LXL04_011047 | RubberDandelionOmics

Gene overview

LXL04_011047

Reference: OH-1004 Chr: Chr02 Coordinates: 156932349-156945457 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

4386 bp · LXL04_011047|LXL04_011047|OH1004|cDNA

ATGGCATCTGTAAATGAGTCGGCTGCTTCTTCCTCCAAAACTAGGGTTCTTCCTTCATGGGGTTCTTCATCCGTGTCAAGTACTACAGGTTCCCGTGGATCAACTAAAAAGCCTCCTCCTTCTAAAAAGGAATCTACTTCAAACAGTCAAAAGTTGCCGACCagtaaagtttataaaaattcAAGATGGTATACACTCACACATGGAAATCACAAGAAAGCTACTTTAAATCACGAATCTGATAACCAGATACCCCAGAA...

CDS

Download CDS FASTA

4386 bp · LXL04_011047|LXL04_011047|OH1004|CDS

ATGGCATCTGTAAATGAGTCGGCTGCTTCTTCCTCCAAAACTAGGGTTCTTCCTTCATGGGGTTCTTCATCCGTGTCAAGTACTACAGGTTCCCGTGGATCAACTAAAAAGCCTCCTCCTTCTAAAAAGGAATCTACTTCAAACAGTCAAAAGTTGCCGACCAGTAAAGTTTATAAAAATTCAAGATGGTATACACTCACACATGGAAATCACAAGAAAGCTACTTTAAATCACGAATCTGATAACCAGATACCCCAGAA...

Protein

Download Protein FASTA

1461 aa · LXL04_011047|LXL04_011047|OH1004|PROTEIN

MASVNESAASSSKTRVLPSWGSSSVSSTTGSRGSTKKPPPSKKESTSNSQKLPTSKVYKNSRWYTLTHGNHKKATLNHESDNQIPQKDTKRILSSYLQNSSSSNSNPTPQRNESYETNDLPASSSHTNFQPQDSFSFANNDVSMKNNNGRRLLPAFMNPHGSVSATQYAGQSGNSRPVVVQETVGDERLIYQVALRDLYQPTTEATLPEGLLSIPLFRHQKIALAWMLDKENSVACSGGILADDQGLGKTISVIALIQMQ...

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_011047`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_011047

Location Chr02:156932349-156945457 (+)

Description Similar to CHR28: Helicase-like transcription factor CHR28

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
`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_011047 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006281 DNA repair Biological Process

GO:0006351 DNA-templated transcription Biological Process

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

GO:0005634 nucleus Cellular Component

GO:0003677 DNA binding Molecular Function

GO:0004386 helicase activity Molecular Function

GO:0005524 ATP binding Molecular Function

GO:0008094 ATP-dependent activity, acting on DNA Molecular Function

GO:0008270 zinc ion binding Molecular Function

GO:0016787 hydrolase activity Molecular Function

KEGG gene cross-reference

ath:AT1G50410

ath:AT3G20010

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.

Nucleus0.913

Rank 1 · LXL04_011047 · OH-1004

Cytoplasm0.113

Rank 2 · LXL04_011047 · OH-1004

Cell membrane0.026

Rank 3 · LXL04_011047 · OH-1004

Plastid0.020

Rank 4 · LXL04_011047 · OH-1004

Mitochondrion0.019

Rank 5 · LXL04_011047 · 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_dom219-601 aa

PF13923.13zf-C3HC4_2641-677 aa

PF00097.32zf-C3HC4641-678 aa

PF00271.38Helicase_C747-848 aa

PF00176.30SNF2-rel_dom1011-1373 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_011047	`PF00176.30`	SNF2-rel_dom	219	601	6.9e-145	482.2
LXL04_011047	`PF13923.13`	zf-C3HC4_2	641	677	2e-06	28.2
LXL04_011047	`PF00097.32`	zf-C3HC4	641	678	2.1e-06	28.2
LXL04_011047	`PF00271.38`	Helicase_C	747	848	1.3e-23	84.0
LXL04_011047	`PF00176.30`	SNF2-rel_dom	1011	1373	6.9e-145	482.2

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	Helicase-like transcription factor CHR28	55.042%	Swiss-Prot	moderate database homology
`Q9LHE4`	Arabidopsis thaliana	Helicase-like transcription factor CHR27	52.509%	Swiss-Prot	moderate database homology
`Q9FIY7`	Arabidopsis thaliana	DNA repair protein RAD5B	33.776%	Swiss-Prot	weak database homology
`Q9FNI6`	Arabidopsis thaliana	DNA repair protein RAD5A	33.141%	Swiss-Prot	weak database homology

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