CDS_variant 2 B129,B91
Chr1:1118652 C T EMS_canonical_SNV CDS_variant 1 B10

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_057789598.1
1536 aa
N
1
768
1536
RVT_1
zf-RVT
RVT_3
C
PF00078 RVT_1 414-673 aa PF13966 zf-RVT 931-1010 aa PF13456 RVT_3 1140-1208 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057789598.1 Pfam PF00078 RVT_1 Domain 414 673 5.1e-27 95.8 Reverse transcriptase (RNA-dependent DNA polymerase)
XP_057789598.1 Pfam PF13966 zf-RVT Domain 931 1010 2e-16 61.1 zinc-binding in reverse transcriptase
XP_057789598.1 Pfam PF13456 RVT_3 Domain 1140 1208 5.6e-07 30.2 Reverse transcriptase-like

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_057933615.1
ATGGTGGTTGTTGACTGTCTTTGGAATAACCACAGGTTCTCGGTAGCAATTGTTCATGGTTCTAATGACTATATACAAAGGCGTCATCTTTGGAGGGACATTCTTGGTTTGGATACTGGCCCTACTATTGTTGCTGGAGATTTTAATGCCGTTAAAGGCGCTCATGAGCGTAGCAGTGATTGTCTTCCGAATGCGGCTTCCTGTCAGGATTTCTGTGAGTTCATTGCGATGTCTAGACTGATTGAATCGCCGTCTATGGG...

CDS

1 records

Download CDS FASTA
LOC131006455
ATGGTGGTTGTTGACTGTCTTTGGAATAACCACAGGTTCTCGGTAGCAATTGTTCATGGTTCTAATGACTATATACAAAGGCGTCATCTTTGGAGGGACATTCTTGGTTTGGATACTGGCCCTACTATTGTTGCTGGAGATTTTAATGCCGTTAAAGGCGCTCATGAGCGTAGCAGTGATTGTCTTCCGAATGCGGCTTCCTGTCAGGATTTCTGTGAGTTCATTGCGATGTCTAGACTGATTGAATCGCCGTCTATGGG...

Protein

1 records

Download Protein FASTA
XP_057789598.1
MVVVDCLWNNHRFSVAIVHGSNDYIQRRHLWRDILGLDTGPTIVAGDFNAVKGAHERSSDCLPNAASCQDFCEFIAMSRLIESPSMGLKFTWSGRKFMPSHVESLLDRVLYSKDFAYLWNSIYTQNLPRLTSDHSPIVLRCVNNQQGGPRFFKFLHMWTMHSSFQDFVRSSWMKGVDTRCPIYLVMVKLKRLREELKTWNKTVFGNVDIMVSDTQKELLEIQNHIATSGYTPDLFDQEVTMQAKVGTALARKNALLQQKC...

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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