LXL04_003570 | RubberDandelionOmics

Gene overview

LXL04_003570

Reference: OH-1004 Chr: Chr01 Coordinates: 86313202-86321762 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

5049 bp · LXL04_003570|LXL04_003570|OH1004|cDNA

ATGGCCTTTTTTAGAAACTATACTAACGGGACAGTTTCAGAGGATGTTTTGAATGATAAGAGTCAGGGTAGAACTATAGAAAGAGCCGAAAGCCTTGTAGGAGGCGTTGATTTGGAAACAACTTCGAGTATTAATAAAGGGTTTGCAACAAGGATGGAAGATGGACAGTATCGTGGTGATGGTGCAGCTGAGGATGATGATAGCTTATTGAACTTAACTGCTTCTAATGCTACTACAAGGAAACCAACCGGGAGATGGGG...

CDS

Download CDS FASTA

5049 bp · LXL04_003570|LXL04_003570|OH1004|CDS

ATGGCCTTTTTTAGAAACTATACTAACGGGACAGTTTCAGAGGATGTTTTGAATGATAAGAGTCAGGGTAGAACTATAGAAAGAGCCGAAAGCCTTGTAGGAGGCGTTGATTTGGAAACAACTTCGAGTATTAATAAAGGGTTTGCAACAAGGATGGAAGATGGACAGTATCGTGGTGATGGTGCAGCTGAGGATGATGATAGCTTATTGAACTTAACTGCTTCTAATGCTACTACAAGGAAACCAACCGGGAGATGGGG...

Protein

Download Protein FASTA

1682 aa · LXL04_003570|LXL04_003570|OH1004|PROTEIN

MAFFRNYTNGTVSEDVLNDKSQGRTIERAESLVGGVDLETTSSINKGFATRMEDGQYRGDGAAEDDDSLLNLTASNATTRKPTGRWGSTFWKDCQPMHQKQGSESGQESKSSSAYNNEDGSGNDLSEVDKANKGQNVDEMLSDDYYELDGDDQSDSKHHKLLNNAAGYNSIPQQGVSANNFVSRKNLKNSSRGAYVEDADFEDDDEEEEDEDDPADADFDPDLVTTSVGRGKKVNDDDWDGEDLEEEDNSEDDELDISDD...

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_003570`
TK1151 ID	TkA01G334950
OH-1004 ID	LXL04_003570
Relationship / confidence	Rbh High Identity Coverage Synteny / Strict
Protein identity (%)	99.300
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_003570

Location Chr01:86313202-86321762 (+)

Description Similar to CHR5: Protein CHROMATIN REMODELING 5

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At2g13370`	DNA-binding helicase that specifically binds to the promoter of target genes, leading to chromatin remodeling, possibly by promoting deposition of histone H3.3 (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_003570 · 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:0006974 DNA damage response Biological Process

GO:0010467 gene expression Biological Process

GO:0034728 nucleosome organization Biological Process

GO:0043923 host-mediated activation of viral transcription Biological Process

GO:0000228 nuclear chromosome Cellular Component

GO:0000775 chromosome, centromeric region Cellular Component

GO:0000785 chromatin Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005654 nucleoplasm Cellular Component

KEGG gene cross-reference

ath:AT2G13370

hsa:1106

mmu:12648

mmu:244059

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.

Nucleus0.966

Rank 1 · LXL04_003570 · OH-1004

Cytoplasm0.085

Rank 2 · LXL04_003570 · OH-1004

Cell membrane0.020

Rank 3 · LXL04_003570 · OH-1004

Endoplasmic reticulum0.011

Rank 4 · LXL04_003570 · OH-1004

Mitochondrion0.010

Rank 5 · LXL04_003570 · 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.

PF00385.31Chromo433-463 aa

PF00385.31Chromo505-545 aa

PF04851.22ResIII587-754 aa

PF00176.30SNF2-rel_dom591-875 aa

PF00270.36DEAD602-760 aa

PF11496.15HDA2-3826-1050 aa

PF00271.38Helicase_C905-1018 aa

PF23588.3HTH_CHD1_Hrp31336-1419 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_003570	`PF00385.31`	Chromo	433	463	6e-18	65.2
LXL04_003570	`PF00385.31`	Chromo	505	545	6e-18	65.2
LXL04_003570	`PF04851.22`	ResIII	587	754	3.2e-12	47.4
LXL04_003570	`PF00176.30`	SNF2-rel_dom	591	875	2.7e-87	293.2
LXL04_003570	`PF00270.36`	DEAD	602	760	1.9e-07	31.7
LXL04_003570	`PF11496.15`	HDA2-3	826	1050	6.1e-14	52.6
LXL04_003570	`PF00271.38`	Helicase_C	905	1018	1.8e-27	96.5
LXL04_003570	`PF23588.3`	HTH_CHD1_Hrp3	1336	1419	2.6e-23	82.5
LXL04_003570	`PF13907.12`	CHD1-like_C	1506	1598	1.5e-16	61.3

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
`F4IV99`	Arabidopsis thaliana	Protein CHROMATIN REMODELING 5	65.025%	Swiss-Prot	strong database homology

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