TkA01G608560 | RubberDandelionOmics

Gene overview

TkA01G608560

Reference: TK1151 Chr: Chr01 Coordinates: 153396068-153402030 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2029 bp · TkA01G608560|TK1151|cDNA

AAAAAATAGAAAAATCAAACCATCAAACGTTAAGATCAGGGTTTATTTTCTATTTGGTCCTGGTATTATGATGGAAAACCTAATCGTTGGATTTTCCCCCTAATCGCTTCTTCCCTCCATCTTCTTAGCTGTGTGAGACAGCACAGAGATTGAGAATGGGTTTTTTCGATCTGAATATCCCCTACAATGAGTCCAACAAGCGAAATCCCACCACCGAAAAGTCTATACGATTGAAACTCGCCGTCAAAGCCATGGAATTG...

CDS

Download CDS FASTA

1641 bp · TkA01G608560|TK1151|CDS

ATGGGTTTTTTCGATCTGAATATCCCCTACAATGAGTCCAACAAGCGAAATCCCACCACCGAAAAGTCTATACGATTGAAACTCGCCGTCAAAGCCATGGAATTGGGTTACACCGGCGTTGCATATAACCGTACTATTACCGGAGTAATGTCGGAAGCAGACCGTTGTTCAATCTCTCTATTCCCTATTTCTTCCGTTCTTAAGGTTTCTCCTTCTATCTCTGCCTCTGTTAACCTTCACCGCCGCCTCCTCAATGTCCC...

Protein

Download Protein FASTA

546 aa · TkA01G608560|TK1151|PROTEIN

MGFFDLNIPYNESNKRNPTTEKSIRLKLAVKAMELGYTGVAYNRTITGVMSEADRCSISLFPISSVLKVSPSISASVNLHRRLLNVPTSTPFRQYTRLTVVVDTPAQGSALNSGNPVLKTYDIIAVRPLKQDSFDQSCKNYEVDIIAIDFSENRFRLKQPLIKAAIERGVYFEITYAGLVLDAQLRRQMITNAKLLVDWTRGKNLIFSSAAPSVTELRGPYDVANLASLLGLSVERAKAAVSRTCRSLLENGIRKKKFYK...

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	`TkA01G608560`
TK1151 ID	TkA01G608560
OH-1004 ID	LXL04_000494
Relationship / confidence	Rbh Sequence Supported / Probable
Protein identity (%)	90.900
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA01G608560

Location Chr01:153396068-153402030 (+)

Description Similar to GAF1: Protein GAMETOPHYTE DEFECTIVE 1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g59980`	Probable component of ribonuclease P, a ribonucleoprotein complex that generates mature tRNA molecules by cleaving their 5'-ends (By similarity).	GAMETOPHYTE DEFECTIVE 1, a putative subunit of RNases P/MRP, is essential for female gametogenesis and male competence in Arabidopsis.2012 · DOI: 10.1371/journal.pone.0033595

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_000494 · 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:0001682 tRNA 5'-leader removal Biological Process

GO:0006364 rRNA processing Biological Process

GO:0006396 RNA processing Biological Process

GO:0008033 tRNA processing Biological Process

GO:0009553 embryo sac development Biological Process

GO:0048868 pollen tube development Biological Process

GO:0000172 ribonuclease MRP complex Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005655 nucleolar ribonuclease P complex Cellular Component

GO:0005739 mitochondrion Cellular Component

GO:0030681 multimeric ribonuclease P complex Cellular Component

KEGG gene cross-reference

ath:AT5G59980

bta:615098

ddi:DDB_G0269980

hsa:10556

mmu:54364

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.

Nucleus0.829

Rank 1 · TkA01G608560 · TK1151

Cytoplasm0.216

Rank 2 · TkA01G608560 · TK1151

Cell membrane0.032

Rank 3 · TkA01G608560 · TK1151

Mitochondrion0.026

Rank 4 · TkA01G608560 · TK1151

Golgi apparatus0.022

Rank 5 · TkA01G608560 · 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.

PF01876RNase_P_p303-257 aa

PF02677QueH3-58 aa

PF10475Vps54_N431-494 aa

PF24231DUF7444436-509 aa

PF02677QueH458-543 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA01G608560	`PF01876`	RNase_P_p30	3	257	3.8e-54	184.2
TkA01G608560	`PF02677`	QueH	3	58	0.041	14.7
TkA01G608560	`PF10475`	Vps54_N	431	494	0.16	12.0
TkA01G608560	`PF24231`	DUF7444	436	509	0.22	12.1
TkA01G608560	`PF02677`	QueH	458	543	0.041	14.7

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
`F4JXF1`	Arabidopsis thaliana	sp\|F4JXF1\|GAF1_ARATH Protein GAMETOPHYTE DEFECTIVE 1	57.100%	Swiss-Prot	Medium

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