TkA06G439560 | RubberDandelionOmics

Gene overview

TkA06G439560

Reference: TK1151 Chr: Chr06 Coordinates: 108644081-108647276 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1998 bp · TkA06G439560|TK1151|cDNA

AAAATATCTCCTTTCCAAAAATAAACATCAGAAGTTAAAGATTAGGTTCAATTATTCCTTCCTCTACCCTCTCTATATCTCCACACTGCATTGCGGCTAGGGTTTCACCAAAACCTTCTCTCGTTCACTCCATCTTCAAGAAATTTCTAGGGTTTTTGTGGGTTAATCGATCTGAATAAGACATGACGATTACGAATTGGAATTAGGCTTCTTATCTGTTGCAAAGACTGAAACTTTGTTCAAAGGGTTCTGTACGAGTG...

CDS

Download CDS FASTA

1173 bp · TkA06G439560|TK1151|CDS

ATGGCCACCGCGAACCCTTTTGATTTGCTCGGGGACGATGACAACGACGACCCTTCACAGCTTCTGCAAAAGATTGTTGATGCGCCGGTGAAGAAAGCTCAGCCAGCTGCTCCCGCCGGTAAAACCGCAGCGCAGCCGGCTAAGCCTTCGGCTAAACTCCCCTCAAAACCTCTCCCTCCAGCTCAAGCCGTTCGAGAATCAAGAACCGAAGGTGGCCGTGGTGGTGGTGGTGGTGGTGGTCGTGGGTATGGCCGTGGCCG...

Protein

Download Protein FASTA

390 aa · TkA06G439560|TK1151|PROTEIN

MATANPFDLLGDDDNDDPSQLLQKIVDAPVKKAQPAAPAGKTAAQPAKPSAKLPSKPLPPAQAVRESRTEGGRGGGGGGGRGYGRGRGGSGGGYNRDPANNNNEVSFGNRGFSGGQGGGEDSDGKSFERRGGGGGGGGGGYGGSRGGFRGGRGGSFGNGDSEEGERPRRTYERRSGTGRGNDIKRDGSGRGNWGTQADDINHEIQEAVIEGEKTVAIEKTGAEEEAVDGKKENNANERVEEPENKEMTLEEYQKVLEEKR...

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	`TkA06G439560`
TK1151 ID	TkA06G439560
OH-1004 ID	LXL04_022818
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	96.700
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

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA06G439560

Location Chr06:108644081-108647276 (-)

Description Similar to RGGB: RGG repeats nuclear RNA binding protein B

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g16830`	Ribosome-binding protein that acts as a regulator of mRNA translation by promoting ribosome inactivation (By similarity).	The Arabidopsis RNA-binding protein AtRGGA regulates tolerance to salt and drought stress.2015 · DOI: 10.1104/pp.114.255802
`At4g17520`	Ribosome-binding protein that acts as a regulator of mRNA translation by promoting ribosome inactivation (By similarity).	No verified direct reference in this release
`At5g47210`	Ribosome-binding protein that acts as a regulator of mRNA translation by promoting ribosome inactivation (By similarity).	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_022818 · 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:0006417 regulation of translation Biological Process

GO:0006970 response to osmotic stress Biological Process

GO:0009414 response to water deprivation Biological Process

GO:0009416 response to light stimulus Biological Process

GO:0009651 response to salt stress Biological Process

GO:0009737 response to abscisic acid Biological Process

GO:0009738 abscisic acid-activated signaling pathway Biological Process

GO:0009787 regulation of abscisic acid-activated signaling pathway Biological Process

GO:0071470 cellular response to osmotic stress Biological Process

GO:0071472 cellular response to salt stress Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

KEGG gene cross-reference

ath:AT4G16830

ath:AT4G17520

ath:AT5G47210

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.

Cytoplasm0.784

Rank 1 · TkA06G439560 · TK1151

Nucleus0.330

Rank 2 · TkA06G439560 · TK1151

Cell membrane0.052

Rank 3 · TkA06G439560 · TK1151

Endoplasmic reticulum0.046

Rank 4 · TkA06G439560 · TK1151

Mitochondrion0.034

Rank 5 · TkA06G439560 · 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.

PF09598Stm1_N1-78 aa

PF04774HABP4_PAI-RBP1126-134 aa

PF04774HABP4_PAI-RBP1167-273 aa

PF19786DUF6270192-277 aa

PF09598Stm1_N214-235 aa

PF04774HABP4_PAI-RBP1290-332 aa

PF09598Stm1_N332-332 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA06G439560	`PF09598`	Stm1_N	1	78	3.6e-23	82.8
TkA06G439560	`PF04774`	HABP4_PAI-RBP1	126	134	4.9e-26	92.4
TkA06G439560	`PF04774`	HABP4_PAI-RBP1	167	273	4.9e-26	92.4
TkA06G439560	`PF19786`	DUF6270	192	277	0.21	12.2
TkA06G439560	`PF09598`	Stm1_N	214	235	3.6e-23	82.8
TkA06G439560	`PF04774`	HABP4_PAI-RBP1	290	332	4.9e-26	92.4
TkA06G439560	`PF09598`	Stm1_N	332	332	3.6e-23	82.8

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
`O23523`	Arabidopsis thaliana	sp\|O23523\|RGGA_ARATH RGG repeats nuclear RNA binding protein A	55.100%	Swiss-Prot	Medium
`O23593`	Arabidopsis thaliana	sp\|O23593\|RGGB_ARATH RGG repeats nuclear RNA binding protein B	40.600%	Swiss-Prot	Medium
`Q9LVT8`	Arabidopsis thaliana	sp\|Q9LVT8\|RGGC_ARATH RGG repeats nuclear RNA binding protein C	39.200%	Swiss-Prot	Medium

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