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.

Resolved gene

`SmilChr03G004327`

Chromosome: Chr03 Coordinates: 61619444-61630075 Strand: - Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr03G004327`
Name	SmilChr03G004327
Description	uncharacterized SmilChr03G004327
Chromosome / SeqID	Chr03 / NC_080389.1
Coordinates and Strand	61619444 - 61630075 / `-`

ID Mapping

NCBI Gene ID	`LOC131015283`
GeneID	`131015283`
locus_tag	`-`
NCBI Name	`LOC131015283`
Original query	`SmilChr03G004327`

Open ID mapping

Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	hit=Os08g0315200; species=rice; confidence=medium
Product	hit=Os08g0315200; species=rice; confidence=medium
Arabidopsis	`-` -
Rice	`Os08g0315200` - identity=35.1; qcov=0.484; evalue=1.64e-27; confidence=medium
GO	GO:0003676 (nucleic acid binding); GO:0008270 (zinc ion binding)
KEGG	-
Pfam	PF00098 (zf-CCHC); PF03732 (PEG10_N-capsid); PF19259 (Ty3_capsid)
InterPro	-
eggNOG	-
NR	GeneID:131015283

Open annotation module

Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Cytoplasm	细胞质	0.80000	`XP_057799613.1`
2	Nucleus	细胞核	0.60000	`XP_057799613.1`
3	Cytoplasmic granule	细胞质颗粒	0.20000	`XP_057799613.1`
4	Cytoplasmic ribonucleoprotein granule	Cytoplasmic ribonucleoprotein granule	0.20000	`XP_057799613.1`
5	Cytosol	细胞质基质	0.20000	`XP_057799613.1`

Open subcellular search

EMS Mutant Variants

No curated EMS CDS / LoF variants are available for this gene yet, or the EMS database is still building.

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_057799613.1

347 aa

174

347

Ty3_capsid

PEG10_N-capsid

zf-CCHC

PF19259 Ty3_capsid 62-224 aa PF03732 PEG10_N-capsid 63-141 aa PF00098 zf-CCHC 322-338 aa

XP_057799614.1

347 aa

174

347

Ty3_capsid

PEG10_N-capsid

zf-CCHC

PF19259 Ty3_capsid 62-224 aa PF03732 PEG10_N-capsid 63-141 aa PF00098 zf-CCHC 322-338 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057799613.1`	Pfam	`PF19259`	Ty3_capsid	Domain	62	224	2.1e-08	34.6	Ty3 transposon capsid-like protein
`XP_057799613.1`	Pfam	`PF03732`	PEG10_N-capsid	Domain	63	141	2.2e-14	54.3	Retrotransposon-derived protein PEG10, N-terminal capsid-like domain
`XP_057799613.1`	Pfam	`PF00098`	zf-CCHC	Domain	322	338	9.4e-06	26.2	Zinc knuckle
`XP_057799614.1`	Pfam	`PF19259`	Ty3_capsid	Domain	62	224	2.1e-08	34.6	Ty3 transposon capsid-like protein
`XP_057799614.1`	Pfam	`PF03732`	PEG10_N-capsid	Domain	63	141	2.2e-14	54.3	Retrotransposon-derived protein PEG10, N-terminal capsid-like domain
`XP_057799614.1`	Pfam	`PF00098`	zf-CCHC	Domain	322	338	9.4e-06	26.2	Zinc knuckle

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

7 records

Download cDNA FASTA

XR_009098486.1
ATTATTGAGCCATTCAATAATTATTATTTTCAAGTTATAACTGACTTAGCAAAGTCATGTTATTTATTAATCGAGAAACGGAAGCAGTTATATTTTATTAATGCTACTAGAAGTCGAGGATTTATTTCCGACAGCAAAGCAGATTAAATCTACGGATTTAATTTAAGTTATATTATAGTTTATCAAGTTAGCAGGCAAGGAAAAAAATATCAAACAGATACAATAACGGATGATAGAGAATAGAAGCCAGTATTTTATTA...

XR_009098483.1
ATTATTGAGCCATTCAATAATTATTATTTTCAAGTTATAACTGACTTAGCAAAGTCATGTTATTTATTAATCGAGAAACGGAAGCAGTTATATTTTATTAATGCTACTAGAAGTCGAGGATTTATTTCCGACAGCAAAGCAGATTAAATCTACGGATTTAATTTAAGTTATATTATAGTTTATCAAGTTAGCAGGCAAGGAAAAAAATATCAAACAGATACAATAACGGATGATAGAGAATAGAAGCCAGTATTTTATTA...

CDS

2 records

Download CDS FASTA

LOC131015283
ATGCTAGAGTGTACTAATTGGCACATCTTTGCTATCAGAATGCCGCCTAAGAGAGGACGCCCTGCGAAAAACAATAACAATCGCAGAAACCGTAACGCTGTACCCGAAGAACCACAAGATGCTCGAGGACATAACCCATCCCCTCCGCCTCCGACTAGGAGAGTCGAAGAACTCTTTTTAAGGCAAAATCCACCTACGTTTGACGGAACGAGTGAACCGGCTGAAGCTGAGATTTGGGTGCGTGCAATGGAACGCATTTT...

Protein

2 records

Download Protein FASTA

XP_057799613.1
MLECTNWHIFAIRMPPKRGRPAKNNNNRRNRNAVPEEPQDARGHNPSPPPPTRRVEELFLRQNPPTFDGTSEPAEAEIWVRAMERIFNFLRCNDEERLSCVSFQLTGSADFWWEARRKILTPEQWASYTWEDFKTGLYDKYIPKSYRKKKEAEFYELKQGKKSVVEYDKEFCNLSRFAPQQVDTDEKMAEKFCAGLRYEIKMALASHGGLSYTESLNRALDIEAAMPSDKSAPPLISTPNDLPGALHTLKGKRKWDNNED...

XP_057799614.1
MLECTNWHIFAIRMPPKRGRPAKNNNNRRNRNAVPEEPQDARGHNPSPPPPTRRVEELFLRQNPPTFDGTSEPAEAEIWVRAMERIFNFLRCNDEERLSCVSFQLTGSADFWWEARRKILTPEQWASYTWEDFKTGLYDKYIPKSYRKKKEAEFYELKQGKKSVVEYDKEFCNLSRFAPQQVDTDEKMAEKFCAGLRYEIKMALASHGGLSYTESLNRALDIEAAMPSDKSAPPLISTPNDLPGALHTLKGKRKWDNNED...

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.

Download upstream Download downstream Download upstream + gene + downstream

JBrowse

Open genome browser