LXL04_028958 | RubberDandelionOmics

Gene overview

LXL04_028958

Reference: OH-1004 Chr: Chr06 Coordinates: 75925477-75931438 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3246 bp · LXL04_028958|LXL04_028958|OH1004|cDNA

ATGGCAAGACGCTCCAAATCGAAAGACTCCACGGAAGAATCTCTATCTAATTCGTCAGAGGAGGAACAGGTCAATGATcaggaagaagaagacgaggAAGAGCTGGAAGCCGTTGCACGGCCTGTTGATTCTGATGAAGATGAAAACGCTACCGCCGCGGTTGATGCCACTGGTGAGGAGCAGGACGAAGATGACGAATCCGAGGTTTGCTTTTTTGGATTTCATGCATTTAGTCTGATTGCTGCTGATTTGGATGGCAA...

CDS

Download CDS FASTA

3246 bp · LXL04_028958|LXL04_028958|OH1004|CDS

ATGGCAAGACGCTCCAAATCGAAAGACTCCACGGAAGAATCTCTATCTAATTCGTCAGAGGAGGAACAGGTCAATGATCAGGAAGAAGAAGACGAGGAAGAGCTGGAAGCCGTTGCACGGCCTGTTGATTCTGATGAAGATGAAAACGCTACCGCCGCGGTTGATGCCACTGGTGAGGAGCAGGACGAAGATGACGAATCCGAGGTTTGCTTTTTTGGATTTCATGCATTTAGTCTGATTGCTGCTGATTTGGATGGCAA...

Protein

Download Protein FASTA

1081 aa · LXL04_028958|LXL04_028958|OH1004|PROTEIN

MARRSKSKDSTEESLSNSSEEEQVNDQEEEDEEELEAVARPVDSDEDENATAAVDATGEEQDEDDESEVCFFGFHAFSLIAADLDGNEEANTEISHREKARLKEMQRLKRQKIQDILDQQNASVEADMNNKGKGRLKFLLQQTELFAHFAKSGASASQKKGKERGRHASKLTEEEEDEEYLKEEEAGAGHTRLLVQPSCITGKMRDYQLAGLNWMIRLYENGINGILADEMGLGKTLQTISLLGYLHEFRGITGPHMVVA...

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_028958`
TK1151 ID	TkA07G254860
OH-1004 ID	LXL04_028958
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	100.000
Protein coverage (%)	TK1151 93.615 / OH-1004 92.229 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_028958

Location Chr06:75925477-75931438 (+)

Description Similar to CHR17: ISWI chromatin-remodeling complex ATPase CHR17

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g18620`	Possesses intrinsic ATP-dependent nucleosome-remodeling activity.	Imitation Switch chromatin remodeling factors and their interacting RINGLET proteins act together in controlling the plant vegetative phase in Arabidopsis.2012 · DOI: 10.1111/j.1365-313x.2012.05074.x ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis.2014 · DOI: 10.1111/tpj.12499
`At3g06400`	Possesses intrinsic ATP-dependent nucleosome-remodeling activity.	CHR11, a chromatin-remodeling factor essential for nuclear proliferation during female gametogenesis in Arabidopsis thaliana.2005 · DOI: 10.1073/pnas.0508186102 Imitation Switch chromatin remodeling factors and their interacting RINGLET proteins act together in controlling the plant vegetative phase in Arabidopsis.2012 · DOI: 10.1111/j.1365-313x.2012.05074.x ISWI proteins participate in the genome-wide nucleosome distribution in Arabidopsis.2014 · DOI: 10.1111/tpj.12499

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0367900`	Possesses intrinsic ATP-dependent nucleosome-remodeling activity.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_028958 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0000183 rDNA heterochromatin formation Biological Process

GO:0006275 regulation of DNA replication Biological Process

GO:0006281 DNA repair Biological Process

GO:0006325 chromatin organization Biological Process

GO:0006334 nucleosome assembly Biological Process

GO:0006338 chromatin remodeling Biological Process

GO:0006346 DNA methylation-dependent constitutive heterochromatin formation Biological Process

GO:0006351 DNA-templated transcription Biological Process

GO:0006352 DNA-templated transcription initiation Biological Process

GO:0006355 regulation of DNA-templated transcription Biological Process

GO:0006974 DNA damage response Biological Process

GO:0009553 embryo sac development Biological Process

KEGG gene cross-reference

ath:AT3G06400

ath:AT5G18620

dosa:Os01g0367900

mmu:93761

mmu:93762

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.

Nucleus0.955

Rank 1 · LXL04_028958 · OH-1004

Cytoplasm0.121

Rank 2 · LXL04_028958 · OH-1004

Cell membrane0.018

Rank 3 · LXL04_028958 · OH-1004

Mitochondrion0.017

Rank 4 · LXL04_028958 · OH-1004

Endoplasmic reticulum0.008

Rank 5 · LXL04_028958 · 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.

PF04851.22ResIII203-363 aa

PF00176.30SNF2-rel_dom207-484 aa

PF00271.38Helicase_C506-619 aa

PF09110.17HAND768-855 aa

PF09111.17SLIDE913-1023 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_028958	`PF04851.22`	ResIII	203	363	6.9e-10	39.8
LXL04_028958	`PF00176.30`	SNF2-rel_dom	207	484	1.8e-101	339.7
LXL04_028958	`PF00271.38`	Helicase_C	506	619	7e-25	88.1
LXL04_028958	`PF09110.17`	HAND	768	855	4.2e-07	31.5
LXL04_028958	`PF09111.17`	SLIDE	913	1023	6.4e-43	146.2

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`F4JY24`	Arabidopsis thaliana	ISWI chromatin-remodeling complex ATPase CHR17	85.370%	Swiss-Prot	strong database homology
`Q8RWY3`	Arabidopsis thaliana	ISWI chromatin-remodeling complex ATPase CHR11	85.102%	Swiss-Prot	strong database homology
`Q7G8Y3`	Oryza sativa subsp. japonica	Probable chromatin-remodeling complex ATPase chain	86.323%	Swiss-Prot	strong database homology

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