TkA02G505280 | RubberDandelionOmics

Gene overview

TkA02G505280

Reference: TK1151 Chr: Chr02 Coordinates: 129631378-129633625 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1554 bp · TkA02G505280|TK1151|cDNA

AAATGTGAAGTTATCATAAGTTGGAATTCATTTGTGGGTAGAACATACGGGAATGCTCCAAGATATTCACCAAAGAGACCAATTGAGAACGATTCTAATGTCACGAGTCTGGAGTCAAACCCTAGATCCACCTCTGGATCCAAAAGCCAAACAAATGAAGTAAAAAGGCAAAAGAAAACAAACGATTTGTTAAACAATACAAACAATTCTAACTCAATGACCAATATTGAAAAACATCCTTGTGCCTTTTGTCATTCATC...

CDS

Download CDS FASTA

666 bp · TkA02G505280|TK1151|CDS

AAATGTGAAGTTATCATAAGTTGGAATTCATTTGTGGGTAGAACATACGGGAATGCTCCAAGATATTCACCAAAGAGACCAATTGAGAACGATTCTAATGTCACGAGTCTGGAGTCAAACCCTAGATCCACCTCTGGATCCAAAAGCCAAACAAATGAAGTAAAAAGGCAAAAGAAAACAAACGATTTGTTAAACAATACAAACAATTCTAACTCAATGACCAATATTGAAAAACATCCTTGTGCCTTTTGTCATTCATC...

Protein

Download Protein FASTA

221 aa · TkA02G505280|TK1151|PROTEIN

KCEVIISWNSFVGRTYGNAPRYSPKRPIENDSNVTSLESNPRSTSGSKSQTNEVKRQKKTNDLLNNTNNSNSMTNIEKHPCAFCHSSNHTKGSGPMVSYAQGKQVVNNIANFSKVTHVHEKCIHWAPRIYFKDGLIQNLDSEILRANKLKCSSCGKKGGGLGCYLETCPRTYHVPCAFDIPACRWDDTYLMYCPDHANLKFPGEMESDDMKQETEKKYLNL

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	`TkA02G505280`
TK1151 ID	TkA02G505280
OH-1004 ID	LXL04_013323
Relationship / confidence	Sequence Supported Annotation Or Model Conflict / Review
Protein identity (%)	100.000
Protein coverage (%)	TK1151 94.570 / OH-1004 42.653 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 TkA02G505280

Location Chr02:129631378-129633625 (-)

Description Similar to BARD1: BRCA1-associated RING domain protein 1

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g04020`	Binds specifically to H3K4me3 regions of target genes (e.g. WUS and WOX5) promoters to repress their transcription via chromatin remodeling.	A homologue of the breast cancer-associated gene BARD1 is involved in DNA repair in plants.2006 · DOI: 10.1038/sj.emboj.7601313 Mutation of Arabidopsis BARD1 causes meristem defects by failing to confine WUSCHEL expression to the organizing center.2008 · DOI: 10.1105/tpc.108.058867 ROW1 maintains quiescent centre identity by confining WOX5 expression to specific cells.2015 · DOI: 10.1038/ncomms7003

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_013323 · 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:0000724 double-strand break repair via homologous recombination Biological Process

GO:0001894 tissue homeostasis Biological Process

GO:0006281 DNA repair Biological Process

GO:0006282 regulation of DNA repair Biological Process

GO:0006310 DNA recombination Biological Process

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006357 regulation of transcription by RNA polymerase II Biological Process

GO:0006974 DNA damage response Biological Process

GO:0007283 spermatogenesis Biological Process

GO:0009934 regulation of meristem structural organization Biological Process

GO:0010078 maintenance of root meristem identity Biological Process

KEGG gene cross-reference

ath:AT4G21070

hsa:580

mmu:12021

rno:64557

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.

Nucleus0.907

Rank 1 · TkA02G505280 · TK1151

Cytoplasm0.198

Rank 2 · TkA02G505280 · TK1151

Mitochondrion0.026

Rank 3 · TkA02G505280 · TK1151

Cell membrane0.019

Rank 4 · TkA02G505280 · TK1151

Golgi apparatus0.008

Rank 5 · TkA02G505280 · 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.

PF21842DUF690149-138 aa

PF13771zf-HC5HC2H53-87 aa

PF14376Haem_bd53-89 aa

PF13832zf-HC5HC2H_266-87 aa

PF26413DUF810875-88 aa

PF22908PHD_NSD78-91 aa

PF23004PHDvar_NSD81-91 aa

PF13832zf-HC5HC2H_2113-179 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA02G505280	`PF21842`	DUF6901	49	138	0.16	12.1
TkA02G505280	`PF13771`	zf-HC5HC2H	53	87	1.5e-11	45.0
TkA02G505280	`PF14376`	Haem_bd	53	89	0.073	13.7
TkA02G505280	`PF13832`	zf-HC5HC2H_2	66	87	7.9e-07	30.0
TkA02G505280	`PF26413`	DUF8108	75	88	0.6	10.9
TkA02G505280	`PF22908`	PHD_NSD	78	91	0.00089	20.2
TkA02G505280	`PF23004`	PHDvar_NSD	81	91	0.059	14.1
TkA02G505280	`PF13832`	zf-HC5HC2H_2	113	179	7.9e-07	30.0
TkA02G505280	`PF13771`	zf-HC5HC2H	119	196	1.5e-11	45.0
TkA02G505280	`PF23004`	PHDvar_NSD	119	124	0.059	14.1
TkA02G505280	`PF26413`	DUF8108	134	197	0.6	10.9
TkA02G505280	`PF22908`	PHD_NSD	148	196	0.00089	20.2
TkA02G505280	`PF23004`	PHDvar_NSD	151	198	0.059	14.1
TkA02G505280	`PF21842`	DUF6901	181	199	0.16	12.1

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
`F4I443`	Arabidopsis thaliana	sp\|F4I443\|BARD1_ARATH BRCA1-associated RING domain protein 1	43.200%	Swiss-Prot	Medium

JBrowse

View in Genome Browser

Gene Card