TkA01G390700 | RubberDandelionOmics

Gene overview

TkA01G390700

Reference: TK1151 Chr: Chr01 Coordinates: 97559014-97560883 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1042 bp · TkA01G390700|TK1151|cDNA

TTGCTCTTAGCTTTTTCTTATCTGTTACATGAGTTAACGGCGGTTAACTATTTGTAATGGTGAACCTAAAAACAACCCGACACGAAAGGAAACACTCACATTTGCAAGCTTCAAAACCAGTCAGCCGTGCTAGAAGAGTCAACCATGGTGCATAAGAAGGCGATGGAACCGGCGGCGAAGGAGCAGAAGAGCCGGAAGCTGAGTAACGTGGAGCGTTCTTCATACTTCGCCCGCCGAGAGGCGGCTAAGGTCTTGAAGAG...

CDS

Download CDS FASTA

597 bp · TkA01G390700|TK1151|CDS

ATGATGTACATAATCACATATGACATTCTTTTTGGACAGGATGCATCTCTAACAGGAGATCCAGAAAAGTACCTTATTTTAAGGAAAAGTCAACTACAGTCAGCTCTAGCAAAGATTCTAGCAAAGAAGGGAGCAAAACGTATAGAAGATTTGATGGCTCAGTACAAGATTCCTTTCTCCGATGTTAAAAAACCTCGATACGTCCGAGTCAACACTCTGAAATTGGACGTTGAAACTGCTATTCTTGAACTTAGCAAAAG...

Protein

Download Protein FASTA

198 aa · TkA01G390700|TK1151|PROTEIN

MMYIITYDILFGQDASLTGDPEKYLILRKSQLQSALAKILAKKGAKRIEDLMAQYKIPFSDVKKPRYVRVNTLKLDVETAILELSKRIRVEKDDMIPDLLVLPPGTDLHNHPLVTEGKVFMQGKASSMVAVALAPKPGWEVIDACASPGNKTVHVAAVMKGEGKIIACELNKDRVKRLEHTHKVGGSHQYPYITLFSH

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	`TkA01G390700`
TK1151 ID	TkA01G390700
OH-1004 ID	LXL04_037286
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	37.500
Protein coverage (%)	TK1151 36.364 / OH-1004 13.662 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	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA01G390700

Location Chr01:97559014-97560883 (+)

Description Similar to rsmB: Probable ribosomal RNA small subunit methyltransferase B (Bacillus subtilis (strain 168)

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g26180`	May methylate the C5 position of cytosine 2268 in 25S rRNA.	Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae.2015 · DOI: 10.1186/s12870-015-0580-8

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_037286 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

GO annotations (OH1004 source)

GO:0001510 RNA methylation Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0070475 rRNA base methylation Biological Process

GO:0005737 cytoplasm Cellular Component

GO:0005829 cytosol Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0008649 rRNA methyltransferase activity Molecular Function

GO:0009383 rRNA (cytosine-C5-)-methyltransferase activity Molecular Function

KEGG gene cross-reference

bsu:BSU15740

syn:slr0679

ypg:YpAngola_A0613

ypo:BZ17_2920

yps:YPTB3667

ypy:YPK_0314

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

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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.

Cytoplasm0.535

Rank 1 · TkA01G390700 · TK1151

Nucleus0.300

Rank 2 · TkA01G390700 · TK1151

Mitochondrion0.129

Rank 3 · TkA01G390700 · TK1151

Plastid0.061

Rank 4 · TkA01G390700 · TK1151

Peroxisome0.053

Rank 5 · TkA01G390700 · TK1151

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

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

PF21153NSUN5_N4-52 aa

PF01728FtsJ29-46 aa

PF02515CoA_transf_329-68 aa

PF22458RsmF-B_ferredox63-103 aa

PF21148NSUN5_fdxn-like65-85 aa

PF21148NSUN5_fdxn-like90-122 aa

PF21801ASPP2-like_RA119-169 aa

PF01189Methyltr_RsmB-F131-182 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G390700	`PF21153`	NSUN5_N	4	52	3e-05	25.3
TkA01G390700	`PF01728`	FtsJ	29	46	0.027	15.1
TkA01G390700	`PF02515`	CoA_transf_3	29	68	0.07	13.0
TkA01G390700	`PF22458`	RsmF-B_ferredox	63	103	0.018	15.9
TkA01G390700	`PF21148`	NSUN5_fdxn-like	65	85	2.6e-13	50.9
TkA01G390700	`PF21148`	NSUN5_fdxn-like	90	122	2.6e-13	50.9
TkA01G390700	`PF21801`	ASPP2-like_RA	119	169	0.016	15.8
TkA01G390700	`PF01189`	Methyltr_RsmB-F	131	182	6.7e-12	46.2
TkA01G390700	`PF01209`	Ubie_methyltran	132	189	0.049	13.7
TkA01G390700	`PF01728`	FtsJ	136	176	0.027	15.1

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q8GYE8`	Arabidopsis thaliana	sp\|Q8GYE8\|NSUN5_ARATH 25S rRNA (cytosine-C(5))-methyltransferase NSUN5	56.700%	Swiss-Prot	High

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