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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

SmilChr05G000748

Chromosome: Chr05 Coordinates: 5797285-5801799 Strand: + Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr05G000748
NameSmilChr05G000748
Descriptionribosome biogenesis protein NOP53
Chromosome / SeqIDChr05 / NC_080391.1
Coordinates and Strand5797285 - 5801799 / +

ID Mapping

NCBI Gene IDLOC130985462
GeneID130985462
locus_tag-
NCBI NameLOC130985462
Original querySmilChr05G000748

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionribosome biogenesis protein NOP53
Productribosome biogenesis protein NOP53
ArabidopsisAT2G40430 (AT2G40430)
Nop53 protein [Source:NCBI gene (formerly Entrezgene);Acc:818636]
identity=53.1; qcov=0.648; evalue=4.46e-73; confidence=high
RiceOs05g0144200
-
identity=57.5; qcov=1.04; evalue=7.59e-142; confidence=high
GOGO:0000027 (ribosomal large subunit assembly); GO:0005730 (nucleolus); GO:0006364 (rRNA processing); GO:0008097 (5S rRNA binding)
KEGG-
PfamPF07767 (Nop53)
InterPro-
eggNOG-
NRGeneID:130985462

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Nucleus 细胞核 1.00000 XP_057764430.1
2 Nucleolus 核仁 1.00000 XP_057764430.1
3 Nucleolus rim Nucleolus rim 0.20000 XP_057764430.1
4 Chromosome 染色体 0.00000 XP_057764430.1
5 Centromere 着丝粒 0.00000 XP_057764430.1

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
Chr5:5799264 C T EMS_canonical_SNV CDS_variant 4 B1,B7,C11,C69
Chr5:5799418 C T EMS_canonical_SNV CDS_variant 1 B82
Chr5:5799458 C T EMS_canonical_SNV CDS_variant 1 C35
Chr5:5799474 C T EMS_canonical_SNV CDS_variant 1 B88
Chr5:5800283 G A EMS_canonical_SNV CDS_variant 1 D10

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_057764430.1
372 aa
N
1
186
372
Nop53
C
PF07767 Nop53 8-357 aa
XP_057764433.1
372 aa
N
1
186
372
Nop53
C
PF07767 Nop53 8-357 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057764430.1 Pfam PF07767 Nop53 Family 8 357 3.2e-65 221.7 Nop53 (60S ribosomal biogenesis)
XP_057764433.1 Pfam PF07767 Nop53 Family 8 357 3.2e-65 221.7 Nop53 (60S ribosomal biogenesis)

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

2 records

Download cDNA FASTA
XM_057908447.1
ATGGGTTAGAAACCCTTTTCAAAAGCGGCATTTCTATCTTCGCAGCGTCTTCTTCTATATGCGTTTTGCGTCCGCCTCTTTCGGTCGCCGTCGCCAGCCTCGCTTCGCCTAGGAATCTCTGCAGAAGCAGCCTGTGCCCCACCTCGTCTCAGTGCGCCGCTTCACGCTCCAGCATTTCCCGTCGTCAGGCCTCCTTCGACCTCGGCGCAGAACCAGCATCAACGCCGCCCCCCAGCCAAACAGCCGGGCCAACAGCAGGC...
XM_057908450.1
CGGCATTTCTATCTTCGCAGCGTCTTCTTCTATATGCGTTTTGCGTCCGCCTCTTTCGGTCGCCGTCGCCAGCCTCGCTTCGCCTAGGAATCTCTGCAGAAGCAGCCTGTGCCCCACCTCGTCTCAGTGCGCCGCTTCACGCTCCAGCATTTCCCGTCGTCAGGCCTCCTTCGACCTCGGCGCAGAACCAGCATCAACGCCGCCCCCCAGCCAAACAGCCGGGCCAACAGCAGTGCCGCAGGCTTCTCTATTTCGTGAGA...

CDS

2 records

Download CDS FASTA
LOC130985462
ATGGGTAAGAGAGCCAAGAGTTCAAGGAAGGGAAAGAAAGAATGGAGGGCTAACATAAGCACTGAAGATATAGAAGATTATTTTGAGAAATCCACAAAAGACGCTCTTTCCGGTGGTTCTTTGGCTGATGTGCCCAGTGATTCTCTTTTCTTCGTTGATAAATCCAGAGATCTTTCTATTAAGCGGAAGATTGAGAAAAACAGAGAGAAAGTATTGCGATGTGATAGTCTGTTGCAGAGAAACCCTTTTATTAAAGCTAT...
LOC130985462
ATGGGTAAGAGAGCCAAGAGTTCAAGGAAGGGAAAGAAAGAATGGAGGGCTAACATAAGCACTGAAGATATAGAAGATTATTTTGAGAAATCCACAAAAGACGCTCTTTCCGGTGGTTCTTTGGCTGATGTGCCCAGTGATTCTCTTTTCTTCGTTGATAAATCCAGAGATCTTTCTATTAAGCGGAAGATTGAGAAAAACAGAGAGAAAGTATTGCGATGTGATAGTCTGTTGCAGAGAAACCCTTTTATTAAAGCTAT...

Protein

2 records

Download Protein FASTA
XP_057764430.1
MGKRAKSSRKGKKEWRANISTEDIEDYFEKSTKDALSGGSLADVPSDSLFFVDKSRDLSIKRKIEKNREKVLRCDSLLQRNPFIKAIPSSIQNKKKSKRKGKALPTAADENVAQGSLKDESAHDSGVLDLWEEKGEVKAKIKKKPKSCVIPAVEVEHPGCSFNPHPESHQDALARAVADEMQKIYQHELGPQPIPLVVPGEAIDEEYKYFLEADADDGTDEDDDEQSENQADDADVDAEKSSQKTKRVTRVEFNRRARRK...
XP_057764433.1
MGKRAKSSRKGKKEWRANISTEDIEDYFEKSTKDALSGGSLADVPSDSLFFVDKSRDLSIKRKIEKNREKVLRCDSLLQRNPFIKAIPSSIQNKKKSKRKGKALPTAADENVAQGSLKDESAHDSGVLDLWEEKGEVKAKIKKKPKSCVIPAVEVEHPGCSFNPHPESHQDALARAVADEMQKIYQHELGPQPIPLVVPGEAIDEEYKYFLEADADDGTDEDDDEQSENQADDADVDAEKSSQKTKRVTRVEFNRRARRK...

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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