LXL04_019530 | RubberDandelionOmics

Gene overview

LXL04_019530

Reference: OH-1004 Chr: Chr04 Coordinates: 33018595-33023601 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

3051 bp · LXL04_019530|LXL04_019530|OH1004|cDNA

ATGACGCGGACCTTCAAAGACCTCCAGCTGACGGAGCTTGGGGGCCGTGATAGGGGCGGCGGTCGTGTTTCGTCGGCGATCGACATAAGCAGTAACCTCGAGGACGTTAGGCTTTTAGATTCTTATGAGGATgttaataatgataataatgaTCATAGTGTCGGTAATAGTAGGAAAGGTAAAGAGAAAGGAGGCGTTACCAGAATTCAGGTGCGAGTCACTGGGATGACATGTGCAGCGTGTTCGAATTCCGTCGAAAT...

CDS

Download CDS FASTA

3051 bp · LXL04_019530|LXL04_019530|OH1004|CDS

ATGACGCGGACCTTCAAAGACCTCCAGCTGACGGAGCTTGGGGGCCGTGATAGGGGCGGCGGTCGTGTTTCGTCGGCGATCGACATAAGCAGTAACCTCGAGGACGTTAGGCTTTTAGATTCTTATGAGGATGTTAATAATGATAATAATGATCATAGTGTCGGTAATAGTAGGAAAGGTAAAGAGAAAGGAGGCGTTACCAGAATTCAGGTGCGAGTCACTGGGATGACATGTGCAGCGTGTTCGAATTCCGTCGAAAT...

Protein

Download Protein FASTA

1016 aa · LXL04_019530|LXL04_019530|OH1004|PROTEIN

MTRTFKDLQLTELGGRDRGGGRVSSAIDISSNLEDVRLLDSYEDVNNDNNDHSVGNSRKGKEKGGVTRIQVRVTGMTCAACSNSVEIALMSLNGVVSASVALLQNKADVAFDPNLVEEDDIKNAIEDAGFDAEILQEHGGKPHGTLVGQFIIGGMTCAACVNSIEGILRKLHGVKKAVVALTTSLGEVEYDPSIISKDEIINAIEDAGFEASLAQSSGQDRMMFLITGILDQLDENTLDGILGNLKGVKQFDFNKMTSEV...

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_019530`
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_019530

Location Chr04:33018595-33023601 (+)

Description Similar to RAN1: Copper-transporting ATPase RAN1

Arabidopsis / Rice Reference Genes and Papers

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Arabidopsis

Reference gene ID	Possible function	Papers / DOI
`At5g44790`	Involved in copper import into the cell.	No verified direct reference in this release
`At1g63440`	Involved in copper import into the cell.	The Arabidopsis heavy metal P-type ATPase HMA5 interacts with metallochaperones and functions in copper detoxification of roots.2006 · DOI: 10.1111/j.1365-313x.2005.02601.x

Rice

Reference gene ID	Possible function	Papers / DOI
`Os06g0665800`	Metal efflux transporter that may play a role in detoxification of heavy metals, such as zinc, copper, lead and cadmium, especially in the shoots.	Rice P1B-type heavy-metal ATPase, OsHMA9, is a metal efflux protein.2007 · DOI: 10.1104/pp.107.102236
`Os04g0556000`	Copper (Cu) transporter that plays an essential role in promoting translocation of Cu from roots to shoots.	A member of the heavy metal P-type ATPase OsHMA5 is involved in xylem loading of copper in rice.2013 · DOI: 10.1104/pp.113.226225
`Os02g0196600`	Copper (Cu) transporter that mediates Cu transport in root vacuoles.	A heavy metal P-type ATPase OsHMA4 prevents copper accumulation in rice grain.2016 · DOI: 10.1038/ncomms12138

Functional annotation source

View annotation sources

Functional annotation source: OH1004 · LXL04_019530 · GCA_047496595.1_OSU_TarKok_2.0.

GO annotations (OH1004 source)

GO:0009636 response to toxic substance Biological Process

GO:0009723 response to ethylene Biological Process

GO:0009873 ethylene-activated signaling pathway Biological Process

GO:0010119 regulation of stomatal movement Biological Process

GO:0010273 detoxification of copper ion Biological Process

GO:0046688 response to copper ion Biological Process

GO:0055070 copper ion homeostasis Biological Process

GO:0055085 transmembrane transport Biological Process

GO:0071280 cellular response to copper ion Biological Process

GO:0005768 endosome Cellular Component

GO:0005794 Golgi apparatus Cellular Component

GO:0005802 trans-Golgi network Cellular Component

KEGG gene cross-reference

ath:AT1G63440

ath:AT5G44790

dosa:Os04g0556000

dosa:Os06g0665800

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 reticulum0.285

Rank 1 · LXL04_019530 · OH-1004

Lysosome / Vacuole0.228

Rank 2 · LXL04_019530 · OH-1004

Golgi apparatus0.184

Rank 3 · LXL04_019530 · OH-1004

Cell membrane0.175

Rank 4 · LXL04_019530 · OH-1004

Cytoplasm0.120

Rank 5 · LXL04_019530 · 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.

PF00403.33HMA71-131 aa

PF00403.33HMA150-210 aa

PF00122.26E1-E2_ATPase468-556 aa

PF00702.33Hydrolase665-904 aa

Gene ID	Domain ID	Domain Name	Start aa	End aa	E-value	Score
LXL04_019530	`PF00403.33`	HMA	71	131	2.1e-34	118.4
LXL04_019530	`PF00403.33`	HMA	150	210	2.1e-34	118.4
LXL04_019530	`PF00122.26`	E1-E2_ATPase	468	556	5.8e-24	84.6
LXL04_019530	`PF00702.33`	Hydrolase	665	904	5.1e-28	99.5

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
`Q9S7J8`	Arabidopsis thaliana	Copper-transporting ATPase RAN1	67.717%	Swiss-Prot	strong database homology
`Q9SH30`	Arabidopsis thaliana	Probable copper-transporting ATPase HMA5	48.903%	Swiss-Prot	moderate database homology
`A0A0P0X004`	Oryza sativa subsp. japonica	Cation-transporting ATPase HMA5	64.134%	Swiss-Prot	strong database homology
`A3AWA4`	Oryza sativa subsp. japonica	Copper-transporting ATPase HMA5	48.188%	Swiss-Prot	moderate database homology
`Q6H7M3`	Oryza sativa subsp. japonica	Copper-transporting ATPase HMA4	48.729%	Swiss-Prot	moderate database homology

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