LXL04_036790 | RubberDandelionOmics

Gene overview

LXL04_036790

Reference: OH-1004 Chr: Chr08 Coordinates: 48339894-48347315 Strand: - Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

2316 bp · LXL04_036790|LXL04_036790|OH1004|cDNA

ATGGTGGATCCTGCTGCATGTTGCTCCACCCATCTCATTGATGGAGATGGTACATTTGATGCAACAGGACTTGACAAGTTCATGAAGGAAGTAAAACTCAATGAATGTGGGCTTTCTTATGCGGTTGTCTCTATCATGGGCCCACAAAGTAGCGGGAAGAGCACACTTTTAAATTATCTGTTTCATACCAACTTCAGGGAAATGGATGCATTTAAGGGAAGGTCTCAAACCACTAAAGGTATTTGGATGGCTAGATGTGC...

CDS

Download CDS FASTA

2316 bp · LXL04_036790|LXL04_036790|OH1004|CDS

ATGGTGGATCCTGCTGCATGTTGCTCCACCCATCTCATTGATGGAGATGGTACATTTGATGCAACAGGACTTGACAAGTTCATGAAGGAAGTAAAACTCAATGAATGTGGGCTTTCTTATGCGGTTGTCTCTATCATGGGCCCACAAAGTAGCGGGAAGAGCACACTTTTAAATTATCTGTTTCATACCAACTTCAGGGAAATGGATGCATTTAAGGGAAGGTCTCAAACCACTAAAGGTATTTGGATGGCTAGATGTGC...

Protein

Download Protein FASTA

771 aa · LXL04_036790|LXL04_036790|OH1004|PROTEIN

MVDPAACCSTHLIDGDGTFDATGLDKFMKEVKLNECGLSYAVVSIMGPQSSGKSTLLNYLFHTNFREMDAFKGRSQTTKGIWMARCAGIEPCTIVMDLEGTDGRERGEDDTAFEKQSALFALAVSDIVLINMWCHDIGREHAANKPLLKTVFQVMMRLFSPRKTTLIFVIRDKTRTPLENLEPVLREDIQKIWDSVPKPEAHKETPLSTFFNIEVVALSSFEEKEEQFKEQVANLRQRFYHSIAPGGLAGDRQGVVPASG...

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_036790`
Source version	OH-1004 / GCA_047496595.1_OSU_TarKok_2.0

Open Full ID Mapping

SNP / Indel variants and carrier samplesCRA009020 · OH-1004

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene ID LXL04_036790

Location Chr08:48339894-48347315 (-)

Description Similar to RHD3: Protein ROOT HAIR DEFECTIVE 3

Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At1g72960`	Probable GTP-binding protein that may be involved in cell development.	No verified direct reference in this release
`At3g13870`	Probable GTP-binding protein involved in cell wall expansion.	Regulation of the cell expansion gene RHD3 during Arabidopsis development.2002 · DOI: 10.1104/pp.002675 The Arabidopsis RHD3 gene is required for cell wall biosynthesis and actin organization.2003 · DOI: 10.1007/s00425-003-1067-7 A GFP-based assay reveals a role for RHD3 in transport between the endoplasmic reticulum and Golgi apparatus.2004 · DOI: 10.1046/j.1365-313x.2003.01969.x Loss-of-function mutations of ROOT HAIR DEFECTIVE3 suppress root waving, skewing, and epidermal cell file rotation in Arabidopsis.2005 · DOI: 10.1104/pp.105.059774 Growth and ultrastructure of Arabidopsis root hairs: the rhd3 mutation alters vacuole enlargement and tip growth.1997 · DOI: 10.1007/bf01007706 The ROOT HAIR DEFECTIVE3 gene encodes an evolutionarily conserved protein with GTP-binding motifs and is required for regulated cell enlargement in Arabidopsis.1997 · DOI: 10.1101/gad.11.6.799
`At5g45160`	Probable GTP-binding protein that may be involved in cell development.	No verified direct reference in this release

Rice

Reference gene ID	Possible function	Papers / DOI
`Os01g0575000`	Probable GTP-binding protein that may be involved in cell development.	No verified direct reference in this release
`Os12g0604600`	Probable GTP-binding protein that may be involved in cell development.	No verified direct reference in this release

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_036790 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0006888 endoplasmic reticulum to Golgi vesicle-mediated transport Biological Process

GO:0009832 plant-type cell wall biogenesis Biological Process

GO:0009932 cell tip growth Biological Process

GO:0010053 root epidermal cell differentiation Biological Process

GO:0016320 endoplasmic reticulum membrane fusion Biological Process

GO:0030036 actin cytoskeleton organization Biological Process

GO:0000139 Golgi membrane Cellular Component

GO:0000325 plant-type vacuole Cellular Component

GO:0005634 nucleus Cellular Component

GO:0005737 cytoplasm Cellular Component

GO:0005783 endoplasmic reticulum Cellular Component

GO:0005789 endoplasmic reticulum membrane Cellular Component

KEGG gene cross-reference

ath:AT1G72960

ath:AT3G13870

ath:AT5G45160

dosa:Os01g0575000

dosa:Os12g0604600

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.

Endoplasmic reticulum0.457

Rank 1 · LXL04_036790 · OH-1004

Golgi apparatus0.257

Rank 2 · LXL04_036790 · OH-1004

Cytoplasm0.257

Rank 3 · LXL04_036790 · OH-1004

Cell membrane0.190

Rank 4 · LXL04_036790 · OH-1004

Nucleus0.128

Rank 5 · LXL04_036790 · 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.

PF25683.2URGCP_GTPase24-164 aa

PF05879.19RHD3_GTPase46-281 aa

PF20428.4Sey1_3HB323-757 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_036790	`PF25683.2`	URGCP_GTPase	24	164	9.6e-08	31.9
LXL04_036790	`PF05879.19`	RHD3_GTPase	46	281	3.4e-115	384.3
LXL04_036790	`PF20428.4`	Sey1_3HB	323	757	4.5e-128	428.4

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
`Q9SSN0`	Arabidopsis thaliana	Protein ROOT HAIR DEFECTIVE 3 homolog 1	69.241%	Swiss-Prot	strong database homology
`P93042`	Arabidopsis thaliana	Protein ROOT HAIR DEFECTIVE 3	69.661%	Swiss-Prot	strong database homology
`Q9FKE9`	Arabidopsis thaliana	Protein ROOT HAIR DEFECTIVE 3 homolog 2	64.729%	Swiss-Prot	strong database homology
`Q0JLS6`	Oryza sativa subsp. japonica	Protein ROOT HAIR DEFECTIVE 3	68.110%	Swiss-Prot	strong database homology
`Q2QMH2`	Oryza sativa subsp. japonica	Protein ROOT HAIR DEFECTIVE 3 homolog 1	62.005%	Swiss-Prot	strong database homology

JBrowse

View in Genome Browser

Gene Card