TkA04G174820 | RubberDandelionOmics

Gene overview

TkA04G174820

Reference: TK1151 Chr: Chr04 Coordinates: 45258134-45270054 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2261 bp · TkA04G174820|TK1151|cDNA

TCTTAGCTTTCGCTAACCTATTCTCACGCTTAAACCCTTCTTCGCCTTCTCCATCTTACAGCCGGCGCTAAATACTCTTCTCCATCTCCGCACCCGGCTTCTCCTGGACTCTGTCTACTTCAGTTCTCAAGCAGAGCAGCTGTAGGTTCAATGGCTGCGAAAGGCAAAATGTCTGAAAAGAAAGCAAGCAGAAAGGAGCAAAGTAAGGAGGCTGTTTCTGTGAAAAGTAAAAAGAAGAATGAGATTGTGAGCGAGTCTGA...

CDS

Download CDS FASTA

1722 bp · TkA04G174820|TK1151|CDS

ATGGCTGCGAAAGGCAAAATGTCTGAAAAGAAAGCAAGCAGAAAGGAGCAAAGTAAGGAGGCTGTTTCTGTGAAAAGTAAAAAGAAGAATGAGATTGTGAGCGAGTCTGATAGTGATGAAGGAGGGGATTCGGGGTCTGAATTGTCGTTGGATACATTGGGAGACGTATTCTCACAAGGCAGCGATGATGAAGATATGGGGTCGGGGTCAGGTTTGGATTCTGATTCTGATTCTGATGATGATGCTGAGAAGAAGTCAAA...

Protein

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573 aa · TkA04G174820|TK1151|PROTEIN

MAAKGKMSEKKASRKEQSKEAVSVKSKKKNEIVSESDSDEGGDSGSELSLDTLGDVFSQGSDDEDMGSGSGLDSDSDSDDDAEKKSKAIDEAKEMEEKEGEEELQLNIKEQPDEFRLPTHEELEEEARGPPDLTGLQQRIKEIVRILSNFGNLRQEGATRKEYVEQLKLDLGSYYGYNEFLISSFVEMFPPVELMELIEAFEKPRPVTLRTNTLKTRRRDLAGVLLNRGINLDPLSKWSKVGLVVYDHQVPYGATPEYMA...

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	`TkA04G174820`
TK1151 ID	TkA04G174820
OH-1004 ID	LXL04_035052
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	97.200
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	TK1151 / GWHBCHF00000000

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SNP / Indel variants and carrier samplesCRA009020 · TK1151

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Basic Information and Functional Annotation

Gene ID TkA04G174820

Location Chr04:45258134-45270054 (-)

Description Similar to NOP2B: 26S rRNA (cytosine-C(5))-methyltransferase NOP2B

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g26600`	Involved in ribosomal large subunit assembly (By similarity).	No verified direct reference in this release
`At5g55920`	Involved in ribosomal large subunit assembly, required for normal progression of rRNA processing.	Coordination of cell proliferation and cell expansion mediated by ribosome-related processes in the leaves of Arabidopsis thaliana.2009 · DOI: 10.1111/j.1365-313x.2009.03886.x Conservation of tRNA and rRNA 5-methylcytosine in the kingdom Plantae.2015 · DOI: 10.1186/s12870-015-0580-8 Two Nucleolar Proteins, GDP1 and OLI2, Function As Ribosome Biogenesis Factors and Are Preferentially Involved in Promotion of Leaf Cell Proliferation without Strongly Affecting Leaf Adaxial-Abaxial Patterning in Arabidopsis thaliana .2017 · DOI: 10.3389/fpls.2017.02240
`At5g57930`	May be involved in the stable assembly of several 4Fe-4S cluster-containing complexes of chloroplasts.	No verified direct reference in this release
`At1g64810`	Involved in the stable assembly of several 4Fe-4S cluster- containing complexes of chloroplasts.	ACCUMULATION OF PHOTOSYSTEM ONE1, a member of a novel gene family, is required for accumulation of [4Fe-4S] cluster-containing chloroplast complexes and antenna proteins.2004 · DOI: 10.1105/tpc.104.024935
`At5g61930`	May be involved in the stable assembly of several 4Fe-4S cluster-containing complexes of mitochondria.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_035052 · 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:0000027 ribosomal large subunit assembly Biological Process

GO:0000470 maturation of LSU-rRNA Biological Process

GO:0006364 rRNA processing Biological Process

GO:0008284 positive regulation of cell population proliferation Biological Process

GO:0009965 leaf morphogenesis Biological Process

GO:0010015 root morphogenesis Biological Process

GO:0040018 positive regulation of multicellular organism growth Biological Process

GO:0042127 regulation of cell population proliferation Biological Process

GO:0042273 ribosomal large subunit biogenesis Biological Process

GO:0045727 positive regulation of translation Biological Process

GO:0051301 cell division Biological Process

GO:0070475 rRNA base methylation Biological Process

KEGG gene cross-reference

ath:AT4G26600

ath:AT5G55920

cel:CELE_W07E6.1

hsa:4839

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.

Nucleus0.933

Rank 1 · TkA04G174820 · TK1151

Cytoplasm0.116

Rank 2 · TkA04G174820 · TK1151

Mitochondrion0.022

Rank 3 · TkA04G174820 · TK1151

Cell membrane0.021

Rank 4 · TkA04G174820 · TK1151

Endoplasmic reticulum0.013

Rank 5 · TkA04G174820 · TK1151

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.

PF04360Serglycin50-95 aa

PF13847Methyltransf_3185-105 aa

PF22458RsmF-B_ferredox158-168 aa

PF22458RsmF-B_ferredox179-244 aa

PF17125Methyltr_RsmF_N188-268 aa

PF01189Methyltr_RsmB-F274-484 aa

PF01728FtsJ281-413 aa

PF13847Methyltransf_31281-417 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G174820	`PF04360`	Serglycin	50	95	9.5	6.9
TkA04G174820	`PF13847`	Methyltransf_31	85	105	0.018	15.5
TkA04G174820	`PF22458`	RsmF-B_ferredox	158	168	1.3e-05	26.0
TkA04G174820	`PF22458`	RsmF-B_ferredox	179	244	1.3e-05	26.0
TkA04G174820	`PF17125`	Methyltr_RsmF_N	188	268	2.9e-07	31.5
TkA04G174820	`PF01189`	Methyltr_RsmB-F	274	484	2.6e-69	233.6
TkA04G174820	`PF01728`	FtsJ	281	413	0.012	16.3
TkA04G174820	`PF13847`	Methyltransf_31	281	417	0.018	15.5
TkA04G174820	`PF29631`	EnP1_N	316	352	0.11	13.2
TkA04G174820	`PF29631`	EnP1_N	400	435	0.11	13.2
TkA04G174820	`PF01189`	Methyltr_RsmB-F	504	547	2.6e-69	233.6

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
`Q8VYM6`	Arabidopsis thaliana	sp\|Q8VYM6\|NOP2B_ARATH 26S rRNA (cytosine-C(5))-methyltransferase NOP2B	75.000%	Swiss-Prot	High
`Q9FG73`	Arabidopsis thaliana	sp\|Q9FG73\|NOP2A_ARATH 25S rRNA (cytosine-C(5))-methyltransferase NOP2A	71.200%	Swiss-Prot	High
`Q8W4A5`	Arabidopsis thaliana	sp\|Q8W4A5\|APO2_ARATH APO protein 2, chloroplastic	66.300%	Swiss-Prot	High
`Q9XIR4`	Arabidopsis thaliana	sp\|Q9XIR4\|APO1_ARATH APO protein 1, chloroplastic	43.400%	Swiss-Prot	Medium
`Q9FH50`	Arabidopsis thaliana	sp\|Q9FH50\|APO3_ARATH APO protein 3, mitochondrial	41.400%	Swiss-Prot	Medium

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