LXL04_029626 | RubberDandelionOmics

Gene overview

LXL04_029626

Reference: OH-1004 Chr: Chr06 Coordinates: 95712382-95715032 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

594 bp · LXL04_029626|LXL04_029626|OH1004|cDNA

ATGGCATTCACCGGGACATTAGAGAAATGCAAAGTTTGCGAGAAAACTGTTTATTTTATAGAAATGATATCAGCTGATGGAATCAATTATCATAAAACATGCTTCAAATGCAGCCAATGTAACGGCAAGCTTACGATTAGCACATATTCCTCATTGGATGGAGTGTTATTTTGCAAACCACACTTTGAGCAAAAGTTCAAGGAGAGAGGAGGTCTTCCCAAAGTCACACCAGCGACTAAAACAAGTGATACGGGAAAAGC...

CDS

Download CDS FASTA

594 bp · LXL04_029626|LXL04_029626|OH1004|CDS

ATGGCATTCACCGGGACATTAGAGAAATGCAAAGTTTGCGAGAAAACTGTTTATTTTATAGAAATGATATCAGCTGATGGAATCAATTATCATAAAACATGCTTCAAATGCAGCCAATGTAACGGCAAGCTTACGATTAGCACATATTCCTCATTGGATGGAGTGTTATTTTGCAAACCACACTTTGAGCAAAAGTTCAAGGAGAGAGGAGGTCTTCCCAAAGTCACACCAGCGACTAAAACAAGTGATACGGGAAAAGC...

Protein

Download Protein FASTA

197 aa · LXL04_029626|LXL04_029626|OH1004|PROTEIN

MAFTGTLEKCKVCEKTVYFIEMISADGINYHKTCFKCSQCNGKLTISTYSSLDGVLFCKPHFEQKFKERGGLPKVTPATKTSDTGKAPSKLAALFSGTQEKCAVCKKTVYPLEKVTVEGEFYHKACFRCTRGGCFLTPSNYAALDGNLFCKPHFSQLFKEKGSYSHLKEAVKKVEAASAEGTPTGEATNEGGAPEED

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_029626`
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_029626

Location Chr06:95712382-95715032 (-)

Description Similar to PLIM2C: LIM domain-containing protein PLIM2c

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At3g61230`	Binds to actin filaments and promotes cross-linking into thick bundles.	Arabidopsis LIM proteins: a family of actin bundlers with distinct expression patterns and modes of regulation.2010 · DOI: 10.1105/tpc.110.075960
`At3g55770`	Binds to actin filaments and promotes cross-linking into thick bundles.	Arabidopsis LIM proteins: a family of actin bundlers with distinct expression patterns and modes of regulation.2010 · DOI: 10.1105/tpc.110.075960
`At2g39900`	Binds to actin filaments and promotes cross-linking into thick bundles.	No verified direct reference in this release
`At2g45800`	Binds to actin filaments and promotes cross-linking into thick bundles.	Arabidopsis LIM proteins: a family of actin bundlers with distinct expression patterns and modes of regulation.2010 · DOI: 10.1105/tpc.110.075960

Rice

Reference gene ID	Possible function	Papers / DOI
`Os04g0532500`	LIM domain-containing protein PLIM2b.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_029626 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0051017 actin filament bundle assembly Biological Process

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005856 cytoskeleton Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0003729 mRNA binding Molecular Function

GO:0046872 metal ion binding Molecular Function

GO:0051015 actin filament binding Molecular Function

KEGG gene cross-reference

ath:AT2G39900

ath:AT2G45800

ath:AT3G55770

ath:AT3G61230

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.

Cytoplasm0.769

Rank 1 · LXL04_029626 · OH-1004

Nucleus0.204

Rank 2 · LXL04_029626 · OH-1004

Cell membrane0.095

Rank 3 · LXL04_029626 · OH-1004

Golgi apparatus0.067

Rank 4 · LXL04_029626 · OH-1004

Endoplasmic reticulum0.043

Rank 5 · LXL04_029626 · 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.

PF00412.29LIM10-66 aa

PF00412.29LIM102-158 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_029626	`PF00412.29`	LIM	10	66	5.3e-23	81.7
LXL04_029626	`PF00412.29`	LIM	102	158	5.3e-23	81.7

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
`Q500W4`	Arabidopsis thaliana	LIM domain-containing protein PLIM2c	54.286%	Swiss-Prot	strong database homology
`Q9M047`	Arabidopsis thaliana	LIM domain-containing protein WLIM2b	60.694%	Swiss-Prot	strong database homology
`O04193`	Arabidopsis thaliana	LIM domain-containing protein WLIM2a	60.920%	Swiss-Prot	strong database homology
`O80839`	Arabidopsis thaliana	LIM domain-containing protein PLIM2a	58.378%	Swiss-Prot	strong database homology
`Q7F9R9`	Oryza sativa subsp. japonica	LIM domain-containing protein PLIM2b	59.218%	Swiss-Prot	strong database homology

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