TkA03G479960 | RubberDandelionOmics

Gene overview

TkA03G479960

Reference: TK1151 Chr: Chr03 Coordinates: 120030559-120034891 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2880 bp · TkA03G479960|TK1151|cDNA

ATGAGGGTAGTCGACAACATTGACAAAACAATGGCGAGTCTAGATGGCTCTAAACAGAGAGTACATCACGTAAAAGGCGGTGCCATTGAATTGCATCAAACAAGAAAGAAGCTAAAGATCAAACTGACATTCCCTCTCAATTCTAATACCATCTTTTCTTCTCAATTCAAAGTTCCATCCCTAATGTCGTTAAACAGCTTCAAGGAAATCCTCAAACCCTGTACATACCAATCCCAATCACAAACTTCCTCCTCGTACTC...

CDS

Download CDS FASTA

2880 bp · TkA03G479960|TK1151|CDS

ATGAGGGTAGTCGACAACATTGACAAAACAATGGCGAGTCTAGATGGCTCTAAACAGAGAGTACATCACGTAAAAGGCGGTGCCATTGAATTGCATCAAACAAGAAAGAAGCTAAAGATCAAACTGACATTCCCTCTCAATTCTAATACCATCTTTTCTTCTCAATTCAAAGTTCCATCCCTAATGTCGTTAAACAGCTTCAAGGAAATCCTCAAACCCTGTACATACCAATCCCAATCACAAACTTCCTCCTCGTACTC...

Protein

Download Protein FASTA

959 aa · TkA03G479960|TK1151|PROTEIN

MRVVDNIDKTMASLDGSKQRVHHVKGGAIELHQTRKKLKIKLTFPLNSNTIFSSQFKVPSLMSLNSFKEILKPCTYQSQSQTSSSYSQTSSTLNPRKPPKSSLAQQLLRLEGDYSSFPTSLPTKQSKEFSQIKQQEPQLDDVIEVKIDDEEEEFKDLDKQNGFRIARPKLEAPQFFDPTGPYEPLVLSESGQDPVVQVPASINCRLLEHQREGVKFLYNLYKKNHGGILGDDMGLGKTIQAIAFLSAIYKKDEEHDTTTP...

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	`TkA03G479960`
TK1151 ID	TkA03G479960
OH-1004 ID	LXL04_009884
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 96.038 / OH-1004 99.032 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 TkA03G479960

Location Chr03:120030559-120034891 (+)

Description Similar to SWI2: Switch 2

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g03750`	May be involved in early DNA damage response (By similarity).	Involvement of the Arabidopsis SWI2/SNF2 chromatin remodeling gene family in DNA damage response and recombination.2006 · DOI: 10.1534/genetics.105.051664

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_009884 · 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:0006974 DNA damage response Biological Process

GO:0007131 reciprocal meiotic recombination Biological Process

GO:0010332 response to gamma radiation Biological Process

GO:0034614 cellular response to reactive oxygen species Biological Process

GO:0036297 interstrand cross-link repair Biological Process

GO:0045003 double-strand break repair via synthesis-dependent strand annealing Biological Process

GO:0051301 cell division Biological Process

GO:0051701 biological process involved in interaction with host Biological Process

GO:0071248 cellular response to metal ion Biological Process

GO:0071480 cellular response to gamma radiation Biological Process

GO:0097680 double-strand break repair via classical nonhomologous end joining Biological Process

KEGG gene cross-reference

ath:AT1G03750

ath:AT3G19210

hsa:375748

mmu:76251

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.

Nucleus0.884

Rank 1 · TkA03G479960 · TK1151

Cytoplasm0.153

Rank 2 · TkA03G479960 · TK1151

Mitochondrion0.035

Rank 3 · TkA03G479960 · TK1151

Cell membrane0.023

Rank 4 · TkA03G479960 · TK1151

Endoplasmic reticulum0.016

Rank 5 · TkA03G479960 · 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.

PF25806RHH_ERCC6L2134-155 aa

PF04851ResIII205-373 aa

PF00176SNF2-rel_dom209-480 aa

PF18766SWI2_SNF2217-252 aa

PF00270DEAD228-374 aa

PF00271Helicase_C265-319 aa

PF18766SWI2_SNF2304-384 aa

PF00271Helicase_C349-383 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA03G479960	`PF25806`	RHH_ERCC6L2	134	155	3.7	8.6
TkA03G479960	`PF04851`	ResIII	205	373	1.5e-10	42.0
TkA03G479960	`PF00176`	SNF2-rel_dom	209	480	4.9e-67	226.7
TkA03G479960	`PF18766`	SWI2_SNF2	217	252	0.16	12.3
TkA03G479960	`PF00270`	DEAD	228	374	7.7e-08	33.0
TkA03G479960	`PF00271`	Helicase_C	265	319	2.2e-25	89.8
TkA03G479960	`PF18766`	SWI2_SNF2	304	384	0.16	12.3
TkA03G479960	`PF00271`	Helicase_C	349	383	2.2e-25	89.8
TkA03G479960	`PF11496`	HDA2-3	596	734	0.013	15.5
TkA03G479960	`PF16203`	ERCC3_RAD25_C	597	686	0.064	13.3
TkA03G479960	`PF00271`	Helicase_C	598	710	2.2e-25	89.8
TkA03G479960	`PF25806`	RHH_ERCC6L2	888	931	3.7	8.6
TkA03G479960	`PF00271`	Helicase_C	913	929	2.2e-25	89.8

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
`F4I2H2`	Arabidopsis thaliana	sp\|F4I2H2\|CHR9_ARATH Switch 2	63.300%	Swiss-Prot	High

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