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

`SmilChr03G000192`

Chromosome: Chr03 Coordinates: 2133929-2149729 Strand: + Biotype: protein_coding

Basic Information

Standard Gene ID	`SmilChr03G000192`
Name	SmilChr03G000192
Description	uncharacterized SmilChr03G000192
Chromosome / SeqID	Chr03 / NC_080389.1
Coordinates and Strand	2133929 - 2149729 / `+`

ID Mapping

NCBI Gene ID	`LOC131016881`
GeneID	`131016881`
locus_tag	`-`
NCBI Name	`LOC131016881`
Original query	`SmilChr03G000192`

Open ID mapping

Functional Annotation

Source	GFF basic annotation; NCBI GO GAF; Pfam-A/HMMER; Arabidopsis/Rice homolog
Description	Ribosomal RNA processing Brix domain protein [Source:NCBI gene (formerly Entrezgene);Acc:828136]; symbol=MEE49; hit=AT4G01560; species=arabidopsis; confidence=high
Product	Ribosomal RNA processing Brix domain protein [Source:NCBI gene (formerly Entrezgene);Acc:828136]; symbol=MEE49; hit=AT4G01560; species=arabidopsis; confidence=high
Arabidopsis	`AT4G01560` (MEE49) Ribosomal RNA processing Brix domain protein [Source:NCBI gene (formerly Entrezgene);Acc:828136] identity=77.7; qcov=0.727; evalue=0; confidence=high
Rice	`Os06g0137500` (P0548D03.36-1) - identity=74.5; qcov=0.725; evalue=0; confidence=high
GO	GO:0000460 (maturation of 5.8S rRNA); GO:0000470 (maturation of LSU-rRNA); GO:0005730 (nucleolus); GO:0030687 (preribosome, large subunit precursor); GO:0042134 (rRNA primary transcript binding)
KEGG	-
Pfam	PF04427 (Brix)
InterPro	-
eggNOG	-
NR	GeneID:131016881

Open annotation module

Subcellular Localization Top 5

Rank	Location	Chinese	Score	Protein ID
1	Nucleus	细胞核	1.00000	`XP_057801646.1`
2	Nucleolus	核仁	1.00000	`XP_057801646.1`
3	Nucleolus rim	Nucleolus rim	0.80000	`XP_057801646.1`
4	Nucleolar fibrillar center	Nucleolar fibrillar center	0.40000	`XP_057801646.1`
5	Nucleoplasm	核质	0.40000	`XP_057801646.1`

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
`Chr3:2133995`	`G`	`GT`	1bp_insertion	frameshift_variant	4	B3,B60,B92,C56
`Chr3:2133995`	`G`	`GT`	1bp_insertion	CDS_variant	4	B3,B60,B92,C56
`Chr3:2133999`	`AC`	`A`	1bp_deletion	frameshift_variant	6	B135,B22,B23,B6,B94,C48
`Chr3:2134004`	`AG`	`A`	1bp_deletion	frameshift_variant	112	A18,A2,A21,A24,A5,A9,B100,B101,B102,B103,B105,B107,B114,B117,B118,B123,B127,B129,B132,B134,B137,B139,B16,B17,B19,B2,B20,B27,B28,B31,B33,B34,B35,B38,B39,B40,B42,B43,B46,B49,B5,B50,B51,B52,B54,B55,B56,B59,B60,B62,B65,B66,B69,B70,B74,B75,B78,B81,B82,B85,B87,B9,B90,B92,B93,B96,B97,B98,B99,C10,C11,C14,C15,C16,C18,C2,C26,C3,C31,C38,C4,C49,C50,C52,C53,C54,C55,C56,C59,C60,C61,C63,C65,C67,C69,C7,C71,C75,C77,C79,C8,C82,C9,D1,D11,D2,D4,D5,D6,D7,D8,D9
`Chr3:2134007`	`T`	`TG`	1bp_insertion	frameshift_variant	1	B60
`Chr3:2134007`	`T`	`TG`	1bp_insertion	CDS_variant	1	B60
`Chr3:2134024`	`G`	`A`	EMS_canonical_SNV	CDS_variant	3	B132,B41,C10
`Chr3:2134052`	`TG`	`T`	1bp_deletion	frameshift_variant	1	A1
`Chr3:2134052`	`TG`	`T`	1bp_deletion	CDS_variant	1	A1
`Chr3:2134053`	`GT`	`G`	1bp_deletion	frameshift_variant	176	A1,A10,A11,A13,A14,A15,A16,A18,A19,A2,A22,A23,A24,A25,A4,A6,A7,A8,A9,B1,B10,B100,B101,B104,B106,B107,B108,B11,B110,B111,B112,B113,B118,B12,B120,B121,B127,B128,B13,B130,B131,B132,B133,B135,B136,B138,B14,B140,B15,B16,B17,B18,B2,B21,B22,B25,B26,B27,B29,B30,B31,B36,B37,B38,B39,B4,B41,B42,B43,B44,B46,B47,B48,B50,B51,B53,B54,B56,B57,B58,B59,B6,B60,B61,B66,B67,B69,B7,B72,B73,B74,B75,B77,B78,B79,B8,B80,B83,B84,B85,B86,B87,B88,B9,B94,B95,B97,C1,C10,C12,C13,C14,C17,C19,C2,C20,C21,C22,C23,C25,C26,C27,C29,C3,C30,C32,C33,C34,C35,C36,C37,C38,C40,C41,C42,C43,C44,C47,C48,C5,C51,C57,C58,C59,C6,C62,C63,C64,C66,C67,C68,C71,C73,C74,C75,C76,C77,C78,C79,C8,C80,C81,C83,C84,C85,C86,C87,C9,D10,D11,D2,D3,D5,D6,D8,D9
`Chr3:2134061`	`T`	`TC`	1bp_insertion	frameshift_variant	1	B91
`Chr3:2134061`	`T`	`TC`	1bp_insertion	CDS_variant	1	B91

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_057801646.1

455 aa

228

455

Brix

PF04427 Brix 238-424 aa

XP_057801648.1

444 aa

222

444

Brix

PF04427 Brix 227-413 aa

Protein ID	Source	Domain ID	Domain name	Type	Start aa	End aa	E-value	Score	Description
`XP_057801646.1`	Pfam	`PF04427`	Brix	Domain	238	424	3.2e-34	119.3	Brix domain
`XP_057801648.1`	Pfam	`PF04427`	Brix	Domain	227	413	3.1e-34	119.4	Brix domain

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_057945663.1
TAGTTTTTGGGTTAGATGCGGGTTAAAAGCGGGTTAGGGTACAATCCGGGTGTATGGTACACCCGGGTGTACCCAAGATCACCTCTTTTTCATTTGGTCAGGTCTAGTCCTTCCTCTTTTAATTGTTTTTTTTTTCTTTTTTTCATATATTGCTTACGTGGCGGTCGACCACTCCCAAAAATACTACCGATAAACTTGGTCTTACAGCCACCCCACCCGCCGCCGCTTCTCCCACCAACACCTGCCGCCCCGCCGCCCAT...

XM_057945665.1
TAGTTTTTGGGTTAGATGCGGGTTAAAAGCGGGTTAGGGTACAATCCGGGTGTATGGTACACCCGGGTGTACCCAAGATCACCTCTTTTTCATTTGGTCAGGTCTAGTCCTTCCTCTTTTAATTGTTTTTTTTTTCTTTTTTTCATATATTGCTTACGTGGCGGTCGACCACTCCCAAAAATACTACCGATAAACTTGGTCTTACAGCCACCCCACCCGCCGCCGCTTCTCCCACCAACACCTGCCGCCCCGTCGCCCAT...

CDS

2 records

Download CDS FASTA

LOC131016881
ATGCGGGTTAAAAGCGGGTTAGGGTACAATCCGGGTGTATGGTACACCCGGGTGTACCCAAGATCACCTCTTTTTCATTTGGTCAGGTCTAGTCCTTCCTCTTTTAATTGTTTTTTTTTTCTTTTTTTCATATATTGCTTACGTGGCGGTCGACCACTCCCAAAAATACTACCGATAAACTTGGTCTTACAGCCACCCCACCCGCCGCCGCTTCTCCCACCAACACCTGCCGCCCCGCCGCCCATTCTCCCACGCACCTC...

Protein

2 records

Download Protein FASTA

XP_057801646.1
MRVKSGLGYNPGVWYTRVYPRSPLFHLVRSSPSSFNCFFFLFFIYCLRGGRPLPKILPINLVLQPPHPPPLLPPTPAAPPPILPRTSVAPSPILPAVRRPPQSASRLNHLNGSAVDIKKAELKKYIKEKMKDREALLPSAIKNKEKRSAVHAKLKHQKKLEKKKKAKVREAEEKKALELGEEPPARPIPRTIENTRELDETVCKPDDEELFAGNDADEFSCILKEERTPKVLITTSRFHSSRGPAFIQELISVIPNAHYH...

XP_057801648.1
MRVKSGLGYNPGVWYTRVYPRSPLFHLVRSSPSSFNCFFFLFFIYCLRGGRPLPKILPINLVLQPPHPPPLLPPTPAAPSPILPAVRRPPQSASRLNHLNGSAVDIKKAELKKYIKEKMKDREALLPSAIKNKEKRSAVHAKLKHQKKLEKKKKAKVREAEEKKALELGEEPPARPIPRTIENTRELDETVCKPDDEELFAGNDADEFSCILKEERTPKVLITTSRFHSSRGPAFIQELISVIPNAHYHKRGTYDLKKIV...

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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