LXL04_009352 | RubberDandelionOmics

Gene overview

LXL04_009352

Reference: OH-1004 Chr: Chr02 Coordinates: 123826692-123829594 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

1707 bp · LXL04_009352|LXL04_009352|OH1004|cDNA

ATGGCTTCCGATATGGAAACCCTAGAGggcaataaacaagacgacgCTCCCACCGTTGTAGAAGAAGTCGAAATGAAGGACAAGGAGGAATCCGAAAACGAAGTCGAAGAAGAGTCAAAGCCTAAAGAGCCAGAAGAGGAGGAAGAGACtaaagaggaagaagaagctaAAGAGGAAGAGAGCTATGCTGAAGAAGAAGCTAAAGACAAAGAGAGCGATGATGAAGAAGAGGCTAAAGACAAAGAGAGCGAAGGCGATGA...

CDS

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1707 bp · LXL04_009352|LXL04_009352|OH1004|CDS

ATGGCTTCCGATATGGAAACCCTAGAGGGCAATAAACAAGACGACGCTCCCACCGTTGTAGAAGAAGTCGAAATGAAGGACAAGGAGGAATCCGAAAACGAAGTCGAAGAAGAGTCAAAGCCTAAAGAGCCAGAAGAGGAGGAAGAGACTAAAGAGGAAGAAGAAGCTAAAGAGGAAGAGAGCTATGCTGAAGAAGAAGCTAAAGACAAAGAGAGCGATGATGAAGAAGAGGCTAAAGACAAAGAGAGCGAAGGCGATGA...

Protein

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568 aa · LXL04_009352|LXL04_009352|OH1004|PROTEIN

MASDMETLEGNKQDDAPTVVEEVEMKDKEESENEVEEESKPKEPEEEEETKEEEEAKEEESYAEEEAKDKESDDEEEAKDKESEGDEEADESKGSRKKGRKRSSSKSPATPIERPTRERKTVDRYTATTPTLSATKPFSIQQGPGTQLKDIPNVAFKLSKRTADENLQSLHSILFGKRAKPNVCKKNIGMFSGFVWTDDEQEKHNTRVKEKLDKCVKERLMDFCDVLNLQLSKSTRKEDVASKLLEFLKSPHATTEVLLA...

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_009352`
TK1151 ID	TkA03G428340
OH-1004 ID	LXL04_009352
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	98.600
Protein coverage (%)	TK1151 89.391 / OH-1004 90.669 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_009352

Location Chr02:123826692-123829594 (-)

Description Similar to Dek: Protein DEK

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g48710`	Chromatin-associated protein which contributes to the modulation of chromatin structure (such as super-helical structure of DNA) and function (By similarity).	No verified direct reference in this release
`At5g63550`	Chromatin-associated protein which contributes to the modulation of chromatin structure (such as super-helical structure of DNA) and function (By similarity).	No verified direct reference in this release
`At4g26630`	Chromatin-associated protein which contributes to the modulation of chromatin structure (such as super-helical structure of DNA) and function.	A DEK domain-containing protein modulates chromatin structure and function in Arabidopsis.2014 · DOI: 10.1105/tpc.114.129254
`At5g55660`	Chromatin-associated protein which contributes to the modulation of chromatin structure (such as super-helical structure of DNA) and function (By similarity).	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

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Functional annotation source: OH1004 · LXL04_009352 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006325 chromatin organization Biological Process

GO:0006338 chromatin remodeling Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0009651 response to salt stress Biological Process

GO:0045892 negative regulation of DNA-templated transcription Biological Process

GO:0045945 positive regulation of transcription by RNA polymerase III Biological Process

GO:2000779 regulation of double-strand break repair Biological Process

GO:2001032 regulation of double-strand break repair via nonhomologous end joining Biological Process

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

GO:0005730 nucleolus Cellular Component

KEGG gene cross-reference

ath:AT3G48710

ath:AT4G26630

ath:AT5G55660

ath:AT5G63550

rno:306817

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.

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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.

Nucleus0.966

Rank 1 · LXL04_009352 · OH-1004

Cytoplasm0.088

Rank 2 · LXL04_009352 · OH-1004

Cell membrane0.021

Rank 3 · LXL04_009352 · OH-1004

Endoplasmic reticulum0.011

Rank 4 · LXL04_009352 · OH-1004

Extracellular0.010

Rank 5 · LXL04_009352 · 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.

PF08766.17DEK_C439-491 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_009352	`PF08766.17`	DEK_C	439	491	3.2e-13	50.1

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.

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Protein	Organism	Description	Identity	Database	Confidence
`Q9SMM8`	Arabidopsis thaliana	DEK domain-containing chromatin-associated protein 1	46.804%	Swiss-Prot	moderate database homology
`Q84JB7`	Arabidopsis thaliana	DEK domain-containing chromatin-associated protein 2	46.005%	Swiss-Prot	moderate database homology
`Q9SUA1`	Arabidopsis thaliana	DEK domain-containing chromatin-associated protein 3	36.275%	Swiss-Prot	weak database homology
`F4K4Y5`	Arabidopsis thaliana	DEK domain-containing chromatin-associated protein 4	37.864%	Swiss-Prot	weak database homology

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