LXL04_016201 | RubberDandelionOmics

Gene overview

LXL04_016201

Reference: OH-1004 Chr: Chr03 Coordinates: 115011535-115018210 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3681 bp · LXL04_016201|LXL04_016201|OH1004|cDNA

ATGTCTGCTTCGCGCAGACCACGCGCAGACCTAAGGGGTTGCAGCGTGTTTGTTTTTTTGAAGTGTGAAGAGGTTTTTACCTCTGCCCGCGGTCTTCTTGGGACAGACCTGGTTCATTGTCTTCAAACCTCTTCTAATTTCAACCTAATAACATTTTGCGATTCAACGGCCGCTCTCCTCCATCGCGATTCAACACCCGTCGTCTTCAGCATCGAACGTCACCTGTCTTCAGCTCCGATCGTCGCCATCTTCAGCACCGC...

CDS

Download CDS FASTA

3681 bp · LXL04_016201|LXL04_016201|OH1004|CDS

ATGTCTGCTTCGCGCAGACCACGCGCAGACCTAAGGGGTTGCAGCGTGTTTGTTTTTTTGAAGTGTGAAGAGGTTTTTACCTCTGCCCGCGGTCTTCTTGGGACAGACCTGGTTCATTGTCTTCAAACCTCTTCTAATTTCAACCTAATAACATTTTGCGATTCAACGGCCGCTCTCCTCCATCGCGATTCAACACCCGTCGTCTTCAGCATCGAACGTCACCTGTCTTCAGCTCCGATCGTCGCCATCTTCAGCACCGC...

Protein

Download Protein FASTA

1226 aa · LXL04_016201|LXL04_016201|OH1004|PROTEIN

MSASRRPRADLRGCSVFVFLKCEEVFTSARGLLGTDLVHCLQTSSNFNLITFCDSTAALLHRDSTPVVFSIERHLSSAPIVAIFSTAPLLHTNRRFQATTRSISVPISADFTLFHPISSRRFPPDRRHLQHRSSPPYKPSISSHKDRKRLSLHKDSWNKVGRVLKDNFGVDLAQKQLKNAYDNLKAKYTGWIYLKNKTGNLYNPQTNTFNLTAEEWDEFKKGTSEGSVIENYPTGHNQRYVIIKRRFQHSKQTIHKFFHE...

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_016201`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

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SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_016201

Location Chr03:115011535-115018210 (-)

Description Similar to GDPDL3: Glycerophosphodiester phosphodiesterase GDPDL3

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At4g26690`	Involved in primary cell wall organization.	The glycerophosphoryl diester phosphodiesterase-like proteins SHV3 and its homologs play important roles in cell wall organization.2008 · DOI: 10.1093/pcp/pcn120
`At5g55480`	Involved in primary cell wall organization.	The glycerophosphoryl diester phosphodiesterase-like proteins SHV3 and its homologs play important roles in cell wall organization.2008 · DOI: 10.1093/pcp/pcn120
`At1g66970`	Hydrolyzes glycerolphosphoglycerol, glycerophosphocholine and glycerophosphoethanolamine in vitro.	Characterization of the Arabidopsis glycerophosphodiester phosphodiesterase (GDPD) family reveals a role of the plastid-localized AtGDPD1 in maintaining cellular phosphate homeostasis under phosphate starvation.2011 · DOI: 10.1111/j.1365-313x.2011.04538.x
`At1g66980`	Atypical receptor-like kinase involved in disease resistance.	Activation of plant immune responses by a gain-of-function mutation in an atypical receptor-like kinase.2010 · DOI: 10.1104/pp.110.158501
`At3g20520`	Glycerophosphodiester phosphodiesterase GDPDL5.	No verified direct reference in this release

Rice

No hit for this species in the current source table.

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_016201 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006071 glycerol metabolic process Biological Process

GO:0006629 lipid metabolic process Biological Process

GO:0009932 cell tip growth Biological Process

GO:0010053 root epidermal cell differentiation Biological Process

GO:0048765 root hair cell differentiation Biological Process

GO:0071555 cell wall organization Biological Process

GO:0005829 cytosol Cellular Component

GO:0005886 plasma membrane Cellular Component

GO:0009506 plasmodesma Cellular Component

GO:0009536 plastid Cellular Component

GO:0016020 membrane Cellular Component

GO:0099503 secretory vesicle Cellular Component

KEGG gene cross-reference

ath:AT4G26690

ath:AT5G55480

These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.

Open Annotation Module

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.

Extracellular0.333

Rank 1 · LXL04_016201 · OH-1004

Cell membrane0.222

Rank 2 · LXL04_016201 · OH-1004

Cytoplasm0.149

Rank 3 · LXL04_016201 · OH-1004

Endoplasmic reticulum0.147

Rank 4 · LXL04_016201 · OH-1004

Lysosome / Vacuole0.128

Rank 5 · LXL04_016201 · 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.

PF12776.14Myb_DNA-bind_3148-219 aa

PF26138.1DUF8040233-266 aa

PF13359.13DDE_Tnp_4304-464 aa

PF03009.24GDPD842-1132 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_016201	`PF12776.14`	Myb_DNA-bind_3	148	219	1e-06	30.3
LXL04_016201	`PF26138.1`	DUF8040	233	266	9.1e-07	29.4
LXL04_016201	`PF13359.13`	DDE_Tnp_4	304	464	1.5e-17	64.4
LXL04_016201	`PF03009.24`	GDPD	842	1132	9.8e-30	105.2

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
`Q9SZ11`	Arabidopsis thaliana	Glycerophosphodiester phosphodiesterase GDPDL3	48.904%	Swiss-Prot	weak database homology
`Q9FJ62`	Arabidopsis thaliana	Glycerophosphodiester phosphodiesterase GDPDL4	44.672%	Swiss-Prot	weak database homology
`Q7Y208`	Arabidopsis thaliana	Glycerophosphodiester phosphodiesterase GDPDL1	47.277%	Swiss-Prot	weak database homology
`D7SFH9`	Arabidopsis thaliana	Protein SUPPRESSOR OF NPR1-1 CONSTITUTIVE 4	44.615%	Swiss-Prot	weak database homology
`F4JEQ1`	Arabidopsis thaliana	Glycerophosphodiester phosphodiesterase GDPDL5	44.045%	Swiss-Prot	weak database homology

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