TkA02G551520 | RubberDandelionOmics

Gene overview

TkA02G551520

Reference: TK1151 Chr: Chr02 Coordinates: 142312418-142315416 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1916 bp · TkA02G551520|TK1151|cDNA

GAACGATATATTAGACATCAAAGTATAATTAGTCGTGTAAAACTATAAATAATTAATCGTTCCTAACTTCCTATCTATCTCTTCCGACCCCAAACTGGTGACCAGAAAACCTCCATAAACCCCCTCTATCCCCACCATCCACCACTGCTTCCATGGCGGCAGCCGCCATAACAACAGCCCTCTCCACCTTCCACATCTCGAAACCCTACTCTATTGCCCGCAACCACCTGCGCTATCATACATTGTCCACATACTCTCTC...

CDS

Download CDS FASTA

1125 bp · TkA02G551520|TK1151|CDS

ATGGCGGCAGCCGCCATAACAACAGCCCTCTCCACCTTCCACATCTCGAAACCCTACTCTATTGCCCGCAACCACCTGCGCTATCATACATTGTCCACATACTCTCTCTCCTCAAGCTCCTCCGAATTCATCACCACCTCTGGATATTTATTAACTGATAAGAAACTCGTTGATCCATGGAGAGGAGACGCTTCTTCAGGACGAGTATTTCATGTCATGGCGGACGCGTCCGCCGTGAATTCACCGACGAAGAAGAAATT...

Protein

Download Protein FASTA

374 aa · TkA02G551520|TK1151|PROTEIN

MAAAAITTALSTFHISKPYSIARNHLRYHTLSTYSLSSSSSEFITTSGYLLTDKKLVDPWRGDASSGRVFHVMADASAVNSPTKKKLRPSRELRPIREMTSEPRYSKAARRFYNENFKESSSQRLSKVLAAAGVASRRSCEELIFEGKVTVNGSVCNTPQTKVDPKKDMIYVNGNRLPKKLPPKVYLALNKPKGYICSSGETQTKSVISLFNDYMKSWDKRNPGQPKPRLFTVGRLDVATTGLIIVTNDGEFAQKISHPS...

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	`TkA02G551520`
TK1151 ID	TkA02G551520
OH-1004 ID	LXL04_012583
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	91.700
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 TkA02G551520

Location Chr02:142312418-142315416 (-)

Description Similar to SVR1: Putative ribosomal large subunit pseudouridine synthase SVR1, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g39140`	Responsible for synthesis of pseudouridine in chloroplastic 23S ribosomal RNA (Probable).	Mutations in SUPPRESSOR OF VARIEGATION1, a factor required for normal chloroplast translation, suppress var2-mediated leaf variegation in Arabidopsis.2008 · DOI: 10.1105/tpc.107.054965

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_012583 · 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:0000455 enzyme-directed rRNA pseudouridine synthesis Biological Process

GO:0000488 maturation of LSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) Biological Process

GO:0000489 maturation of SSU-rRNA from tetracistronic rRNA transcript (SSU-rRNA, LSU-rRNA, 4.5S-rRNA, 5S-rRNA) Biological Process

GO:0001522 pseudouridine synthesis Biological Process

GO:0032544 plastid translation Biological Process

GO:0005829 cytosol Cellular Component

GO:0009501 amyloplast Cellular Component

GO:0009507 chloroplast Cellular Component

GO:0003723 RNA binding Molecular Function

GO:0003729 mRNA binding Molecular Function

GO:0009982 pseudouridine synthase activity Molecular Function

GO:0120159 rRNA pseudouridine synthase activity Molecular Function

KEGG gene cross-reference

aae:aq_1464

ath:AT2G39140

bsu:BSU23160

mbo:BQ2027_MB1738

mtu:Rv1711

mtv:RVBD_1711

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.

Plastid0.883

Rank 1 · TkA02G551520 · TK1151

Mitochondrion0.097

Rank 2 · TkA02G551520 · TK1151

Nucleus0.036

Rank 3 · TkA02G551520 · TK1151

Cytoplasm0.013

Rank 4 · TkA02G551520 · TK1151

Cell membrane0.008

Rank 5 · TkA02G551520 · 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.

PF22421SYY_C-terminal120-168 aa

PF01479S4123-165 aa

PF22421SYY_C-terminal166-177 aa

PF00849PseudoU_synth_2186-328 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA02G551520	`PF22421`	SYY_C-terminal	120	168	0.033	14.8
TkA02G551520	`PF01479`	S4	123	165	3.3e-12	46.7
TkA02G551520	`PF22421`	SYY_C-terminal	166	177	0.033	14.8
TkA02G551520	`PF00849`	PseudoU_synth_2	186	328	5e-21	76.2

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
`Q8L960`	Arabidopsis thaliana	sp\|Q8L960\|SVR1_ARATH Putative ribosomal large subunit pseudouridine synthase SVR1, chloroplastic	76.800%	Swiss-Prot	High

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