LXL04_017552 | RubberDandelionOmics

Gene overview

LXL04_017552

Reference: OH-1004 Chr: Chr03 Coordinates: 153116008-153121758 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2670 bp · LXL04_017552|LXL04_017552|OH1004|cDNA

ATGAAGCTTCGTTCTCGCTCATCTGATCCTTCCGACAAAGGTAAAGGCATTATCGAGCTCTCAGACGAAGAAGACAATGATCAGTTGTCTTCAGATTCCGAATACTATTCTTATAGTTTTGAACGTCTTGCCAATGAAGAAGCGGTTCCAGATTTTGTAACAGAATCCGAAGATGAAAAGCCAAAGAGAAATAAAAGCAGTTCACAAAGGTGGAAGAGAAAAGCCGAACAATCAGATGAAGAAATAGCGGTTATAATTGC...

CDS

Download CDS FASTA

2670 bp · LXL04_017552|LXL04_017552|OH1004|CDS

ATGAAGCTTCGTTCTCGCTCATCTGATCCTTCCGACAAAGGTAAAGGCATTATCGAGCTCTCAGACGAAGAAGACAATGATCAGTTGTCTTCAGATTCCGAATACTATTCTTATAGTTTTGAACGTCTTGCCAATGAAGAAGCGGTTCCAGATTTTGTAACAGAATCCGAAGATGAAAAGCCAAAGAGAAATAAAAGCAGTTCACAAAGGTGGAAGAGAAAAGCCGAACAATCAGATGAAGAAATAGCGGTTATAATTGC...

Protein

Download Protein FASTA

889 aa · LXL04_017552|LXL04_017552|OH1004|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	`LXL04_017552`
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	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

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Basic Information and Functional Annotation

Gene ID LXL04_017552

Location Chr03:153116008-153121758 (-)

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
`At3g20010`	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.

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.

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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.

Nucleus0.928

Rank 1 · LXL04_017552 · OH-1004

Cytoplasm0.127

Rank 2 · LXL04_017552 · OH-1004

Mitochondrion0.028

Rank 3 · LXL04_017552 · OH-1004

Cell membrane0.019

Rank 4 · LXL04_017552 · OH-1004

Endoplasmic reticulum0.010

Rank 5 · LXL04_017552 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

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Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF00176.30SNF2-rel_dom163-468 aa

PF00176.30SNF2-rel_dom496-612 aa

PF00271.38Helicase_C719-833 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_017552	`PF00176.30`	SNF2-rel_dom	163	468	3.3e-53	181.4
LXL04_017552	`PF00176.30`	SNF2-rel_dom	496	612	3.3e-53	181.4
LXL04_017552	`PF00271.38`	Helicase_C	719	833	1.8e-23	83.6

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
`Q9LHE4`	Arabidopsis thaliana	Helicase-like transcription factor CHR27	29.663%	Swiss-Prot	weak database homology
`Q9FIY7`	Arabidopsis thaliana	DNA repair protein RAD5B	34.043%	Swiss-Prot	moderate database homology
`Q9FNI6`	Arabidopsis thaliana	DNA repair protein RAD5A	34.291%	Swiss-Prot	moderate database homology

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