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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

SmilChr04G000583

Chromosome: Chr04 Coordinates: 6473034-6479637 Strand: + Biotype: protein_coding

Basic Information

Standard Gene IDSmilChr04G000583
NameSmilChr04G000583
Descriptionribosome biogenesis protein WDR12 homolog
Chromosome / SeqIDChr04 / NC_080390.1
Coordinates and Strand6473034 - 6479637 / +

ID Mapping

NCBI Gene IDLOC131022464
GeneID131022464
locus_tag-
NCBI NameLOC131022464
Original querySmilChr04G000583

Open ID mapping

Functional Annotation

SourceGFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Descriptionribosome biogenesis protein WDR12 homolog
Productribosome biogenesis protein WDR12 homolog
ArabidopsisAT5G15550 (AT5G15550)
Transducin/WD40 repeat-like superfamily protein [Source:NCBI gene (formerly Entrezgene);Acc:831408]
identity=58.3; qcov=1.12; evalue=0; confidence=high
RiceOs07g0600400 (OsWD40-147)
-
identity=53; qcov=1.11; evalue=2.26e-157; confidence=high
GOGO:0005515 (protein binding); GO:0030687 (preribosome, large subunit precursor); GO:0042254 (ribosome biogenesis)
KEGG-
PfamPF00400 (WD40); PF08154 (NLE)
InterPro-
eggNOG-
NRGeneID:131022464

Open annotation module

Subcellular Localization Top 5

RankLocationChineseScoreProtein ID
1 Nucleus 细胞核 1.00000 XP_057807935.1
2 Cytoplasm 细胞质 0.60000 XP_057807935.1
3 Nucleolus 核仁 0.20000 XP_057807935.1
4 Chromosome 染色体 0.00000 XP_057807935.1
5 Centromere 着丝粒 0.00000 XP_057807935.1

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
Chr4:6473411 CA C 1bp_deletion frameshift_variant 1 A10
Chr4:6473411 CA C 1bp_deletion CDS_variant 1 A10
Chr4:6473420 G A EMS_canonical_SNV CDS_variant 1 A18
Chr4:6473424 G A EMS_canonical_SNV CDS_variant 3 B38,B39,C13
Chr4:6473624 C T EMS_canonical_SNV CDS_variant 1 B114
Chr4:6474306 G A EMS_canonical_SNV CDS_variant 1 B47
Chr4:6474713 C T EMS_canonical_SNV CDS_variant 1 B114
Chr4:6475306 C T EMS_canonical_SNV CDS_variant 4 A13,B140,B70,C13
Chr4:6475342 G A EMS_canonical_SNV CDS_variant 4 B31,B41,B66,C79
Chr4:6475513 C T EMS_canonical_SNV CDS_variant 1 B49
Chr4:6477683 C T EMS_canonical_SNV CDS_variant 4 B31,B41,B66,C79
Chr4:6477810 C T EMS_canonical_SNV CDS_variant 1 B114

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_057807935.1
436 aa
N
1
218
436
NLE
WD40
WD40
WD40
WD40
WD40
C
PF08154 NLE 14-81 aa PF00400 WD40 111-138 aa PF00400 WD40 143-185 aa PF00400 WD40 201-237 aa PF00400 WD40 266-302 aa PF00400 WD40 352-390 aa
XP_057807936.1
436 aa
N
1
218
436
NLE
WD40
WD40
WD40
WD40
WD40
C
PF08154 NLE 14-81 aa PF00400 WD40 111-138 aa PF00400 WD40 143-185 aa PF00400 WD40 201-237 aa PF00400 WD40 266-302 aa PF00400 WD40 352-390 aa
XP_057807937.1
436 aa
N
1
218
436
NLE
WD40
WD40
WD40
WD40
WD40
C
PF08154 NLE 14-81 aa PF00400 WD40 111-138 aa PF00400 WD40 143-185 aa PF00400 WD40 201-237 aa PF00400 WD40 266-302 aa PF00400 WD40 352-390 aa
XP_057807938.1
436 aa
N
1
218
436
NLE
WD40
WD40
WD40
WD40
WD40
C
PF08154 NLE 14-81 aa PF00400 WD40 111-138 aa PF00400 WD40 143-185 aa PF00400 WD40 201-237 aa PF00400 WD40 266-302 aa PF00400 WD40 352-390 aa
XP_057807939.1
436 aa
N
1
218
436
NLE
WD40
WD40
WD40
WD40
WD40
C
PF08154 NLE 14-81 aa PF00400 WD40 111-138 aa PF00400 WD40 143-185 aa PF00400 WD40 201-237 aa PF00400 WD40 266-302 aa PF00400 WD40 352-390 aa
XP_057807940.1
436 aa
N
1
218
436
NLE
WD40
WD40
WD40
WD40
WD40
C
PF08154 NLE 14-81 aa PF00400 WD40 111-138 aa PF00400 WD40 143-185 aa PF00400 WD40 201-237 aa PF00400 WD40 266-302 aa PF00400 WD40 352-390 aa
XP_057807941.1
388 aa
N
1
194
388
NLE
WD40
WD40
WD40
WD40
C
PF08154 NLE 14-81 aa PF00400 WD40 111-138 aa PF00400 WD40 143-185 aa PF00400 WD40 201-237 aa PF00400 WD40 304-342 aa
Protein ID Source Domain ID Domain name Type Start aa End aa E-value Score Description
XP_057807935.1 Pfam PF08154 NLE Domain 14 81 1e-20 74.7 NLE (NUC135) domain
XP_057807935.1 Pfam PF00400 WD40 Repeat 111 138 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807935.1 Pfam PF00400 WD40 Repeat 143 185 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807935.1 Pfam PF00400 WD40 Repeat 201 237 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807935.1 Pfam PF00400 WD40 Repeat 266 302 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807935.1 Pfam PF00400 WD40 Repeat 352 390 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807936.1 Pfam PF08154 NLE Domain 14 81 1e-20 74.7 NLE (NUC135) domain
XP_057807936.1 Pfam PF00400 WD40 Repeat 111 138 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807936.1 Pfam PF00400 WD40 Repeat 143 185 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807936.1 Pfam PF00400 WD40 Repeat 201 237 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807936.1 Pfam PF00400 WD40 Repeat 266 302 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807936.1 Pfam PF00400 WD40 Repeat 352 390 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807937.1 Pfam PF08154 NLE Domain 14 81 1e-20 74.7 NLE (NUC135) domain
XP_057807937.1 Pfam PF00400 WD40 Repeat 111 138 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807937.1 Pfam PF00400 WD40 Repeat 143 185 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807937.1 Pfam PF00400 WD40 Repeat 201 237 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807937.1 Pfam PF00400 WD40 Repeat 266 302 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807937.1 Pfam PF00400 WD40 Repeat 352 390 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807938.1 Pfam PF08154 NLE Domain 14 81 1e-20 74.7 NLE (NUC135) domain
XP_057807938.1 Pfam PF00400 WD40 Repeat 111 138 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807938.1 Pfam PF00400 WD40 Repeat 143 185 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807938.1 Pfam PF00400 WD40 Repeat 201 237 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807938.1 Pfam PF00400 WD40 Repeat 266 302 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807938.1 Pfam PF00400 WD40 Repeat 352 390 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807939.1 Pfam PF08154 NLE Domain 14 81 1e-20 74.7 NLE (NUC135) domain
XP_057807939.1 Pfam PF00400 WD40 Repeat 111 138 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807939.1 Pfam PF00400 WD40 Repeat 143 185 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807939.1 Pfam PF00400 WD40 Repeat 201 237 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807939.1 Pfam PF00400 WD40 Repeat 266 302 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807939.1 Pfam PF00400 WD40 Repeat 352 390 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807940.1 Pfam PF08154 NLE Domain 14 81 1e-20 74.7 NLE (NUC135) domain
XP_057807940.1 Pfam PF00400 WD40 Repeat 111 138 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807940.1 Pfam PF00400 WD40 Repeat 143 185 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807940.1 Pfam PF00400 WD40 Repeat 201 237 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807940.1 Pfam PF00400 WD40 Repeat 266 302 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807940.1 Pfam PF00400 WD40 Repeat 352 390 4.5e-35 119.3 WD domain, G-beta repeat
XP_057807941.1 Pfam PF08154 NLE Domain 14 81 8.3e-21 74.9 NLE (NUC135) domain
XP_057807941.1 Pfam PF00400 WD40 Repeat 111 138 5.3e-29 100.1 WD domain, G-beta repeat
XP_057807941.1 Pfam PF00400 WD40 Repeat 143 185 5.3e-29 100.1 WD domain, G-beta repeat
XP_057807941.1 Pfam PF00400 WD40 Repeat 201 237 5.3e-29 100.1 WD domain, G-beta repeat
XP_057807941.1 Pfam PF00400 WD40 Repeat 304 342 5.3e-29 100.1 WD domain, G-beta repeat

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
XM_057951958.1
TTCTCTCGAATTCATTTCCATTTCTCCTTTCCTCTCTCATTTTTTCCACATAGGAAAAATGACATCTTCTTCTTCGTCTTCTTCATCCTTCCCACATACCAAAACGACTTTATTTTCCCCTTCTTCTTCGTCCGATGGAGACTTCGAGAGAATTGTGGAAATGATTGTCGATATGCAAACGATTGTCAAAGAACATTTCATCAACCAAGCACCCGAAAGAAGGATATTCACCGACACGACATTTCATCAACCTGCCCTCT...
XM_057951952.1
TCTCGAATTCATTTCCATTTCTCCTTTCCTCTCTCATTTTTTCCACATAGGAAAAATGACATCTTCTTCTTCGTCTTCTTCATCCTTCCCACATACCAAAACGACTTTATTTTCCCCTTCTTCTTCGTCCGATGGAGACTTCGAGAGAATTGTGGAAATGATTGTCGATATGCAAACGATTGTCAAAGAACATTTCATCAACCAAGCACCCGAAAGAAGGATATTCACCGACACGACATTTCATCAACCTGCCCTCTCTC...

CDS

7 records

Download CDS FASTA
LOC131022464
ATGGATATTCACCCAGACGAAGAAGGAGAAGCTAAGCAGGTTCAAGTGCGCTTCATAACGAAGCTACAACAGCCGTACAAAGTGCAGCAAGCTTCTATCTCCATACCTGCCAATCTCACTCGCTTCGGCCTCTCTGCACTCGTCAACAATCTCCTCCTCACATCGAATGCGGATTGGACAACGGAGCCTTTTGATTTTCTCATTGATGGAGAGCTGGTTCGCATGTCACTTGAAGAGTTCCTTCTTGCCAAAGGCATTTC...
LOC131022464
ATGGATATTCACCCAGACGAAGAAGGAGAAGCTAAGCAGGTTCAAGTGCGCTTCATAACGAAGCTACAACAGCCGTACAAAGTGCAGCAAGCTTCTATCTCCATACCTGCCAATCTCACTCGCTTCGGCCTCTCTGCACTCGTCAACAATCTCCTCCTCACATCGAATGCGGATTGGACAACGGAGCCTTTTGATTTTCTCATTGATGGAGAGCTGGTTCGCATGTCACTTGAAGAGTTCCTTCTTGCCAAAGGCATTTC...

Protein

7 records

Download Protein FASTA
XP_057807935.1
MDIHPDEEGEAKQVQVRFITKLQQPYKVQQASISIPANLTRFGLSALVNNLLLTSNADWTTEPFDFLIDGELVRMSLEEFLLAKGISAEKVLEIEYIKAVAPRNQEEPSLHDDWVSAVDGSNDGYILTGCYDDLGRVWKAGGICTHVLDGHSGPLTSVCNLMPKVDSIVGQVVATGSKDRTLRLWKFGEEDPIDQTKKIRSVKVLRGHTDAVQSIAAIPSGDVVCSGSWDCTINLWNTTANDPEDSVSVKKRKKGGQDKE...
XP_057807936.1
MDIHPDEEGEAKQVQVRFITKLQQPYKVQQASISIPANLTRFGLSALVNNLLLTSNADWTTEPFDFLIDGELVRMSLEEFLLAKGISAEKVLEIEYIKAVAPRNQEEPSLHDDWVSAVDGSNDGYILTGCYDDLGRVWKAGGICTHVLDGHSGPLTSVCNLMPKVDSIVGQVVATGSKDRTLRLWKFGEEDPIDQTKKIRSVKVLRGHTDAVQSIAAIPSGDVVCSGSWDCTINLWNTTANDPEDSVSVKKRKKGGQDKE...

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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