TkA02G032080 | RubberDandelionOmics

Gene overview

TkA02G032080

Reference: TK1151 Chr: Chr02 Coordinates: 7776144-7782307 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3084 bp · TkA02G032080|TK1151|cDNA

AGAAAACGCAAACCCTACTCCCTTTTATCATCTATTAACCCTAAGTTCGATTACACTGTTAAGCATCATGAAGCTTCGTTCTCGCTCATCTGATCCTTCCGACAAAGGTAAAGGCATTATCGAGCTCTCAGACGAAGAAGACAATGATCAGTTGTCTTCAGATTCCGAATACTATTCTTATAGTTTTGAACGTCTTGCCAATGAAGAAGCGGTTCCAGATTTTGTAACAGAATCCGAAGATGAAAAGCCAAAGAGAAATA...

CDS

Download CDS FASTA

2670 bp · TkA02G032080|TK1151|CDS

ATGAAGCTTCGTTCTCGCTCATCTGATCCTTCCGACAAAGGTAAAGGCATTATCGAGCTCTCAGACGAAGAAGACAATGATCAGTTGTCTTCAGATTCCGAATACTATTCTTATAGTTTTGAACGTCTTGCCAATGAAGAAGCGGTTCCAGATTTTGTAACAGAATCCGAAGATGAAAAGCCAAAGAGAAATAAAAGCAGTTCACAAAGGTGGAAGAGAAAAGCCGAACAATCAGATGAAGAAATAGCGGTTATAATTGC...

Protein

Download Protein FASTA

889 aa · TkA02G032080|TK1151|PROTEIN

MKLRSRSSDPSDKGKGIIELSDEEDNDQLSSDSEYYSYSFERLANEEAVPDFVTESEDEKPKRNKSSSQRWKRKAEQSDEEIAVIIAELSLDEEDIAVVKKSTNRKKKKKKTKPTLLWEIWEEETEKWLDQHMTEDVDLDNLNEIVAETVEPSPDLIMPLLRYQKEWLAWGLKQEESPSRGGILADEMGMGKTIQAIALVLAKRALHVEFGQPVDQSTNPSSSSSSSSLLPRVKATLVICPLIAVMQWVNEIERFTAKGS...

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	`TkA02G032080`
TK1151 ID	TkA02G032080
OH-1004 ID	LXL04_017552
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.900
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 TkA02G032080

Location Chr02:7776144-7782307 (+)

Description Similar to rhp16: ATP-dependent helicase rhp16 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g50410`	Probable helicase-like transcription factor involved in transcriptional gene silencing.	SUVR2 is involved in transcriptional gene silencing by associating with SNF2-related chromatin-remodeling proteins in Arabidopsis.2014 · DOI: 10.1038/cr.2014.156 SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation.2014 · DOI: 10.1073/pnas.1420515111
`At5g43530`	Possesses intrinsic ATP-dependent nucleosome-remodeling activity.	A homolog of ScRAD5 is involved in DNA repair and homologous recombination in Arabidopsis.2008 · DOI: 10.1104/pp.108.116806
`At5g22750`	Functions in error-free postreplication DNA repair or DNA- damage tolerance (DTT) pathway.	A homolog of ScRAD5 is involved in DNA repair and homologous recombination in Arabidopsis.2008 · DOI: 10.1104/pp.108.116806 RAD5A, RECQ4A, and MUS81 have specific functions in homologous recombination and define different pathways of DNA repair in Arabidopsis thaliana.2010 · DOI: 10.1105/tpc.110.078568 RAD5a and REV3 function in two alternative pathways of DNA-damage tolerance in Arabidopsis.2011 · DOI: 10.1016/j.dnarep.2011.04.009 AtRAD5A is a DNA translocase harboring a HIRAN domain which confers binding to branched DNA structures and is required for DNA repair in vivo.2016 · DOI: 10.1111/tpj.13283

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_017552 · 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:0000715 nucleotide-excision repair, DNA damage recognition Biological Process

GO:0000720 pyrimidine dimer repair by nucleotide-excision repair Biological Process

GO:0006281 DNA repair Biological Process

GO:0006289 nucleotide-excision repair Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006511 ubiquitin-dependent protein catabolic process Biological Process

GO:0008104 intracellular protein localization Biological Process

GO:0009411 response to UV Biological Process

GO:0034644 cellular response to UV Biological Process

GO:0070911 global genome nucleotide-excision repair Biological Process

GO:0080188 gene silencing by siRNA-directed DNA methylation Biological Process

GO:0000113 nucleotide-excision repair factor 4 complex Cellular Component

KEGG gene cross-reference

ath:AT3G20010

sce:YBR114W

spo:2538860

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.

Nucleus0.928

Rank 1 · TkA02G032080 · TK1151

Cytoplasm0.127

Rank 2 · TkA02G032080 · TK1151

Mitochondrion0.028

Rank 3 · TkA02G032080 · TK1151

Cell membrane0.019

Rank 4 · TkA02G032080 · TK1151

Endoplasmic reticulum0.010

Rank 5 · TkA02G032080 · 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.

PF04851ResIII81-94 aa

PF00176SNF2-rel_dom114-133 aa

PF04851ResIII158-295 aa

PF00176SNF2-rel_dom163-468 aa

PF00270DEAD187-293 aa

PF00271Helicase_C237-289 aa

PF04851ResIII359-447 aa

PF00270DEAD377-428 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
TkA02G032080	`PF04851`	ResIII	81	94	2e-05	25.3
TkA02G032080	`PF00176`	SNF2-rel_dom	114	133	3.3e-53	181.4
TkA02G032080	`PF04851`	ResIII	158	295	2e-05	25.3
TkA02G032080	`PF00176`	SNF2-rel_dom	163	468	3.3e-53	181.4
TkA02G032080	`PF00270`	DEAD	187	293	2.1e-05	25.0
TkA02G032080	`PF00271`	Helicase_C	237	289	1.8e-23	83.6
TkA02G032080	`PF04851`	ResIII	359	447	2e-05	25.3
TkA02G032080	`PF00270`	DEAD	377	428	2.1e-05	25.0
TkA02G032080	`PF13920`	zf-C3HC4_3	470	493	9e-05	22.9
TkA02G032080	`PF14634`	zf-RING_5	470	491	0.014	16.1
TkA02G032080	`PF13923`	zf-C3HC4_2	471	491	1.7e-05	25.2
TkA02G032080	`PF00097`	zf-C3HC4	471	491	3e-05	24.5
TkA02G032080	`PF13445`	zf-RING_UBOX	471	489	4.9e-05	24.0
TkA02G032080	`PF13639`	zf-RING_2	471	491	0.015	16.2
TkA02G032080	`PF14447`	Prok-RING_4	472	494	0.016	15.8
TkA02G032080	`PF00176`	SNF2-rel_dom	496	612	3.3e-53	181.4

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q94BR5`	Arabidopsis thaliana	sp\|Q94BR5\|CHR28_ARATH Helicase-like transcription factor CHR28	31.000%	Swiss-Prot	Medium
`Q9FIY7`	Arabidopsis thaliana	sp\|Q9FIY7\|SM3L3_ARATH DNA repair protein RAD5B	29.500%	Swiss-Prot	Low
`Q9FNI6`	Arabidopsis thaliana	sp\|Q9FNI6\|SM3L2_ARATH DNA repair protein RAD5A	29.900%	Swiss-Prot	Low

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