LXL04_017946 | RubberDandelionOmics

Gene overview

LXL04_017946

Reference: OH-1004 Chr: Chr04 Coordinates: 4147826-4149346 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

891 bp · LXL04_017946|LXL04_017946|OH1004|cDNA

ATGTCGTCGAGGCCGGAGTTACAAGCACCACCTGAGATATTCTACGACGATGTTGAAGCTCGAAAATACACTTCATCCTCTCGTATAGTCGGAATTCAGGCAGAGCTTTCTGAAAGAGCACTAGAGCTTCTCGCGTTACCTGACGATGACGTCCCTAGATTGCTTCTTGACATTGGTTGTGGTTCCGGACTTAGTGGCGAAACAATATCCGAGAACGGACATGAATGGATTGGTCTCGATATATCACGATCAATGCTTGA...

CDS

Download CDS FASTA

891 bp · LXL04_017946|LXL04_017946|OH1004|CDS

ATGTCGTCGAGGCCGGAGTTACAAGCACCACCTGAGATATTCTACGACGATGTTGAAGCTCGAAAATACACTTCATCCTCTCGTATAGTCGGAATTCAGGCAGAGCTTTCTGAAAGAGCACTAGAGCTTCTCGCGTTACCTGACGATGACGTCCCTAGATTGCTTCTTGACATTGGTTGTGGTTCCGGACTTAGTGGCGAAACAATATCCGAGAACGGACATGAATGGATTGGTCTCGATATATCACGATCAATGCTTGA...

Protein

Download Protein FASTA

296 aa · LXL04_017946|LXL04_017946|OH1004|PROTEIN

MSSRPELQAPPEIFYDDVEARKYTSSSRIVGIQAELSERALELLALPDDDVPRLLLDIGCGSGLSGETISENGHEWIGLDISRSMLDVALERETDGDLILGDMGQGLGLRPGVIDGAISISAVQWLCNADKSCHEPRLRLKAFFGSLYRCLGRGARAVFQLYPENNAQRELILSFAMRAGFAGGVVIDYPHSSKKRKEYLVLTCGPPSMSTTTPSGKGVEENSCSDDGSSEDDDDDDEDNQAVCISDRHRPRKKQKMTKK...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

ID Mapping

Input ID	`LXL04_017946`
TK1151 ID	TkA08G037570
OH-1004 ID	LXL04_017946
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 100.000 / OH-1004 100.000 Coverage and evidence Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_017946

Location Chr04:4147826-4149346 (+)

Description Similar to RID2: 18S rRNA (guanine-N(7))-methyltransferase RID2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g57280`	Essential protein.	Genetic analysis of adventitious root formation with a novel series of temperature-sensitive mutants of Arabidopsis thaliana.2003 · DOI: 10.1242/dev.00794 Genetic identification of Arabidopsis RID2 as an essential factor involved in pre-rRNA processing.2011 · DOI: 10.1111/j.1365-313x.2011.04574.x

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_017946 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006325 chromatin organization Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006364 rRNA processing Biological Process

GO:0010078 maintenance of root meristem identity Biological Process

GO:0048364 root development Biological Process

GO:0048527 lateral root development Biological Process

GO:0070476 rRNA (guanine-N7)-methylation Biological Process

GO:2000234 positive regulation of rRNA processing Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

GO:0043527 tRNA methyltransferase complex Cellular Component

KEGG gene cross-reference

ath:AT5G57280

bta:513878

ddi:DDB_G0269722

hsa:114049

mmu:66138

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene

Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.798

Rank 1 · LXL04_017946 · OH-1004

Cytoplasm0.252

Rank 2 · LXL04_017946 · OH-1004

Mitochondrion0.038

Rank 3 · LXL04_017946 · OH-1004

Cell membrane0.033

Rank 4 · LXL04_017946 · OH-1004

Endoplasmic reticulum0.026

Rank 5 · LXL04_017946 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF08241.19Methyltransf_1156-151 aa

PF13649.13Methyltransf_2556-130 aa

PF12589.14WBS_methylT202-294 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017946	`PF08241.19`	Methyltransf_11	56	151	7.1e-09	36.9
LXL04_017946	`PF13649.13`	Methyltransf_25	56	130	5.7e-08	34.1
LXL04_017946	`PF12589.14`	WBS_methylT	202	294	3.2e-20	73.4

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`Q9LVD0`	Arabidopsis thaliana	18S rRNA (guanine-N(7))-methyltransferase RID2	72.973%	Swiss-Prot	strong database homology

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