TkA04G124870 | RubberDandelionOmics

Gene overview

TkA04G124870

Reference: TK1151 Chr: Chr04 Coordinates: 32474242-32476213 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1288 bp · TkA04G124870|TK1151|cDNA

CCCATACCTAGGGAGAGAAAACACTTCGAAAATAGACCCACGACATTGCCGCCCCGAACAATTTGTATCGTCTCGACGCTTCTCCCAACTCCCACAACCGAGCAACTCCTCACGCGGTACACCATGAACCCTAGAGCTATGCTGAAGCTCTCTCGCTTCCTTAATTCCGGGTAACCGTTCTCATCTTCAAATTTACACATCTGCAAACTACATTCATCTATCGATTTTTGGTGTATATACTGCGAGTGTATGAACATATA...

CDS

Download CDS FASTA

852 bp · TkA04G124870|TK1151|CDS

CCCATACCTAGGGAGAGAAAACACTTCGAAAATAGACCCACGACATTGCCGCCCCGAACAATTTGTATCGTCTCGACGCTTCTCCCAACTCCCACAACCGAGCAACTCCTCACGCGGTACACCATGAACCCTAGAGCTATGCTGAAGCTCTCTCGCTTCCTTAATTCCGGGAACAACTTCCTCCAGCGTAGATTACTTGGCGAAAATGGTGGAAGTTCTTTCAATTTGATGTCCTCTGCTGCCATTGCTACTGCAAGACA...

Protein

Download Protein FASTA

283 aa · TkA04G124870|TK1151|PROTEIN

PIPRERKHFENRPTTLPPRTICIVSTLLPTPTTEQLLTRYTMNPRAMLKLSRFLNSGNNFLQRRLLGENGGSSFNLMSSAAIATARHSYGSEGRTPSRIFADYTVFKGKAALSASPVLPTFSKMDSGHTKVDRRGVILLTFRPAIGERKYDSEKKQFFALSVTEVGSFISLGPGDSCEFFHDPSMQSRDAGQVRKSLSIKPHTDGYFISLSVANNILKINERITVPVSTAEFAVMRSAFSFALPHIMGWAHSTSQVAGNV...

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	`TkA04G124870`
TK1151 ID	TkA04G124870
OH-1004 ID	LXL04_025205
Relationship / confidence	Multi Source To Oh1004 / Complex relationship
Protein identity (%)	48.700
Protein coverage (%)	TK1151 53.710 / OH-1004 61.111 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

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID TkA04G124870

Location Chr04:32474242-32476213 (+)

Description Similar to WHY1: Single-stranded DNA-binding protein WHY1, chloroplastic

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g71260`	Single-stranded DNA-binding protein that associates with mitochondrial DNA and may play a role in the regulation of the gene expression machinery.	Overexpression of mtDNA-associated AtWhy2 compromises mitochondrial function.2008 · DOI: 10.1186/1471-2229-8-42 A RAD52-like single-stranded DNA binding protein affects mitochondrial DNA repair by recombination.2012 · DOI: 10.1111/j.1365-313x.2012.05097.x
`At1g14410`	Single-stranded DNA-binding protein that functions in both chloroplasts and nucleus.	A "Whirly" transcription factor is required for salicylic acid-dependent disease resistance in Arabidopsis.2004 · DOI: 10.1016/s1534-5807(04)00028-0 Single-stranded DNA binding factor AtWHY1 modulates telomere length homeostasis in Arabidopsis.2007 · DOI: 10.1111/j.1365-313x.2006.02974.x Whirly proteins maintain plastid genome stability in Arabidopsis.2009 · DOI: 10.1073/pnas.0901710106 Recruitment of AtWHY1 and AtWHY3 by a distal element upstream of the kinesin gene AtKP1 to mediate transcriptional repression.2009 · DOI: 10.1007/s11103-009-9533-7

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_025205 · 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:0006281 DNA repair Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006952 defense response Biological Process

GO:0009627 systemic acquired resistance Biological Process

GO:0009863 salicylic acid mediated signaling pathway Biological Process

GO:0032204 regulation of telomere maintenance Biological Process

GO:0032211 negative regulation of telomere maintenance via telomerase Biological Process

GO:0045893 positive regulation of DNA-templated transcription Biological Process

GO:0045910 negative regulation of DNA recombination Biological Process

GO:0050832 defense response to fungus Biological Process

GO:0000781 chromosome, telomeric region Cellular Component

KEGG gene cross-reference

ath:AT1G14410

ath:AT2G02740

sot:102577544

sot:102577630

zma:100170235

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

Open Annotation Module

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.

Mitochondrion0.759

Rank 1 · TkA04G124870 · TK1151

Plastid0.135

Rank 2 · TkA04G124870 · TK1151

Nucleus0.122

Rank 3 · TkA04G124870 · TK1151

Cytoplasm0.051

Rank 4 · TkA04G124870 · TK1151

Cell membrane0.012

Rank 5 · TkA04G124870 · 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.

PF08536Whirly105-238 aa

PF29262SlaB_N180-268 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA04G124870	`PF08536`	Whirly	105	238	1.9e-54	183.9
TkA04G124870	`PF29262`	SlaB_N	180	268	0.031	15.4

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
`Q8VYF7`	Arabidopsis thaliana	sp\|Q8VYF7\|WHY2_ARATH Single-stranded DNA-binding protein WHY2, mitochondrial	60.700%	Swiss-Prot	High
`Q9M9S3`	Arabidopsis thaliana	sp\|Q9M9S3\|WHY1_ARATH Single-stranded DNA-binding protein WHY1, chloroplastic	48.700%	Swiss-Prot	Medium

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