LXL04_002956 | RubberDandelionOmics

Gene overview

LXL04_002956

Reference: OH-1004 Chr: Chr01 Coordinates: 62478743-62483665 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3039 bp · LXL04_002956|LXL04_002956|OH1004|cDNA

ATGGCTGTTTCTATGAGAGAAGTGGATCCAGCCTTTCAAGGAGCTGGACAAAAAGAATCTAATTTCCTTTTGTATGCTACTTTAAATATAAACTATTTCAAAGCATTATTAATGTTAATCTTTACATCATGGGTGACAATTAGAGGAATTGAGGTATGGCGGATTGAAAACTCTAAGCCAGTGGCTGTCCCGGAGGAATCTTACGGTAAATTTTACACAGGGGaatcatatattattttaaagACCAATACTACAAAAAG...

CDS

Download CDS FASTA

3039 bp · LXL04_002956|LXL04_002956|OH1004|CDS

ATGGCTGTTTCTATGAGAGAAGTGGATCCAGCCTTTCAAGGAGCTGGACAAAAAGAATCTAATTTCCTTTTGTATGCTACTTTAAATATAAACTATTTCAAAGCATTATTAATGTTAATCTTTACATCATGGGTGACAATTAGAGGAATTGAGGTATGGCGGATTGAAAACTCTAAGCCAGTGGCTGTCCCGGAGGAATCTTACGGTAAATTTTACACAGGGGAATCATATATTATTTTAAAGACCAATACTACAAAAAG...

Protein

Download Protein FASTA

1012 aa · LXL04_002956|LXL04_002956|OH1004|PROTEIN

MAVSMREVDPAFQGAGQKESNFLLYATLNINYFKALLMLIFTSWVTIRGIEVWRIENSKPVAVPEESYGKFYTGESYIILKTNTTKSGAFRYAIHYWLGKDASEDDGATAAIKTLELDAALGGRAVQYRELQQHETEKFLSLFNPCIIPEKSEPLEHKTRMFVCKGKHVAHVPCARSSLNHDDIFILDSKNKIFQFNGSNTSIQERAKALEVVQYLRDTYHQKKCDVATIDDGRLMADAEAGEFWGFFGGFAPLPKKTAT...

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_002956`
TK1151 ID	TkA08G034610
OH-1004 ID	LXL04_002956
Relationship / confidence	Rbh Below Probable Coverage Or Synteny Threshold / Review
Protein identity (%)	60.300
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_002956

Location Chr01:62478743-62483665 (-)

Description Similar to VLN4: Villin-4

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g30160`	Binds actin and actin bundles independently of Ca²⁺, but caps filament barbed ends and severs filaments in a calcium-dependent manner.	Arabidopsis VILLIN4 is involved in root hair growth through regulating actin organization in a Ca2+-dependent manner.2011 · DOI: 10.1111/j.1469-8137.2010.03632.x The universal bundling activity of AtVLN4 in diffusely growing cells.2011 · DOI: 10.4161/psb.6.9.16501
`At5g57320`	Major actin filament stabilizing factor and regulator of actin dynamics.	Arabidopsis VILLIN5, an actin filament bundling and severing protein, is necessary for normal pollen tube growth.2010 · DOI: 10.1105/tpc.110.076257 Arabidopsis villins promote actin turnover at pollen tube tips and facilitate the construction of actin collars.2013 · DOI: 10.1105/tpc.113.110940

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0659300`	Ca(2+)-regulated actin-binding protein.	No verified direct reference in this release
`Os08g0240800`	Ca(2+)-regulated actin-binding protein (By similarity).	No verified direct reference in this release
`Os04g0604000`	Ca(2+)-regulated actin-binding protein (By similarity).	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_002956 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0007015 actin filament organization Biological Process

GO:0030042 actin filament depolymerization Biological Process

GO:0048767 root hair elongation Biological Process

GO:0051014 actin filament severing Biological Process

GO:0051592 response to calcium ion Biological Process

GO:0051693 actin filament capping Biological Process

GO:0051764 actin crosslink formation Biological Process

GO:0099636 cytoplasmic streaming Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0015629 actin cytoskeleton Cellular Component

KEGG gene cross-reference

ath:AT4G30160

ath:AT5G57320

dosa:Os04g0604000

dosa:Os06g0659300

dosa:Os08g0240800

osa:4341731

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.

Cytoplasm0.646

Rank 1 · LXL04_002956 · OH-1004

Nucleus0.204

Rank 2 · LXL04_002956 · OH-1004

Cell membrane0.188

Rank 3 · LXL04_002956 · OH-1004

Golgi apparatus0.082

Rank 4 · LXL04_002956 · OH-1004

Endoplasmic reticulum0.072

Rank 5 · LXL04_002956 · OH-1004

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

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

PF00626.28Gelsolin58-140 aa

PF00626.28Gelsolin169-233 aa

PF00626.28Gelsolin266-337 aa

PF00626.28Gelsolin676-747 aa

PF02209.25VHP977-1012 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_002956	`PF00626.28`	Gelsolin	58	140	1.3e-53	179.5
LXL04_002956	`PF00626.28`	Gelsolin	169	233	1.3e-53	179.5
LXL04_002956	`PF00626.28`	Gelsolin	266	337	1.3e-53	179.5
LXL04_002956	`PF00626.28`	Gelsolin	676	747	1.3e-53	179.5
LXL04_002956	`PF02209.25`	VHP	977	1012	3.1e-14	53.3

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.

Download current result

Protein	Organism	Description	Identity	Database	Confidence
`O65570`	Arabidopsis thaliana	Villin-4	55.807%	Swiss-Prot	strong database homology
`Q9LVC6`	Arabidopsis thaliana	Villin-5	51.905%	Swiss-Prot	strong database homology
`Q67U26`	Oryza sativa subsp. japonica	Villin-3	54.175%	Swiss-Prot	strong database homology
`Q0J716`	Oryza sativa subsp. japonica	Villin-5	54.737%	Swiss-Prot	strong database homology
`Q0JAD9`	Oryza sativa subsp. japonica	Villin-4	52.919%	Swiss-Prot	strong database homology

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